
                         MODELLER 9.25, 2020/09/03, r11894

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                     Copyright(c) 1989-2020 Andrej Sali
                            All Rights Reserved

                             Written by A. Sali
                               with help from
              B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
          M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
             A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
                     F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK


Kind, OS, HostName, Kernel, Processor: 4, WinNT 10.0 build 19041, LAPTOP-QO80AMMP, SMP, unknown
Date and time of compilation         : 2020/09/03 08:23:39
MODELLER executable type             : x86_64-w64
Job starting time (YY/MM/DD HH:MM:SS): 2021/02/06 13:56:51


check_ali___> Checking the sequence-structure alignment. 

Implied intrachain target CA(i)-CA(i+1) distances longer than  8.0 angstroms:

ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file:        3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    42837    39547
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   710670
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -49628.0898




<< end of ENERGY.
DOPE score               : -49628.089844
>> Normalized DOPE z score: -0.631
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.116318
Native energy (pair)     :  -422.607068
Native energy (surface)  :   -11.091902
Native energy (combined) :   -10.939647
Z score (pair)           :   -10.642705
Z score (surface)        :    -7.204480
Z score (combined)       :   -12.479662
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   710670
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -49628.0898




<< end of ENERGY.
DOPE score               : -49628.089844
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   710670
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -39483.8125




<< end of ENERGY.
DOPE-HR score               : -39483.812500


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     8684
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        2795.2649





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    3676       0      0   0.005   0.005      28.408       1.000
 2 Bond angle potential               :    4978       0     18   2.096   2.096      434.20       1.000
 3 Stereochemical cosine torsion poten:    2202       0     60  46.133  46.133      726.80       1.000
 4 Stereochemical improper torsion pot:    1476       0      1   1.465   1.465      75.345       1.000
 5 Soft-sphere overlap restraints     :    8684       0      1   0.003   0.003      12.026       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    9560       0      0   0.144   0.144      142.62       1.000
10 Distance restraints 2 (N-O)        :    9747       0     10   0.243   0.243      356.37       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     461       0      4   4.752   4.752      122.77       1.000
14 Sidechain Chi_1 dihedral restraints:     404       0     11  72.114  72.114      121.62       1.000
15 Sidechain Chi_2 dihedral restraints:     308       0      6  78.175  78.175      154.95       1.000
16 Sidechain Chi_3 dihedral restraints:     130       0      0  82.970  82.970      89.606       1.000
17 Sidechain Chi_4 dihedral restraints:      51       0      0  85.723  85.723      34.248       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    4393       0      0   0.388   0.388      120.00       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     460      49     59  27.872  55.303      148.36       1.000
26 Distance restraints 4 (SDCH-SDCH)  :    1701       0      3   0.889   0.889      227.94       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: pkp2a.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   49811.5273



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  12333   1E   2M C   N       8   10  -71.93  -63.40   12.84    1.63   56.30  144.09   26.67
    1          2M   2M N   CA     10   11  -30.91  -40.50                   34.80
    2  12350  18P  19S C   N     140  142  -42.46  -72.40   61.44    2.83  -64.10  135.50   11.25
    2         19S  19S N   CA    142  143   98.76  152.40                  -35.00
    3  12351  19S  20R C   N     146  148 -166.64 -125.20  121.15    4.82  -63.00  122.05   22.25
    3         20R  20R N   CA    148  149 -105.56  140.60                  -41.10
    4  12477 145W 146P C   N    1157 1159  -68.36  -64.50   11.40    0.69  -58.70  171.84   14.99
    4        146P 146P N   CA   1159 1160  157.93  147.20                  -30.50
    5  12478 146P 147E C   N    1164 1166 -117.54 -117.80    9.56    0.49  -63.60 -178.46   27.26
    5        147E 147E N   CA   1166 1167  146.36  136.80                  -40.30
    6  12479 147E 148G C   N    1173 1175  134.74   78.70   57.57    2.53   82.20 -179.95   11.26
    6        148G 148G N   CA   1175 1176 -179.29 -166.10                    8.50
    7  12481 149D 150Y C   N    1185 1187 -129.15 -124.30   14.83    0.61  -63.50  179.61   31.78
    7        150Y 150Y N   CA   1187 1188  149.41  135.40                  -43.40
    8  12484 152K 153A C   N    1213 1215 -104.71 -134.00   30.97    0.73  -62.50 -177.22   28.20
    8        153A 153A N   CA   1215 1216  136.94  147.00                  -40.90
    9  12485 153A 154N C   N    1218 1220 -118.58 -119.90    2.67    0.14  -63.20 -172.08   26.65
    9        154N 154N N   CA   1220 1221  139.33  137.00                  -41.10
   10  12486 154N 155G C   N    1226 1228  170.04 -167.20   42.18    1.69   82.20  157.38   11.45
   10        155G 155G N   CA   1228 1229  139.08  174.60                    8.50
   11  12488 156L 157L C   N    1238 1240   68.95   60.20   88.10    6.00 -108.50  178.11    8.31
   11        157L 157L N   CA   1240 1241  117.26   29.60                  132.50
   12  12509 177A 178D C   N    1397 1399  -74.08  -63.30  108.03   12.72  -63.30  108.03   12.72
   12        178D 178D N   CA   1399 1400   67.49  -40.00                  -40.00
   13  12510 178D 179G C   N    1405 1407  120.06   82.20   69.71    1.91  -62.40  177.76   32.10
   13        179G 179G N   CA   1407 1408  -50.03    8.50                  -41.20
   14  12535 203D 204Y C   N    1599 1601   72.13   55.90   16.60    1.67  -63.50  157.17   29.68
   14        204Y 204Y N   CA   1601 1602   36.02   39.50                  -43.40
   15  12536 204Y 205Q C   N    1611 1613 -117.63 -121.10   82.18    3.85  -63.80  111.72   14.38
   15        205Q 205Q N   CA   1613 1614   57.59  139.70                  -40.30
   16  12570 238Y 239I C   N    1888 1890  -95.62 -120.60   58.31    2.50  -63.40  125.43   19.57
   16        239I 239I N   CA   1890 1891   77.62  130.30                  -43.60
   17  12571 239I 240Q C   N    1896 1898  -66.36  -63.80    2.98    0.54 -121.10 -173.32    9.58
   17        240Q 240Q N   CA   1898 1899  -41.83  -40.30                  139.70
   18  12572 240Q 241N C   N    1905 1907 -137.56 -119.90   37.52    1.26  -63.20  166.35   24.98
   18        241N 241N N   CA   1907 1908  170.10  137.00                  -41.10
   19  12573 241N 242R C   N    1913 1915  -72.92  -72.10   10.63    0.80  -63.00  166.70   23.19
   19        242R 242R N   CA   1915 1916  152.50  141.90                  -41.10
   20  12574 242R 243N C   N    1924 1926 -123.63 -119.90   21.69    0.89  -63.20  171.54   24.88
   20        243N 243N N   CA   1926 1927  158.36  137.00                  -41.10
   21  12576 244I 245Q C   N    1940 1942 -103.30 -121.10   30.30    1.58  -63.80  160.41   25.70
   21        245Q 245Q N   CA   1942 1943  164.22  139.70                  -40.30
   22  12577 245Q 246T C   N    1949 1951  -74.49  -78.10   10.62    0.58  -63.20  158.51   21.07
   22        246T 246T N   CA   1951 1952  159.79  149.80                  -42.10
   23  12578 246T 247D C   N    1956 1958  -99.41  -96.50   24.19    1.01  -63.30  135.11   14.87
   23        247D 247D N   CA   1958 1959   90.19  114.20                  -40.00
   24  12580 248N 249N C   N    1972 1974 -163.25  -63.20  110.89   18.19  -63.20  110.89   18.19
   24        249N 249N N   CA   1974 1975  -88.91  -41.10                  -41.10
   25  12581 249N 250K C   N    1980 1982 -154.48 -118.00   50.29    1.76  -62.90  171.91   27.76
   25        250K 250K N   CA   1982 1983  173.72  139.10                  -40.80
   26  12582 250K 251S C   N    1989 1991 -119.44 -136.60   29.39    1.67  -64.10  159.82   15.48
   26        251S 251S N   CA   1991 1992  175.06  151.20                  -35.00
   27  12583 251S 252I C   N    1995 1997  -60.58  -63.40    6.49    1.17 -120.60  178.46    8.05
   27        252I 252I N   CA   1997 1998  -37.76  -43.60                  130.30
   28  12586 254C 255F C   N    2013 2015 -147.58 -124.20   30.79    0.81  -63.20  174.17   29.54
   28        255F 255F N   CA   2015 2016  163.34  143.30                  -44.30
   29  12588 256G 257S C   N    2028 2030 -150.47 -136.60   25.46    1.45  -64.10 -173.90   11.96
   29        257S 257S N   CA   2030 2031  129.84  151.20                  -35.00
   30  12589 257S 258R C   N    2034 2036 -124.27 -125.20   61.86    2.97  -63.00  134.60   15.29
   30        258R 258R N   CA   2036 2037   78.74  140.60                  -41.10
   31  12590 258R 259S C   N    2045 2047 -123.34 -136.60   33.53    1.37  -64.10  166.31   10.27
   31        259S 259S N   CA   2047 2048  120.40  151.20                  -35.00
   32  12592 260R 261K C   N    2062 2064 -135.67 -118.00   34.50    1.36  -62.90  167.14   26.06
   32        261K 261K N   CA   2064 2065  168.74  139.10                  -40.80
   33  12594 262V 263K C   N    2078 2080  -91.84  -70.20   32.56    2.72  -62.90  159.51   19.32
   33        263K 263K N   CA   2080 2081  116.07  140.40                  -40.80
   34  12595 263K 264E C   N    2087 2089   57.01  -69.30  134.90   11.69  -63.60  177.21   20.95
   34        264E 264E N   CA   2089 2090 -170.13  142.50                  -40.30
   35  12596 264E 265Q C   N    2096 2098  -51.10  -73.00   43.79    3.29  -63.80  141.64   20.18
   35        265Q 265Q N   CA   2098 2099  178.63  140.70                  -40.30
   36  12597 265Q 266Y C   N    2105 2107 -104.20 -124.30   35.89    2.73  -63.50  156.83   26.96
   36        266Y 266Y N   CA   2107 2108  165.14  135.40                  -43.40
   37  12598 266Y 267Q C   N    2117 2119  -81.47  -73.00   51.37    3.19  -63.80  129.54   19.99
   37        267Q 267Q N   CA   2119 2120 -168.63  140.70                  -40.30
   38  12599 267Q 268D C   N    2126 2128 -110.44  -96.50   49.62    2.07  -63.30  116.54   12.42
   38        268D 268D N   CA   2128 2129   66.58  114.20                  -40.00
   39  12601 269V 270P C   N    2141 2143  -70.45  -58.70   13.74    1.93  -64.50  175.30   12.77
   39        270P 270P N   CA   2143 2144  -37.61  -30.50                  147.20
   40  12602 270P 271M C   N    2148 2150  -76.55  -73.00    9.69    0.61   56.30  177.17   17.45
   40        271M 271M N   CA   2150 2151  152.01  143.00                   34.80
   41  12605 273E 274E C   N    2172 2174  110.90   54.60   99.21   11.82   54.60   99.21   11.82
   41        274E 274E N   CA   2174 2175  124.08   42.40                   42.40
   42  12607 275K 276S C   N    2190 2192  -89.95 -136.60   47.02    1.72  -64.10 -178.49   14.84
   42        276S 276S N   CA   2192 2193  145.34  151.20                  -35.00
   43  12664 332V 333Q C   N    2623 2625 -108.47  -63.80   52.15    9.47  -63.80   52.15    9.47
   43        333Q 333Q N   CA   2625 2626  -67.21  -40.30                  -40.30
   44  12715 383S 384I C   N    3021 3023  -92.14 -120.60   81.63    3.65  -63.40  101.55   15.78
   44        384I 384I N   CA   3023 3024   53.80  130.30                  -43.60
   45  12716 384I 385I C   N    3029 3031 -145.75  -63.40   87.37   14.55  -63.40   87.37   14.55
   45        385I 385I N   CA   3031 3032  -14.43  -43.60                  -43.60
   46  12720 388T 389V C   N    3059 3061 -107.70 -125.40   92.87    4.14  -62.40  104.82   11.50
   46        389V 389V N   CA   3061 3062   52.13  143.30                  -42.40
   47  12767 435G 436D C   N    3407 3409  -34.92  -96.50   72.60    2.96  -63.30  169.73   19.40
   47        436D 436D N   CA   3409 3410  152.66  114.20                  -40.00
   48  12786 454L 455W C   N    3545 3547 -116.18  -63.00   91.27   10.27  -63.00   91.27   10.27
   48        455W 455W N   CA   3547 3548   29.97  -44.20                  -44.20
   49  12792 460L 461H C   N    3598 3600 -177.54  -63.20  119.80   20.31   56.30  173.32   16.83
   49        461H 461H N   CA   3600 3601  -78.04  -42.30                   40.80


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0   39   91  317  362  415  454  520  599  578  685


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   743006
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -49846.6250




<< end of ENERGY.
DOPE score               : -49846.625000
>> Normalized DOPE z score: -0.665
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.113040
Native energy (pair)     :  -209.608153
Native energy (surface)  :    -8.530267
Native energy (combined) :    -5.632548
Z score (pair)           :    -9.331388
Z score (surface)        :    -6.952698
Z score (combined)       :   -10.324391
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   743006
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -49846.6250




<< end of ENERGY.
DOPE score               : -49846.625000
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   743006
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -37652.2617




<< end of ENERGY.
DOPE-HR score               : -37652.261719


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     8900
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        3874.6353





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    3676      15     24   0.016   0.016      257.93       1.000
 2 Bond angle potential               :    4978      16     55   2.821   2.821      772.57       1.000
 3 Stereochemical cosine torsion poten:    2202       0     67  46.443  46.443      739.81       1.000
 4 Stereochemical improper torsion pot:    1476       3      5   2.129   2.129      139.51       1.000
 5 Soft-sphere overlap restraints     :    8900       0      2   0.007   0.007      51.192       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    9560      13     24   0.262   0.262      485.13       1.000
10 Distance restraints 2 (N-O)        :    9747       9     17   0.292   0.292      578.72       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     461       0      9   5.106   5.106      141.72       1.000
14 Sidechain Chi_1 dihedral restraints:     404       0      9  71.029  71.029      105.15       1.000
15 Sidechain Chi_2 dihedral restraints:     308       0      1  72.612  72.612      115.46       1.000
16 Sidechain Chi_3 dihedral restraints:     130       0      0  78.974  78.974      90.266       1.000
17 Sidechain Chi_4 dihedral restraints:      51       0      0  91.090  91.090      33.117       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    4393       0      0   0.335   0.335      80.424       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     460      53     64  28.252  59.763      169.42       1.000
26 Distance restraints 4 (SDCH-SDCH)  :    1701       0      3   0.642   0.642      114.20       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: pkp2a.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   52238.3672



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   2125 264E 264E C   CA   2096 2090    1.65    1.49    0.16    4.65    1.49    0.16    4.65
    2   2134 265Q 265Q C   CA   2105 2099    1.67    1.49    0.18    5.23    1.49    0.18    5.23
    3   2147 266Y 266Y C   CA   2117 2108    1.66    1.49    0.17    4.83    1.49    0.17    4.83
    4   2154 267Q 267Q N   CA   2119 2120    1.58    1.43    0.15    4.93    1.43    0.15    4.93
    5   2156 267Q 267Q C   CA   2126 2120    1.65    1.49    0.16    4.79    1.49    0.16    4.79
    6   2162 268D 268D N   CA   2128 2129    1.60    1.43    0.17    5.60    1.43    0.17    5.60
    7   2165 268D 269V C   N    2134 2136    1.52    1.35    0.17    6.04    1.35    0.17    6.04
    8   2169 269V 269V N   CA   2136 2137    1.65    1.43    0.22    7.13    1.43    0.22    7.13
    9   2171 269V 269V C   CA   2141 2137    1.77    1.49    0.28    8.06    1.49    0.28    8.06
   10   2172 269V 270P C   N    2141 2143    1.56    1.30    0.26    7.61    1.30    0.26    7.61
   11   2174 270P 270P C   CA   2148 2144    1.78    1.49    0.29    8.36    1.49    0.29    8.36
   12   2175 270P 271M C   N    2148 2150    1.52    1.35    0.17    6.08    1.35    0.17    6.08
   13   2176 270P 270P N   CA   2143 2144    1.66    1.43    0.23    7.58    1.43    0.23    7.58
   14   2185 271M 271M N   CA   2150 2151    1.62    1.43    0.19    6.23    1.43    0.19    6.23
   15   2187 271M 271M C   CA   2156 2151    1.67    1.49    0.18    5.27    1.49    0.18    5.27

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   6546 265Q 265Q N   CA   2098 2099  128.84  107.00   21.84    6.28  107.00   21.84    6.28
    2   6555 265Q 266Y C   N    2105 2107  150.67  120.00   30.67    6.97  120.00   30.67    6.97
    3   6558 266Y 266Y N   CA   2107 2108  139.51  107.00   32.51    9.35  107.00   32.51    9.35
    4   6573 266Y 267Q C   N    2117 2119  145.72  120.00   25.72    5.84  120.00   25.72    5.84
    5   6576 267Q 267Q N   CA   2119 2120  136.24  107.00   29.24    8.41  107.00   29.24    8.41
    6   6585 267Q 268D C   N    2126 2128  155.78  120.00   35.78    8.13  120.00   35.78    8.13
    7   6588 268D 268D N   CA   2128 2129  132.72  107.00   25.72    7.40  107.00   25.72    7.40
    8   6596 268D 269V C   N    2134 2136  158.48  120.00   38.48    8.74  120.00   38.48    8.74
    9   6599 269V 269V N   CA   2136 2137  140.62  107.00   33.62    9.67  107.00   33.62    9.67
   10   6606 269V 270P C   N    2141 2143  144.95  117.00   27.95    6.96  117.00   27.95    6.96
   11   6609 270P 270P N   CA   2143 2144  151.30  108.20   43.10    9.79  108.20   43.10    9.79
   12   6613 270P 270P CA  C    2144 2148  135.97  116.50   19.47    5.60  116.50   19.47    5.60
   13   6621 271M 271M N   CA   2150 2151  127.57  107.00   20.57    5.91  107.00   20.57    5.91
   14   6628 271M 272P C   N    2156 2158  135.19  117.00   18.19    4.53  117.00   18.19    4.53

-------------------------------------------------------------------------------------------------

Feature 10                           : Distance restraints 2 (N-O)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  31799 384I 347V N   O    3023 2748   13.13   10.49    2.65    5.29   10.49    2.65    5.29

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  12333   1E   2M C   N       8   10  -88.18  -73.00   25.83    2.01   56.30  168.81   21.04
    1          2M   2M N   CA     10   11  122.11  143.00                   34.80
    2  12350  18P  19S C   N     140  142  -44.10  -72.40   59.83    2.76  -64.10  136.16   11.18
    2         19S  19S N   CA    142  143   99.68  152.40                  -35.00
    3  12351  19S  20R C   N     146  148 -166.16  -63.00  119.52   21.79  -63.00  119.52   21.79
    3         20R  20R N   CA    148  149 -101.46  -41.10                  -41.10
    4  12477 145W 146P C   N    1157 1159  -71.65  -64.50   22.78    1.39  -58.70  161.19   14.38
    4        146P 146P N   CA   1159 1160  168.83  147.20                  -30.50
    5  12478 146P 147E C   N    1164 1166  -75.15  -69.30   20.70    1.37  -63.60  157.77   21.68
    5        147E 147E N   CA   1166 1167  162.36  142.50                  -40.30
    6  12479 147E 148G C   N    1173 1175  111.97   78.70   73.32    1.09   82.20  123.69    7.45
    6        148G 148G N   CA   1175 1176  128.56 -166.10                    8.50
    7  12480 148G 149D C   N    1177 1179 -123.17  -96.50   38.67    1.62  -63.30 -172.39   27.03
    7        149D 149D N   CA   1179 1180  142.20  114.20                  -40.00
    8  12481 149D 150Y C   N    1185 1187 -127.43 -124.30    9.59    0.40  -63.50 -176.37   32.35
    8        150Y 150Y N   CA   1187 1188  144.46  135.40                  -43.40
    9  12482 150Y 151P C   N    1197 1199  -63.76  -58.70    6.36    0.88  -64.50  178.46   13.36
    9        151P 151P N   CA   1199 1200  -34.34  -30.50                  147.20
   10  12483 151P 152K C   N    1204 1206 -138.17 -118.00   24.29    0.81  -62.90 -177.21   28.24
   10        152K 152K N   CA   1206 1207  152.63  139.10                  -40.80
   11  12484 152K 153A C   N    1213 1215 -140.70 -134.00   10.16    0.33  -62.50 -177.88   34.04
   11        153A 153A N   CA   1215 1216  154.63  147.00                  -40.90
   12  12485 153A 154N C   N    1218 1220 -111.81 -119.90   10.78    0.58  -63.20 -178.58   25.45
   12        154N 154N N   CA   1220 1221  144.12  137.00                  -41.10
   13  12486 154N 155G C   N    1226 1228  -60.65  -80.20   67.06    1.76   82.20  175.21    6.71
   13        155G 155G N   CA   1228 1229  109.96  174.10                    8.50
   14  12535 203D 204Y C   N    1599 1601   72.93   55.90   17.08    1.85  -63.50  158.95   30.03
   14        204Y 204Y N   CA   1601 1602   38.17   39.50                  -43.40
   15  12536 204Y 205Q C   N    1611 1613 -115.97 -121.10   81.41    3.79  -63.80  111.69   14.40
   15        205Q 205Q N   CA   1613 1614   58.45  139.70                  -40.30
   16  12570 238Y 239I C   N    1888 1890 -106.43 -120.60   32.60    1.39  -63.40  150.81   23.42
   16        239I 239I N   CA   1890 1891  100.94  130.30                  -43.60
   17  12571 239I 240Q C   N    1896 1898  -67.33  -63.80    4.07    0.57 -121.10 -174.08    7.81
   17        240Q 240Q N   CA   1898 1899  -38.28  -40.30                  139.70
   18  12572 240Q 241N C   N    1905 1907  -55.05  -71.20   25.81    1.37  -63.20  163.96   20.95
   18        241N 241N N   CA   1907 1908  122.66  142.80                  -41.10
   19  12573 241N 242R C   N    1913 1915 -149.39 -125.20   27.04    0.82  -63.00 -172.69   31.16
   19        242R 242R N   CA   1915 1916  152.70  140.60                  -41.10
   20  12576 244I 245Q C   N    1940 1942  -94.71  -73.00   60.46    4.39  -63.80  128.35   17.40
   20        245Q 245Q N   CA   1942 1943   84.28  140.70                  -40.30
   21  12577 245Q 246T C   N    1949 1951 -133.64 -124.80   50.02    2.41  -63.20  153.49   16.31
   21        246T 246T N   CA   1951 1952   94.26  143.50                  -42.10
   22  12579 247D 248N C   N    1964 1966  -75.49  -71.20   17.24    0.99  -63.20  159.89   20.67
   22        248N 248N N   CA   1966 1967  159.49  142.80                  -41.10
   23  12580 248N 249N C   N    1972 1974  -75.58  -71.20   14.16    0.80  -63.20  163.11   21.08
   23        249N 249N N   CA   1974 1975  156.26  142.80                  -41.10
   24  12581 249N 250K C   N    1980 1982  -77.56  -70.20   10.36    0.62  -62.90  172.14   23.18
   24        250K 250K N   CA   1982 1983  147.68  140.40                  -40.80
   25  12582 250K 251S C   N    1989 1991  -90.78  -72.40   45.17    2.13  -64.10  134.01   11.50
   25        251S 251S N   CA   1991 1992 -166.34  152.40                  -35.00
   26  12584 252I 253G C   N    2003 2005  -66.41  -80.20   24.74    0.61   82.20 -152.33    6.58
   26        253G 253G N   CA   2005 2006  153.56  174.10                    8.50
   27  12586 254C 255F C   N    2013 2015 -123.96 -124.20    0.72    0.03  -63.20 -176.56   29.49
   27        255F 255F N   CA   2015 2016  142.62  143.30                  -44.30
   28  12587 255F 256G C   N    2024 2026  -86.26  -80.20    6.85    0.51   82.20 -126.01    7.47
   28        256G 256G N   CA   2026 2027  170.90  174.10                    8.50
   29  12588 256G 257S C   N    2028 2030  -80.38  -72.40   18.81    1.37  -64.10  171.14   11.53
   29        257S 257S N   CA   2030 2031  135.36  152.40                  -35.00
   30  12590 258R 259S C   N    2045 2047  -48.67  -72.40   26.85    1.49  -64.10  175.51   13.69
   30        259S 259S N   CA   2047 2048  139.83  152.40                  -35.00
   31  12591 259S 260R C   N    2051 2053 -110.55 -125.20   19.04    0.57  -63.00  176.08   21.02
   31        260R 260R N   CA   2053 2054  128.44  140.60                  -41.10
   32  12592 260R 261K C   N    2062 2064 -152.04 -118.00   41.26    1.38  -62.90 -179.64   28.74
   32        261K 261K N   CA   2064 2065  162.41  139.10                  -40.80
   33  12594 262V 263K C   N    2078 2080 -172.69 -118.00   80.22    2.87  -62.90  163.69   27.59
   33        263K 263K N   CA   2080 2081 -162.21  139.10                  -40.80
   34  12595 263K 264E C   N    2087 2089 -168.98 -117.80   53.51    1.64  -63.60 -162.29   32.13
   34        264E 264E N   CA   2089 2090  152.41  136.80                  -40.30
   35  12596 264E 265Q C   N    2096 2098  166.87 -121.10   72.29    2.59  -63.80 -143.25   38.27
   35        265Q 265Q N   CA   2098 2099  145.76  139.70                  -40.30
   36  12597 265Q 266Y C   N    2105 2107   97.58 -124.30  140.76    9.64  -63.50 -137.08   31.09
   36        266Y 266Y N   CA   2107 2108  162.50  135.40                  -43.40
   37  12598 266Y 267Q C   N    2117 2119  -84.81  -73.00   73.01    4.54  -63.80  108.99   17.15
   37        267Q 267Q N   CA   2119 2120 -147.25  140.70                  -40.30
   38  12599 267Q 268D C   N    2126 2128   16.29  -70.90   87.27    6.48  -63.30 -169.04   20.32
   38        268D 268D N   CA   2128 2129  146.42  150.30                  -40.00
   39  12600 268D 269V C   N    2134 2136   32.80  -62.40  132.54   15.36 -125.40  178.22    9.30
   39        269V 269V N   CA   2136 2137 -134.61  -42.40                  143.30
   40  12601 269V 270P C   N    2141 2143  -71.40  -58.70   27.48    3.29  -64.50  158.08   11.44
   40        270P 270P N   CA   2143 2144  -54.87  -30.50                  147.20
   41  12602 270P 271M C   N    2148 2150 -152.48 -125.60   37.43    1.14   56.30 -159.44   34.63
   41        271M 271M N   CA   2150 2151  166.54  140.50                   34.80
   42  12605 273E 274E C   N    2172 2174   92.50   54.60   88.00    9.70   54.60   88.00    9.70
   42        274E 274E N   CA   2174 2175  121.82   42.40                   42.40
   43  12607 275K 276S C   N    2190 2192  -91.86 -136.60   46.07    1.56  -64.10  177.41   11.49
   43        276S 276S N   CA   2192 2193  140.22  151.20                  -35.00
   44  12664 332V 333Q C   N    2623 2625 -111.09  -63.80   52.65    9.52  -63.80   52.65    9.52
   44        333Q 333Q N   CA   2625 2626  -63.46  -40.30                  -40.30
   45  12677 345L 346H C   N    2730 2732 -108.15  -63.20   96.73   10.29  -63.20   96.73   10.29
   45        346H 346H N   CA   2732 2733   43.36  -42.30                  -42.30
   46  12678 346H 347V C   N    2740 2742  -66.54  -62.40    8.85    0.97  -73.50  173.91   14.77
   46        347V 347V N   CA   2742 2743  -34.57  -42.40                  139.20
   47  12679 347V 348G C   N    2747 2749   90.48   82.20   21.74    0.67  -62.40  155.73   28.82
   47        348G 348G N   CA   2749 2750  -11.60    8.50                  -41.20
   48  12715 383S 384I C   N    3021 3023  -88.77 -120.60   89.32    3.98  -63.40   93.94   14.62
   48        384I 384I N   CA   3023 3024   46.85  130.30                  -43.60
   49  12716 384I 385I C   N    3029 3031 -148.63  -63.40   91.29   15.12  -63.40   91.29   15.12
   49        385I 385I N   CA   3031 3032  -10.90  -43.60                  -43.60
   50  12720 388T 389V C   N    3059 3061 -108.93 -125.40   90.12    4.04  -62.40  107.67   11.81
   50        389V 389V N   CA   3061 3062   54.70  143.30                  -42.40
   51  12767 435G 436D C   N    3407 3409  -27.44  -96.50   75.87    3.09  -63.30  178.01   20.06
   51        436D 436D N   CA   3409 3410  145.64  114.20                  -40.00
   52  12786 454L 455W C   N    3545 3547 -116.24  -63.00   89.98   10.15  -63.00   89.98   10.15
   52        455W 455W N   CA   3547 3548   28.35  -44.20                  -44.20
   53  12792 460L 461H C   N    3598 3600 -170.91 -125.60  116.52    3.49   56.30 -156.16   17.95
   53        461H 461H N   CA   3600 3601 -113.85  138.80                   40.80


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    1   36   85  317  321  432  452  505  629  661  697


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   751721
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50001.3477




<< end of ENERGY.
DOPE score               : -50001.347656
>> Normalized DOPE z score: -0.689
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.117056
Native energy (pair)     :  -309.404973
Native energy (surface)  :    -7.700988
Native energy (combined) :    -7.770491
Z score (pair)           :    -9.745124
Z score (surface)        :    -6.978175
Z score (combined)       :   -10.923983
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   751721
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50001.3477




<< end of ENERGY.
DOPE score               : -50001.347656
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   751721
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -37202.7539




<< end of ENERGY.
DOPE-HR score               : -37202.753906


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     9192
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        3048.5537





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    3676       0      0   0.006   0.006      38.826       1.000
 2 Bond angle potential               :    4978       1     29   2.304   2.304      516.01       1.000
 3 Stereochemical cosine torsion poten:    2202       0     67  46.991  46.991      758.11       1.000
 4 Stereochemical improper torsion pot:    1476       0      5   1.852   1.852      109.65       1.000
 5 Soft-sphere overlap restraints     :    9192       0      0   0.004   0.004      20.448       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    9560       0      0   0.156   0.156      166.32       1.000
10 Distance restraints 2 (N-O)        :    9747       2     15   0.250   0.250      422.51       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     461       0      8   4.875   4.875      129.19       1.000
14 Sidechain Chi_1 dihedral restraints:     404       0      6  73.579  73.579      123.09       1.000
15 Sidechain Chi_2 dihedral restraints:     308       0      8  73.574  73.574      163.27       1.000
16 Sidechain Chi_3 dihedral restraints:     130       0      0  83.032  83.032      94.487       1.000
17 Sidechain Chi_4 dihedral restraints:      51       0      0  92.072  92.072      30.907       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    4393       0      0   0.364   0.364      96.139       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     460      53     60  27.401  57.756      151.98       1.000
26 Distance restraints 4 (SDCH-SDCH)  :    1701       0     11   0.900   0.900      227.62       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: pkp2a.V99990003
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   52280.4883



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   6559 266Y 266Y CA  CB   2108 2109  132.79  107.50   25.30    5.85  107.50   25.30    5.85

-------------------------------------------------------------------------------------------------

Feature 10                           : Distance restraints 2 (N-O)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  31799 384I 347V N   O    3023 2748   13.11   10.49    2.62    5.23   10.49    2.62    5.23

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  12333   1E   2M C   N       8   10 -107.69 -125.60   42.67    1.60   56.30  177.13   25.60
    1          2M   2M N   CA     10   11  101.77  140.50                   34.80
    2  12350  18P  19S C   N     140  142  -42.72  -72.40   60.98    2.81  -64.10  135.83   11.25
    2         19S  19S N   CA    142  143   99.13  152.40                  -35.00
    3  12351  19S  20R C   N     146  148 -165.27 -125.20  120.58    4.82  -63.00  120.95   22.05
    3         20R  20R N   CA    148  149 -105.67  140.60                  -41.10
    4  12477 145W 146P C   N    1157 1159  -69.13  -64.50   17.04    1.06  -58.70  166.23   14.59
    4        146P 146P N   CA   1159 1160  163.60  147.20                  -30.50
    5  12478 146P 147E C   N    1164 1166  -71.66  -69.30   13.53    0.95  -63.60  164.08   22.32
    5        147E 147E N   CA   1166 1167  155.82  142.50                  -40.30
    6  12479 147E 148G C   N    1173 1175  -61.82  -62.40    2.95    0.47   82.20  151.44   11.47
    6        148G 148G N   CA   1175 1176  -38.31  -41.20                    8.50
    7  12481 149D 150Y C   N    1185 1187  -73.06  -98.40   26.99    1.30  -63.50  179.16   28.92
    7        150Y 150Y N   CA   1187 1188  137.69  128.40                  -43.40
    8  12483 151P 152K C   N    1204 1206  -77.08  -70.20   15.31    0.96  -62.90  165.73   22.32
    8        152K 152K N   CA   1206 1207  154.08  140.40                  -40.80
    9  12484 152K 153A C   N    1213 1215  -66.66  -68.20    5.46    0.49  -62.50  168.62   27.84
    9        153A 153A N   CA   1215 1216  150.54  145.30                  -40.90
   10  12485 153A 154N C   N    1218 1220  -69.46  -71.20    1.75    0.13  -63.20  176.05   22.36
   10        154N 154N N   CA   1220 1221  142.96  142.80                  -41.10
   11  12486 154N 155G C   N    1226 1228   98.61   78.70   69.35    1.22   82.20  120.10    6.64
   11        155G 155G N   CA   1228 1229  127.47 -166.10                    8.50
   12  12488 156L 157L C   N    1238 1240   82.35   60.20   99.54    7.84 -108.50  169.25    8.13
   12        157L 157L N   CA   1240 1241  126.64   29.60                  132.50
   13  12507 175A 176G C   N    1388 1390   25.84   82.20   66.01    2.76  -62.40  121.87   22.65
   13        176G 176G N   CA   1390 1391   42.86    8.50                  -41.20
   14  12508 176G 177A C   N    1392 1394   33.80  -62.50  121.40   24.56  -62.50  121.40   24.56
   14        177A 177A N   CA   1394 1395   33.02  -40.90                  -40.90
   15  12518 186C 187D C   N    1470 1472    0.20  -63.30  105.43   11.40  -70.90  111.23    8.75
   15        187D 187D N   CA   1472 1473 -124.16  -40.00                  150.30
   16  12519 187D 188G C   N    1478 1480  -64.43  -62.40   41.37    6.08   82.20  146.87   10.15
   16        188G 188G N   CA   1480 1481    0.12  -41.20                    8.50
   17  12535 203D 204Y C   N    1599 1601   74.25   55.90   19.40    1.80  -63.50  157.62   29.72
   17        204Y 204Y N   CA   1601 1602   33.21   39.50                  -43.40
   18  12536 204Y 205Q C   N    1611 1613 -118.35 -121.10   76.78    3.61  -63.80  116.80   15.06
   18        205Q 205Q N   CA   1613 1614   62.97  139.70                  -40.30
   19  12570 238Y 239I C   N    1888 1890 -112.82 -120.60   39.99    1.99  -63.40  143.46   22.10
   19        239I 239I N   CA   1890 1891   91.08  130.30                  -43.60
   20  12572 240Q 241N C   N    1905 1907   50.55   55.90    8.50    0.46  -63.20  143.34   23.48
   20        241N 241N N   CA   1907 1908   46.12   39.50                  -41.10
   21  12573 241N 242R C   N    1913 1915  -81.80  -72.10   42.07    3.43  -63.00  143.30   18.16
   21        242R 242R N   CA   1915 1916  100.96  141.90                  -41.10
   22  12574 242R 243N C   N    1924 1926 -147.52 -119.90   37.26    1.08  -63.20  178.11   26.99
   22        243N 243N N   CA   1926 1927  162.01  137.00                  -41.10
   23  12576 244I 245Q C   N    1940 1942 -126.07 -121.10   10.02    0.37  -63.80 -177.73   30.10
   23        245Q 245Q N   CA   1942 1943  148.40  139.70                  -40.30
   24  12577 245Q 246T C   N    1949 1951 -114.79 -124.80   10.14    0.49  -63.20 -176.57   26.96
   24        246T 246T N   CA   1951 1952  141.88  143.50                  -42.10
   25  12578 246T 247D C   N    1956 1958  -68.04  -70.90   11.60    0.44  -63.30  179.12   21.83
   25        247D 247D N   CA   1958 1959  139.06  150.30                  -40.00
   26  12579 247D 248N C   N    1964 1966 -115.80 -119.90    4.86    0.26  -63.20 -173.16   26.36
   26        248N 248N N   CA   1966 1967  139.62  137.00                  -41.10
   27  12580 248N 249N C   N    1972 1974 -104.67 -119.90   19.87    0.58  -63.20  170.46   19.32
   27        249N 249N N   CA   1974 1975  124.24  137.00                  -41.10
   28  12581 249N 250K C   N    1980 1982 -128.68 -118.00   24.74    1.01  -62.90  170.94   26.14
   28        250K 250K N   CA   1982 1983  161.42  139.10                  -40.80
   29  12582 250K 251S C   N    1989 1991 -123.18 -136.60   17.16    0.53  -64.10 -174.82   11.41
   29        251S 251S N   CA   1991 1992  140.50  151.20                  -35.00
   30  12584 252I 253G C   N    2003 2005 -146.64 -167.20   36.75    1.01   82.20 -171.32   14.42
   30        253G 253G N   CA   2005 2006  144.14  174.60                    8.50
   31  12586 254C 255F C   N    2013 2015 -105.92 -124.20   21.47    0.56  -63.20 -178.55   22.51
   31        255F 255F N   CA   2015 2016  132.04  143.30                  -44.30
   32  12587 255F 256G C   N    2024 2026  156.96 -167.20   41.94    1.38   82.20  162.53   11.28
   32        256G 256G N   CA   2026 2027  152.82  174.60                    8.50
   33  12588 256G 257S C   N    2028 2030 -158.23 -136.60   33.20    1.12  -64.10  175.92   19.54
   33        257S 257S N   CA   2030 2031  176.38  151.20                  -35.00
   34  12589 257S 258R C   N    2034 2036   57.47   57.30    4.03    0.25  -63.00  141.95   25.88
   34        258R 258R N   CA   2036 2037   33.97   38.00                  -41.10
   35  12590 258R 259S C   N    2045 2047  -93.31  -72.40   65.34    4.56  -64.10  128.85    8.08
   35        259S 259S N   CA   2047 2048   90.50  152.40                  -35.00
   36  12591 259S 260R C   N    2051 2053 -122.10 -125.20   23.00    1.04  -63.00  169.54   19.70
   36        260R 260R N   CA   2053 2054  117.81  140.60                  -41.10
   37  12592 260R 261K C   N    2062 2064 -146.43 -118.00   29.31    1.00  -62.90 -167.91   29.94
   37        261K 261K N   CA   2064 2065  146.22  139.10                  -40.80
   38  12594 262V 263K C   N    2078 2080 -161.31 -118.00   53.15    1.79  -62.90  178.79   29.05
   38        263K 263K N   CA   2080 2081  169.92  139.10                  -40.80
   39  12595 263K 264E C   N    2087 2089 -155.10 -117.80   39.05    1.19  -63.60 -165.76   30.98
   39        264E 264E N   CA   2089 2090  148.36  136.80                  -40.30
   40  12596 264E 265Q C   N    2096 2098 -145.28 -121.10   36.97    1.24  -63.80  172.48   29.57
   40        265Q 265Q N   CA   2098 2099  167.67  139.70                  -40.30
   41  12597 265Q 266Y C   N    2105 2107 -119.06 -124.30   31.81    1.91  -63.50  159.79   28.14
   41        266Y 266Y N   CA   2107 2108  166.78  135.40                  -43.40
   42  12598 266Y 267Q C   N    2117 2119 -165.35 -121.10   58.36    1.85  -63.80  174.53   30.72
   42        267Q 267Q N   CA   2119 2120  177.75  139.70                  -40.30
   43  12599 267Q 268D C   N    2126 2128  139.86  -96.50  133.12    5.49  -63.30 -138.44   36.85
   43        268D 268D N   CA   2128 2129  163.52  114.20                  -40.00
   44  12602 270P 271M C   N    2148 2150 -168.07  -63.40  116.11   23.55   56.30 -175.17   17.52
   44        271M 271M N   CA   2150 2151  -90.75  -40.50                   34.80
   45  12605 273E 274E C   N    2172 2174  119.17   54.60  110.77   13.30   54.60  110.77   13.30
   45        274E 274E N   CA   2174 2175  132.40   42.40                   42.40
   46  12677 345L 346H C   N    2730 2732 -106.52  -63.20   91.01    9.68  -63.20   91.01    9.68
   46        346H 346H N   CA   2732 2733   37.74  -42.30                  -42.30
   47  12678 346H 347V C   N    2740 2742  -67.64  -62.40   10.75    1.18  -73.50  172.31   14.65
   47        347V 347V N   CA   2742 2743  -33.01  -42.40                  139.20
   48  12679 347V 348G C   N    2747 2749   97.69   82.20   35.70    1.04  -62.40  161.05   29.42
   48        348G 348G N   CA   2749 2750  -23.67    8.50                  -41.20
   49  12715 383S 384I C   N    3021 3023  -88.10 -120.60   84.04    3.68  -63.40   99.52   15.55
   49        384I 384I N   CA   3023 3024   52.80  130.30                  -43.60
   50  12716 384I 385I C   N    3029 3031 -149.40  -63.40   90.25   15.14  -63.40   90.25   15.14
   50        385I 385I N   CA   3031 3032  -16.24  -43.60                  -43.60
   51  12720 388T 389V C   N    3059 3061 -107.70 -125.40   95.68    4.28  -62.40  102.25   11.20
   51        389V 389V N   CA   3061 3062   49.27  143.30                  -42.40
   52  12767 435G 436D C   N    3407 3409  -38.03  -96.50   71.48    2.92  -63.30  166.60   19.16
   52        436D 436D N   CA   3409 3410  155.33  114.20                  -40.00
   53  12792 460L 461H C   N    3598 3600 -157.52  -63.20  106.94   18.37   56.30 -162.02   19.50
   53        461H 461H N   CA   3600 3601  -92.71  -42.30                   40.80


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    1   45   87  364  335  484  459  504  604  674  725


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   756821
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50752.7070




<< end of ENERGY.
DOPE score               : -50752.707031
>> Normalized DOPE z score: -0.804
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.126006
Native energy (pair)     :  -288.595925
Native energy (surface)  :     1.293338
Native energy (combined) :    -5.721212
Z score (pair)           :    -8.870528
Z score (surface)        :    -5.776669
Z score (combined)       :    -9.192732
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   756821
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50752.7070




<< end of ENERGY.
DOPE score               : -50752.707031
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   756821
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -39683.5977




<< end of ENERGY.
DOPE-HR score               : -39683.597656


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     8817
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        2926.7734





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    3676       0      0   0.007   0.007      47.507       1.000
 2 Bond angle potential               :    4978       0     23   2.223   2.223      487.31       1.000
 3 Stereochemical cosine torsion poten:    2202       0     54  46.449  46.449      740.63       1.000
 4 Stereochemical improper torsion pot:    1476       0      1   1.559   1.559      84.727       1.000
 5 Soft-sphere overlap restraints     :    8817       0      0   0.004   0.004      15.274       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    9560       3     11   0.207   0.207      220.47       1.000
10 Distance restraints 2 (N-O)        :    9747       4     17   0.261   0.261      424.72       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     461       1     12   5.269   5.269      150.94       1.000
14 Sidechain Chi_1 dihedral restraints:     404       0      6  66.716  66.716      102.67       1.000
15 Sidechain Chi_2 dihedral restraints:     308       0      8  71.509  71.509      121.33       1.000
16 Sidechain Chi_3 dihedral restraints:     130       0      0  77.355  77.355      87.826       1.000
17 Sidechain Chi_4 dihedral restraints:      51       0      0  88.787  88.787      31.097       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    4393       0      0   0.327   0.327      76.625       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     460      53     62  28.600  56.273      177.09       1.000
26 Distance restraints 4 (SDCH-SDCH)  :    1701       0      4   0.750   0.750      158.55       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: pkp2a.V99990004
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   49326.3750



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature 10                           : Distance restraints 2 (N-O)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  31799 384I 347V N   O    3023 2748   12.96   10.49    2.48    4.94   10.49    2.48    4.94
    2  32792 427Q 423T N   O    3347 3330    5.39    2.70    2.70    4.84    2.70    2.70    4.84

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  13056 264E 264E CA  C    2090 2096 -151.39 -180.00   28.61    5.72 -180.00   28.61    5.72

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  12349  17L  18P C   N     133  135  -40.32  -58.70   43.57    2.55  -64.50  144.83   12.12
    1         18P  18P N   CA    135  136  -70.00  -30.50                  147.20
    2  12350  18P  19S C   N     140  142 -153.45 -136.60   81.02    4.40  -64.10  139.36   10.45
    2         19S  19S N   CA    142  143   71.94  151.20                  -35.00
    3  12351  19S  20R C   N     146  148 -150.43  -63.00  107.09   19.49  -63.00  107.09   19.49
    3         20R  20R N   CA    148  149 -102.93  -41.10                  -41.10
    4  12477 145W 146P C   N    1157 1159  -67.69  -64.50   12.97    0.82  -58.70  169.96   14.78
    4        146P 146P N   CA   1159 1160  159.78  147.20                  -30.50
    5  12478 146P 147E C   N    1164 1166 -106.88 -117.80   17.17    0.58  -63.60  169.48   20.53
    5        147E 147E N   CA   1166 1167  123.56  136.80                  -40.30
    6  12480 148G 149D C   N    1177 1179  -94.20  -96.50   29.31    1.23  -63.30  128.75   14.30
    6        149D 149D N   CA   1179 1180   84.99  114.20                  -40.00
    7  12481 149D 150Y C   N    1185 1187 -125.09 -124.30   10.99    0.62  -63.50  178.78   25.57
    7        150Y 150Y N   CA   1187 1188  124.44  135.40                  -43.40
    8  12484 152K 153A C   N    1213 1215  -70.48  -68.20    3.07    0.19  -62.50  171.93   28.57
    8        153A 153A N   CA   1215 1216  147.36  145.30                  -40.90
    9  12485 153A 154N C   N    1218 1220  -91.36  -71.20   38.38    2.04  -63.20  146.19   19.87
    9        154N 154N N   CA   1220 1221  175.45  142.80                  -41.10
   10  12507 175A 176G C   N    1388 1390   47.60  -62.40  168.79   23.41  -62.40  168.79   23.41
   10        176G 176G N   CA   1390 1391 -169.23  -41.20                  -41.20
   11  12535 203D 204Y C   N    1599 1601   70.62   55.90   14.93    1.54  -63.50  156.37   29.54
   11        204Y 204Y N   CA   1601 1602   36.99   39.50                  -43.40
   12  12536 204Y 205Q C   N    1611 1613 -116.90 -121.10   81.53    3.81  -63.80  111.97   14.42
   12        205Q 205Q N   CA   1613 1614   58.27  139.70                  -40.30
   13  12568 236N 237I C   N    1868 1870 -102.90 -120.60   72.48    3.48  -63.40  110.89   17.06
   13        237I 237I N   CA   1870 1871   60.01  130.30                  -43.60
   14  12569 237I 238Y C   N    1876 1878 -115.80  -63.50   54.28    9.95  -63.50   54.28    9.95
   14        238Y 238Y N   CA   1878 1879  -57.93  -43.40                  -43.40
   15  12570 238Y 239I C   N    1888 1890 -122.23 -120.60   62.28    3.50  -63.40  137.10   24.62
   15        239I 239I N   CA   1890 1891 -167.44  130.30                  -43.60
   16  12572 240Q 241N C   N    1905 1907 -126.98 -119.90   97.40    4.26  -63.20  106.07   16.72
   16        241N 241N N   CA   1907 1908 -125.85  137.00                  -41.10
   17  12573 241N 242R C   N    1913 1915 -117.92 -125.20   29.63    1.56  -63.00  159.35   25.31
   17        242R 242R N   CA   1915 1916  169.31  140.60                  -41.10
   18  12574 242R 243N C   N    1924 1926  -58.34  -71.20   13.09    1.00  -63.20  173.69   21.45
   18        243N 243N N   CA   1926 1927  145.28  142.80                  -41.10
   19  12576 244I 245Q C   N    1940 1942  -62.00  -73.00   11.13    0.82  -63.80  177.28   25.97
   19        245Q 245Q N   CA   1942 1943  142.42  140.70                  -40.30
   20  12577 245Q 246T C   N    1949 1951  -77.84  -78.10   12.15    0.51  -63.20 -179.65   22.19
   20        246T 246T N   CA   1951 1952  137.66  149.80                  -42.10
   21  12579 247D 248N C   N    1964 1966  -59.93  -71.20   12.60    1.01  -63.20  170.52   21.14
   21        248N 248N N   CA   1966 1967  148.41  142.80                  -41.10
   22  12580 248N 249N C   N    1972 1974 -124.80 -119.90   33.73    1.41  -63.20  160.79   23.60
   22        249N 249N N   CA   1974 1975  170.37  137.00                  -41.10
   23  12581 249N 250K C   N    1980 1982  -66.63  -70.20    3.69    0.29  -62.90  177.90   23.31
   23        250K 250K N   CA   1982 1983  141.34  140.40                  -40.80
   24  12582 250K 251S C   N    1989 1991 -138.71 -136.60   18.09    0.87  -64.10  172.77   17.85
   24        251S 251S N   CA   1991 1992  169.16  151.20                  -35.00
   25  12584 252I 253G C   N    2003 2005 -140.48 -167.20   30.37    0.48   82.20 -155.41   15.53
   25        253G 253G N   CA   2005 2006  160.17  174.60                    8.50
   26  12586 254C 255F C   N    2013 2015  -91.56  -71.40   24.66    1.39  -63.20  163.28   24.59
   26        255F 255F N   CA   2015 2016  154.90  140.70                  -44.30
   27  12587 255F 256G C   N    2024 2026 -153.01 -167.20   14.68    0.38   82.20 -149.25   15.56
   27        256G 256G N   CA   2026 2027  178.34  174.60                    8.50
   28  12588 256G 257S C   N    2028 2030  -72.82  -72.40   12.84    0.74  -64.10  160.00   12.13
   28        257S 257S N   CA   2030 2031  165.23  152.40                  -35.00
   29  12589 257S 258R C   N    2034 2036  -70.55  -72.10    1.63    0.13  -63.00  176.67   24.38
   29        258R 258R N   CA   2036 2037  142.39  141.90                  -41.10
   30  12590 258R 259S C   N    2045 2047 -153.24 -136.60   29.62    1.07  -64.10  173.88   19.02
   30        259S 259S N   CA   2047 2048  175.70  151.20                  -35.00
   31  12591 259S 260R C   N    2051 2053 -145.75 -125.20   22.85    0.70  -63.00 -172.45   30.97
   31        260R 260R N   CA   2053 2054  150.59  140.60                  -41.10
   32  12592 260R 261K C   N    2062 2064   74.75   56.60   86.17    7.57  -62.90 -146.17   35.77
   32        261K 261K N   CA   2064 2065  122.83   38.60                  -40.80
   33  12594 262V 263K C   N    2078 2080  154.14 -118.00   88.37    3.18  -62.90 -137.41   37.22
   33        263K 263K N   CA   2080 2081  148.58  139.10                  -40.80
   34  12595 263K 264E C   N    2087 2089 -130.94 -117.80   80.81    3.79  -63.60  123.20   20.10
   34        264E 264E N   CA   2089 2090 -143.47  136.80                  -40.30
   35  12596 264E 265Q C   N    2096 2098 -140.83 -121.10   34.07    1.20  -63.80  170.61   29.09
   35        265Q 265Q N   CA   2098 2099  167.47  139.70                  -40.30
   36  12597 265Q 266Y C   N    2105 2107 -146.89 -124.30   71.31    2.96  -63.50  140.89   26.18
   36        266Y 266Y N   CA   2107 2108 -156.96  135.40                  -43.40
   37  12598 266Y 267Q C   N    2117 2119 -133.05 -121.10   46.25    1.97  -63.80  152.01   25.95
   37        267Q 267Q N   CA   2119 2120 -175.62  139.70                  -40.30
   38  12599 267Q 268D C   N    2126 2128 -139.11  -96.50   59.51    2.49  -63.30 -179.09   27.23
   38        268D 268D N   CA   2128 2129  155.74  114.20                  -40.00
   39  12602 270P 271M C   N    2148 2150  128.92 -125.60  106.55    4.59   56.30  116.13   18.25
   39        271M 271M N   CA   2150 2151  125.43  140.50                   34.80
   40  12603 271M 272P C   N    2156 2158  -52.82  -58.70   46.49    3.39  -64.50  136.68   10.83
   40        272P 272P N   CA   2158 2159  -76.62  -30.50                  147.20
   41  12605 273E 274E C   N    2172 2174  100.86   54.60   95.96   10.91   54.60   95.96   10.91
   41        274E 274E N   CA   2174 2175  126.47   42.40                   42.40
   42  12664 332V 333Q C   N    2623 2625 -111.68  -63.80   52.32    9.43  -63.80   52.32    9.43
   42        333Q 333Q N   CA   2625 2626  -61.40  -40.30                  -40.30
   43  12677 345L 346H C   N    2730 2732 -106.51  -63.20   93.41    9.94  -63.20   93.41    9.94
   43        346H 346H N   CA   2732 2733   40.46  -42.30                  -42.30
   44  12678 346H 347V C   N    2740 2742  -64.12  -62.40    2.37    0.28  -73.50 -179.79   15.27
   44        347V 347V N   CA   2742 2743  -40.76  -42.40                  139.20
   45  12679 347V 348G C   N    2747 2749   92.92   82.20   22.76    0.64  -62.40  158.12   29.25
   45        348G 348G N   CA   2749 2750  -11.58    8.50                  -41.20
   46  12715 383S 384I C   N    3021 3023  -89.08 -120.60   85.82    3.80  -63.40   97.52   15.20
   46        384I 384I N   CA   3023 3024   50.48  130.30                  -43.60
   47  12716 384I 385I C   N    3029 3031 -144.49  -63.40   81.53   14.28  -63.40   81.53   14.28
   47        385I 385I N   CA   3031 3032  -35.12  -43.60                  -43.60
   48  12720 388T 389V C   N    3059 3061 -108.33 -125.40   93.31    4.18  -62.40  104.59   11.46
   48        389V 389V N   CA   3061 3062   51.57  143.30                  -42.40
   49  12754 422N 423T C   N    3322 3324  -65.65 -124.80   59.30    3.24  -63.20  170.17   21.98
   49        423T 423T N   CA   3324 3325  147.75  143.50                  -42.10
   50  12755 423T 424G C   N    3329 3331  102.09   82.20   74.83    2.65  -62.40  166.01   28.66
   50        424G 424G N   CA   3331 3332  -63.63    8.50                  -41.20
   51  12767 435G 436D C   N    3407 3409  -27.87  -96.50   74.93    3.05  -63.30  179.25   20.23
   51        436D 436D N   CA   3409 3410  144.28  114.20                  -40.00
   52  12786 454L 455W C   N    3545 3547 -113.91  -63.00   89.71   10.04  -63.00   89.71   10.04
   52        455W 455W N   CA   3547 3548   29.66  -44.20                  -44.20
   53  12792 460L 461H C   N    3598 3600 -177.17  -63.20  120.64   20.53   56.30  176.22   16.89
   53        461H 461H N   CA   3600 3601  -81.85  -42.30                   40.80


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0   38   57  305  322  466  438  512  566  648  695


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90:      -90.5192
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   728859
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50274.0039




<< end of ENERGY.
DOPE score               : -50274.003906
>> Normalized DOPE z score: -0.731
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.099774
Native energy (pair)     :  -378.095739
Native energy (surface)  :   -10.388280
Native energy (combined) :    -9.417316
Z score (pair)           :    -9.868579
Z score (surface)        :    -7.208857
Z score (combined)       :   -11.318383
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   728859
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50274.0039




<< end of ENERGY.
DOPE score               : -50274.003906
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   728859
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -39426.5352




<< end of ENERGY.
DOPE-HR score               : -39426.535156


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    39547   39547
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     8749
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        3074.6589





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    3676       0      0   0.006   0.006      34.924       1.000
 2 Bond angle potential               :    4978       0     22   2.144   2.144      456.74       1.000
 3 Stereochemical cosine torsion poten:    2202       0     62  46.119  46.119      736.22       1.000
 4 Stereochemical improper torsion pot:    1476       0      1   1.518   1.518      83.520       1.000
 5 Soft-sphere overlap restraints     :    8749       0      0   0.004   0.004      17.809       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    9560       0      0   0.171   0.171      181.09       1.000
10 Distance restraints 2 (N-O)        :    9747       3     36   0.286   0.286      551.44       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     461       0      8   4.915   4.915      131.33       1.000
14 Sidechain Chi_1 dihedral restraints:     404       0      7  75.138  75.138      122.45       1.000
15 Sidechain Chi_2 dihedral restraints:     308       0      4  75.722  75.722      120.50       1.000
16 Sidechain Chi_3 dihedral restraints:     130       0      0  82.730  82.730      88.590       1.000
17 Sidechain Chi_4 dihedral restraints:      51       0      0  91.910  91.910      37.575       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    4393       0      0   0.361   0.361      102.48       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     460      58     70  30.054  58.523      223.78       1.000
26 Distance restraints 4 (SDCH-SDCH)  :    1701       0      6   0.825   0.825      186.20       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: pkp2a.V99990005
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   52215.4570



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature 10                           : Distance restraints 2 (N-O)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  32792 427Q 423T N   O    3347 3330    5.40    2.70    2.71    4.85    2.70    2.71    4.85

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  12333   1E   2M C   N       8   10 -112.84 -125.60   40.95    1.65   56.30 -178.15   26.52
    1          2M   2M N   CA     10   11  101.59  140.50                   34.80
    2  12344  12E  13A C   N      94   96  -57.00  -62.50   36.56    5.75  -68.20  138.11   11.53
    2         13A  13A N   CA     96   97  -77.04  -40.90                  145.30
    3  12345  13A  14D C   N      99  101  170.01  -63.30  126.75   20.30  -63.30  126.75   20.30
    3         14D  14D N   CA    101  102  -44.13  -40.00                  -40.00
    4  12350  18P  19S C   N     140  142  -45.79  -72.40   60.26    2.81  -64.10  134.58   10.94
    4         19S  19S N   CA    142  143   98.33  152.40                  -35.00
    5  12351  19S  20R C   N     146  148 -161.64 -125.20  116.84    4.74  -63.00  119.41   21.75
    5         20R  20R N   CA    148  149 -108.39  140.60                  -41.10
    6  12478 146P 147E C   N    1164 1166 -177.56 -117.80   65.84    1.93  -63.60 -167.40   31.81
    6        147E 147E N   CA   1166 1167  164.43  136.80                  -40.30
    7  12479 147E 148G C   N    1173 1175   96.91   78.70   57.85    0.97   82.20  131.32    7.11
    7        148G 148G N   CA   1175 1176  138.99 -166.10                    8.50
    8  12481 149D 150Y C   N    1185 1187  -94.38  -98.40    4.09    0.18  -63.50  173.78   26.06
    8        150Y 150Y N   CA   1187 1188  127.62  128.40                  -43.40
    9  12483 151P 152K C   N    1204 1206 -128.18 -118.00   11.62    0.38  -62.90 -173.69   28.09
    9        152K 152K N   CA   1206 1207  144.70  139.10                  -40.80
   10  12484 152K 153A C   N    1213 1215 -150.74 -134.00   20.16    0.49  -62.50 -176.51   34.79
   10        153A 153A N   CA   1215 1216  158.23  147.00                  -40.90
   11  12486 154N 155G C   N    1226 1228 -112.92  -80.20   46.85    3.29   82.20 -148.75   16.44
   11        155G 155G N   CA   1228 1229  140.57  174.10                    8.50
   12  12488 156L 157L C   N    1238 1240   72.17   60.20   93.72    6.62 -108.50  179.61    8.67
   12        157L 157L N   CA   1240 1241  122.55   29.60                  132.50
   13  12507 175A 176G C   N    1388 1390   47.47  -62.40  168.55   23.38  -62.40  168.55   23.38
   13        176G 176G N   CA   1390 1391 -169.03  -41.20                  -41.20
   14  12518 186C 187D C   N    1470 1472   -6.65  -63.30   98.12   10.54  -70.90  110.24    8.45
   14        187D 187D N   CA   1472 1473 -120.12  -40.00                  150.30
   15  12519 187D 188G C   N    1478 1480  -63.80  -62.40   40.28    5.95   82.20  146.31   10.15
   15        188G 188G N   CA   1480 1481   -0.94  -41.20                    8.50
   16  12529 197V 198R C   N    1556 1558  -72.59 -125.20   63.14    3.34  -63.00  143.72   20.07
   16        198R 198R N   CA   1558 1559  175.50  140.60                  -41.10
   17  12530 198R 199G C   N    1567 1569   88.01   82.20   82.67    3.72  -62.40  153.94   25.98
   17        199G 199G N   CA   1569 1570  -73.97    8.50                  -41.20
   18  12535 203D 204Y C   N    1599 1601   72.81   55.90   17.00    1.82  -63.50  158.64   29.97
   18        204Y 204Y N   CA   1601 1602   37.77   39.50                  -43.40
   19  12536 204Y 205Q C   N    1611 1613 -119.16 -121.10   80.09    3.78  -63.80  114.24   14.70
   19        205Q 205Q N   CA   1613 1614   59.63  139.70                  -40.30
   20  12569 237I 238Y C   N    1876 1878 -102.39  -63.50   61.26    8.45  -63.50   61.26    8.45
   20        238Y 238Y N   CA   1878 1879    3.93  -43.40                  -43.40
   21  12570 238Y 239I C   N    1888 1890 -123.27 -120.60   34.27    2.06  -63.40  152.03   23.29
   21        239I 239I N   CA   1890 1891   96.14  130.30                  -43.60
   22  12572 240Q 241N C   N    1905 1907 -121.71 -119.90    2.63    0.14  -63.20 -174.34   20.57
   22        241N 241N N   CA   1907 1908  135.10  137.00                  -41.10
   23  12573 241N 242R C   N    1913 1915 -103.37 -125.20   28.43    1.54  -63.00  165.11   25.10
   23        242R 242R N   CA   1915 1916  158.80  140.60                  -41.10
   24  12574 242R 243N C   N    1924 1926 -126.24 -119.90   48.86    2.07  -63.20  147.60   22.01
   24        243N 243N N   CA   1926 1927 -174.55  137.00                  -41.10
   25  12576 244I 245Q C   N    1940 1942  -81.72  -73.00   22.92    1.35  -63.80  158.82   24.31
   25        245Q 245Q N   CA   1942 1943  161.90  140.70                  -40.30
   26  12577 245Q 246T C   N    1949 1951  -92.00  -78.10   27.51    0.90  -63.20  147.20   20.80
   26        246T 246T N   CA   1951 1952  173.54  149.80                  -42.10
   27  12578 246T 247D C   N    1956 1958 -126.47  -70.90   66.59    3.31  -63.30  147.26   22.25
   27        247D 247D N   CA   1958 1959 -173.02  150.30                  -40.00
   28  12579 247D 248N C   N    1964 1966 -168.70 -119.90   51.68    2.53  -63.20 -167.43   20.72
   28        248N 248N N   CA   1966 1967  120.00  137.00                  -41.10
   29  12580 248N 249N C   N    1972 1974 -167.40 -119.90  122.04    4.35  -63.20  125.24   20.58
   29        249N 249N N   CA   1974 1975 -110.59  137.00                  -41.10
   30  12581 249N 250K C   N    1980 1982 -151.72 -118.00   36.81    1.67  -62.90 -172.48   21.54
   30        250K 250K N   CA   1982 1983  124.35  139.10                  -40.80
   31  12582 250K 251S C   N    1989 1991 -178.12 -136.60   47.92    1.46  -64.10 -171.68   21.87
   31        251S 251S N   CA   1991 1992  175.12  151.20                  -35.00
   32  12584 252I 253G C   N    2003 2005  -83.24  -80.20    4.91    0.33   82.20 -128.64    7.33
   32        253G 253G N   CA   2005 2006  170.24  174.10                    8.50
   33  12586 254C 255F C   N    2013 2015  -70.97  -71.40    1.50    0.13  -63.20  173.74   24.65
   33        255F 255F N   CA   2015 2016  142.13  140.70                  -44.30
   34  12587 255F 256G C   N    2024 2026  175.36 -167.20   26.02    0.99   82.20  173.84   12.53
   34        256G 256G N   CA   2026 2027  155.28  174.60                    8.50
   35  12588 256G 257S C   N    2028 2030 -121.58 -136.60   20.84    0.67  -64.10 -178.89   11.16
   35        257S 257S N   CA   2030 2031  136.75  151.20                  -35.00
   36  12589 257S 258R C   N    2034 2036 -123.74 -125.20    6.46    0.34  -63.00 -177.58   28.83
   36        258R 258R N   CA   2036 2037  146.89  140.60                  -41.10
   37  12590 258R 259S C   N    2045 2047 -113.52 -136.60   24.86    0.79  -64.10 -176.26   11.38
   37        259S 259S N   CA   2047 2048  141.96  151.20                  -35.00
   38  12591 259S 260R C   N    2051 2053 -105.81 -125.20   28.50    0.88  -63.00  166.41   19.96
   38        260R 260R N   CA   2053 2054  119.72  140.60                  -41.10
   39  12592 260R 261K C   N    2062 2064 -110.04 -118.00   64.40    3.22  -62.90  125.38   19.10
   39        261K 261K N   CA   2064 2065 -156.99  139.10                  -40.80
   40  12594 262V 263K C   N    2078 2080 -109.15  -62.90   85.00    9.82  -62.90   85.00    9.82
   40        263K 263K N   CA   2080 2081   30.52  -40.80                  -40.80
   41  12595 263K 264E C   N    2087 2089  -85.47  -69.30   16.88    1.10  -63.60  173.77   24.39
   41        264E 264E N   CA   2089 2090  147.31  142.50                  -40.30
   42  12596 264E 265Q C   N    2096 2098  -85.55  -73.00   16.08    0.95  -63.80  170.35   26.21
   42        265Q 265Q N   CA   2098 2099  150.75  140.70                  -40.30
   43  12597 265Q 266Y C   N    2105 2107 -129.18 -124.30   61.40    3.04  -63.50  136.79   24.88
   43        266Y 266Y N   CA   2107 2108 -163.39  135.40                  -43.40
   44  12598 266Y 267Q C   N    2117 2119  -63.11  -73.00   42.10    2.56  -63.80  140.08   20.63
   44        267Q 267Q N   CA   2119 2120   99.78  140.70                  -40.30
   45  12599 267Q 268D C   N    2126 2128 -117.87  -70.90   49.37    3.12  -63.30  163.85   23.75
   45        268D 268D N   CA   2128 2129  165.51  150.30                  -40.00
   46  12602 270P 271M C   N    2148 2150 -173.94 -125.60   50.06    1.67   56.30  175.86   30.05
   46        271M 271M N   CA   2150 2151  153.50  140.50                   34.80
   47  12605 273E 274E C   N    2172 2174   99.14   54.60   88.30   10.17   54.60   88.30   10.17
   47        274E 274E N   CA   2174 2175  118.64   42.40                   42.40
   48  12664 332V 333Q C   N    2623 2625 -108.89  -63.80   52.04    9.44  -63.80   52.04    9.44
   48        333Q 333Q N   CA   2625 2626  -66.28  -40.30                  -40.30
   49  12677 345L 346H C   N    2730 2732 -102.26  -63.20   75.07    7.99  -63.20   75.07    7.99
   49        346H 346H N   CA   2732 2733   21.80  -42.30                  -42.30
   50  12715 383S 384I C   N    3021 3023  -86.96  -63.40   89.06   13.88  -63.40   89.06   13.88
   50        384I 384I N   CA   3023 3024   42.29  -43.60                  -43.60
   51  12716 384I 385I C   N    3029 3031 -142.67  -63.40   84.99   14.07  -63.40   84.99   14.07
   51        385I 385I N   CA   3031 3032  -12.97  -43.60                  -43.60
   52  12720 388T 389V C   N    3059 3061  -75.89 -125.40   78.52    4.50  -62.40  114.15   15.26
   52        389V 389V N   CA   3061 3062 -155.75  143.30                  -42.40
   53  12721 389V 390P C   N    3066 3068 -118.71  -58.70   90.64    6.02  -64.50  122.42   12.02
   53        390P 390P N   CA   3068 3069   37.43  -30.50                  147.20
   54  12754 422N 423T C   N    3322 3324  -64.90 -124.80   60.02    3.26  -63.20  170.57   21.99
   54        423T 423T N   CA   3324 3325  147.33  143.50                  -42.10
   55  12755 423T 424G C   N    3329 3331  101.96   82.20   74.85    2.65  -62.40  165.89   28.64
   55        424G 424G N   CA   3331 3332  -63.69    8.50                  -41.20
   56  12767 435G 436D C   N    3407 3409  -34.71  -96.50   70.85    2.89  -63.30  173.51   19.85
   56        436D 436D N   CA   3409 3410  148.86  114.20                  -40.00
   57  12786 454L 455W C   N    3545 3547 -120.07  -63.00   94.94   10.75  -63.00   94.94   10.75
   57        455W 455W N   CA   3547 3548   31.68  -44.20                  -44.20
   58  12792 460L 461H C   N    3598 3600 -165.29  -63.20  106.40   18.00   56.30  178.74   18.51
   58        461H 461H N   CA   3600 3601  -72.29  -42.30                   40.80


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    3   43   90  324  320  440  460  471  590  636  688


<< end of ENERGY.
readlinef__W> File: pkp2a.B99990001.pdb, Line: 5
              Modeller will only read the first 80 characters of this line.

iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
readlinef__W> File: pkp2a.B99990001.pdb, Line: 5
              Modeller will only read the first 80 characters of this line.

  #      ALGNMT CODE

  1  pkp2a
  2  pkp2a
341 atoms selected for loop refinement
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:     1640     1438
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     6485
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        -239.0852





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349       0      0   0.004   0.004      1.1597       1.000
 2 Bond angle potential               :     473       0      1   0.035   0.035      33.761       1.000
 3 Stereochemical cosine torsion poten:     340       0      9   1.076   1.076      113.74       1.000
 4 Stereochemical improper torsion pot:     138       0      0   0.018   0.018      3.0967       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :    6485       0     30   2.508   2.508      42.966       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       0      0   0.062   0.062      6.6883       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      0   1.278   1.278      9.8877       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      1   1.465   1.465      23.029       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      0   2.077   2.077      15.440       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.694   1.694      4.9490       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :    6485       0     49   2.626   2.626     -22.623       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -471.18       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.



report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0   39   91  317  361  414  453  524  598  578  686


<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    11557
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -1682.7345





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349       0      0   0.014   0.014      19.455       1.000
 2 Bond angle potential               :     473       0     11   0.068   0.068      126.84       1.000
 3 Stereochemical cosine torsion poten:     340       0     16   1.139   1.139      135.74       1.000
 4 Stereochemical improper torsion pot:     138       0      0   0.041   0.041      16.263       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   11557       0      3   2.555   2.555     -155.17       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       0      2   0.106   0.106      19.469       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      2   1.268   1.268      23.624       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      0   1.130   1.130      17.469       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      0   1.899   1.899      14.538       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.326   1.326      4.5643       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   11557       0      0   2.631   2.631     -1401.9       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -503.60       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.



report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0   38   83  310  345  427  446  534  611  604  704


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   734804
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -51304.1250




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -51304.125000
>> Normalized DOPE z score: -0.888
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.128613
Native energy (pair)     :  -417.704653
Native energy (surface)  :   -11.980023
Native energy (combined) :   -10.513864
Z score (pair)           :   -10.562550
Z score (surface)        :    -7.447647
Z score (combined)       :   -11.875894
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    63762
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -3652.2898




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -3652.289795
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    63762
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -3640.0647




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               : -3640.064697
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    12527
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       12422.8262





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      30     45   0.231   0.231      5535.1       1.000
 2 Bond angle potential               :     473      42     86   0.214   0.214      1198.3       1.000
 3 Stereochemical cosine torsion poten:     340       0     40   1.302   1.302      199.69       1.000
 4 Stereochemical improper torsion pot:     138       7     15   0.150   0.150      216.66       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   12527       0    134   2.544   2.544      4302.9       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       7     12   0.294   0.294      150.25       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      8   1.496   1.496      58.187       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      4   1.367   1.367      29.305       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      0   1.783   1.783      17.122       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   2.280   2.280      8.2233       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   12527       0    205   2.716   2.716      1275.2       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -568.05       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    204 255F 255F CB  CA   2017 2016    1.72    1.54    0.19    5.13    1.54    0.19    5.13
    2    205 255F 255F CG  CB   2018 2017    1.95    1.49    0.46   12.76    1.49    0.46   12.76
    3    212 255F 255F N   CA   2015 2016    1.68    1.43    0.25    8.25    1.43    0.25    8.25
    4    215 255F 256G C   N    2024 2026    2.64    1.35    1.29   45.76    1.35    1.29   45.76
    5    216 256G 256G N   CA   2026 2027    2.46    1.43    1.03   33.80    1.43    1.03   33.80
    6    261 261K 261K C   CA   2071 2065    1.72    1.49    0.23    6.59    1.49    0.23    6.59
    7    263 262V 262V CB  CA   2075 2074    1.71    1.50    0.21    5.88    1.50    0.21    5.88
    8    266 262V 262V N   CA   2073 2074    1.61    1.43    0.18    6.07    1.43    0.18    6.07
    9    268 262V 262V C   CA   2078 2074    2.04    1.49    0.55   16.15    1.49    0.55   16.15
   10    269 262V 263K C   N    2078 2080    2.16    1.35    0.82   29.01    1.35    0.82   29.01
   11    270 263K 263K CB  CA   2082 2081    1.73    1.54    0.19    5.22    1.54    0.19    5.22
   12    275 263K 263K N   CA   2080 2081    2.29    1.43    0.86   28.31    1.43    0.86   28.31
   13    277 263K 263K C   CA   2087 2081    3.19    1.49    1.70   49.35    1.49    1.70   49.35
   14    278 263K 264E C   N    2087 2089    1.81    1.35    0.47   16.54    1.35    0.47   16.54
   15    284 264E 264E N   CA   2089 2090    1.83    1.43    0.40   13.24    1.43    0.40   13.24
   16    286 264E 264E C   CA   2096 2090    2.16    1.49    0.67   19.64    1.49    0.67   19.64
   17    287 264E 265Q C   N    2096 2098    1.73    1.35    0.39   13.69    1.35    0.39   13.69
   18    293 265Q 265Q N   CA   2098 2099    1.78    1.43    0.35   11.46    1.43    0.35   11.46
   19    295 265Q 265Q C   CA   2105 2099    1.97    1.49    0.48   13.88    1.49    0.48   13.88
   20    296 265Q 266Y C   N    2105 2107    1.66    1.35    0.31   11.15    1.35    0.31   11.15
   21    297 266Y 266Y CB  CA   2109 2108    2.36    1.54    0.82   22.53    1.54    0.82   22.53
   22    298 266Y 266Y CG  CB   2110 2109    2.20    1.49    0.71   19.76    1.49    0.71   19.76
   23    299 266Y 266Y CD1 CG   2111 2110    2.29    1.38    0.92   29.43    1.38    0.92   29.43
   24    300 266Y 266Y CD2 CG   2112 2110    2.70    1.38    1.33   42.72    1.38    1.33   42.72
   25    301 266Y 266Y CE1 CD1  2113 2111    2.47    1.38    1.10   35.30    1.38    1.10   35.30
   26    302 266Y 266Y CE2 CD2  2114 2112    2.60    1.38    1.22   39.26    1.38    1.22   39.26
   27    303 266Y 266Y CZ  CE1  2115 2113    2.39    1.38    1.02   32.66    1.38    1.02   32.66
   28    304 266Y 266Y CZ  CE2  2115 2114    2.49    1.38    1.11   35.74    1.38    1.11   35.74
   29    306 266Y 266Y N   CA   2107 2108    1.87    1.43    0.44   14.44    1.43    0.44   14.44

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    626 254C 255F C   N    2013 2015  147.17  120.00   27.17    6.17  120.00   27.17    6.17
    2    628 255F 255F N   CA   2015 2016  153.31  113.50   39.81   10.70  113.50   39.81   10.70
    3    630 255F 255F CA  CB   2016 2017  137.51  107.50   30.01    6.94  107.50   30.01    6.94
    4    632 255F 255F CA  C    2016 2024  139.02  116.50   22.52    6.47  116.50   22.52    6.47
    5    633 255F 255F CB  CG   2017 2018  155.25  122.30   32.95    7.16  122.30   32.95    7.16
    6    634 255F 255F CB  CG   2017 2018  155.12  122.30   32.82    7.14  122.30   32.82    7.14
    7    644 256G 256G N   CA   2026 2027  147.05  107.00   40.05   11.51  107.00   40.05   11.51
    8    681 260R 260R CA  CB   2054 2055  133.35  113.50   19.85    4.87  113.50   19.85    4.87
    9    691 260R 261K C   N    2062 2064  151.37  120.00   31.37    7.13  120.00   31.37    7.13
   10    694 261K 261K N   CA   2064 2065  132.67  107.00   25.67    7.38  107.00   25.67    7.38
   11    697 261K 261K CA  C    2065 2071  134.92  116.50   18.42    5.29  116.50   18.42    5.29
   12    705 262V 262V N   CA   2073 2074  142.57  107.00   35.57   10.22  107.00   35.57   10.22
   13    709 262V 262V CA  C    2074 2078  138.51  116.50   22.01    6.33  116.50   22.01    6.33
   14    712 262V 263K C   N    2078 2080  158.16  120.00   38.16    8.67  120.00   38.16    8.67
   15    715 263K 263K N   CA   2080 2081  142.07  107.00   35.07   10.08  107.00   35.07   10.08
   16    716 263K 263K CA  CB   2081 2082  144.49  113.50   30.99    7.61  113.50   30.99    7.61
   17    717 263K 263K CA  C    2081 2087  140.43  121.00   19.43    5.58  121.00   19.43    5.58
   18    723 263K 264E C   N    2087 2089  153.92  120.00   33.92    7.71  120.00   33.92    7.71
   19    726 264E 264E N   CA   2089 2090  136.38  107.00   29.38    8.44  107.00   29.38    8.44
   20    729 264E 264E CA  C    2090 2096  134.90  116.50   18.40    5.29  116.50   18.40    5.29
   21    735 264E 265Q C   N    2096 2098  154.26  120.00   34.26    7.78  120.00   34.26    7.78
   22    738 265Q 265Q N   CA   2098 2099  141.31  107.00   34.31    9.86  107.00   34.31    9.86
   23    741 265Q 265Q CA  C    2099 2105  145.27  116.50   28.77    8.27  116.50   28.77    8.27
   24    747 265Q 266Y C   N    2105 2107  161.99  120.00   41.99    9.54  120.00   41.99    9.54
   25    749 266Y 266Y N   CA   2107 2108  130.71  113.50   17.21    4.63  113.50   17.21    4.63
   26    751 266Y 266Y CA  CB   2108 2109  132.90  107.50   25.40    5.87  107.50   25.40    5.87

-------------------------------------------------------------------------------------------------

Feature  4                           : Stereochemical improper torsion potentia
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    928 263K 263K C   CA   2087 2081   20.08    0.00   20.08    7.07    0.00   20.08    7.07
    2    939 266Y 266Y CB  CG   2109 2110 -151.45  180.00   28.55    8.70  180.00   28.55    8.70

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1329 255F 255F CA  C    2016 2024 -133.82  180.00   46.18    9.24  180.00   46.18    9.24
    2   1335 261K 261K CA  C    2065 2071 -144.68  180.00   35.32    7.06  180.00   35.32    7.06
    3   1337 263K 263K CA  C    2081 2087 -125.64  180.00   54.36   10.87  180.00   54.36   10.87
    4   1338 264E 264E CA  C    2090 2096 -141.76  180.00   38.24    7.65  180.00   38.24    7.65
    5   1344 270P 270P CA  C    2144 2148 -154.30  180.00   25.70    5.14  180.00   25.70    5.14


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1830 2087   2.291
  serious non-bonded atom clash:  1846 2024   2.218
  serious non-bonded atom clash:  1846 2026   1.856
  serious non-bonded atom clash:  1848 2026   2.280
  serious non-bonded atom clash:  1851 2026   2.005
  serious non-bonded atom clash:  1852 2026   1.930
  serious non-bonded atom clash:  1852 2027   2.237
  serious non-bonded atom clash:  1870 2024   2.252
  serious non-bonded atom clash:  1870 2026   2.057
  serious non-bonded atom clash:  1872 2026   2.058
  serious non-bonded atom clash:  1873 2024   2.277
  serious non-bonded atom clash:  1873 2026   2.006
  serious non-bonded atom clash:  2078 2162   2.268
  serious non-bonded atom clash:  2111 2176   2.255
  serious non-bonded atom clash:  2111 2179   2.156
  serious non-bonded atom clash:  2112 2177   2.152
  serious non-bonded atom clash:  2112 2191   2.275
  serious non-bonded atom clash:  2113 2176   2.278
  serious non-bonded atom clash:  2113 2179   2.298
  serious non-bonded atom clash:  2114 2177   2.174
  serious non-bonded atom clash:  2115 2177   2.284

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     6    3   12    7   14   52   97  337  366  435  472  545  636  624  738


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90:      115.9061
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   738933
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -48834.1875




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -48834.187500
>> Normalized DOPE z score: -0.510
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.128613
Native energy (pair)     :  -323.529935
Native energy (surface)  :   -11.162968
Native energy (combined) :    -8.291147
Z score (pair)           :   -10.235914
Z score (surface)        :    -7.210165
Z score (combined)       :   -11.494307
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    67891
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -1182.1267




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -1182.126709
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    67891
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        1565.6411




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :  1565.641113
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    15620
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       33962.4375





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      50     83   0.278   0.278      7790.8       1.000
 2 Bond angle potential               :     473      69    139   0.252   0.252      1861.1       1.000
 3 Stereochemical cosine torsion poten:     340       1     30   1.196   1.196      195.60       1.000
 4 Stereochemical improper torsion pot:     138      20     36   0.259   0.259      550.61       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   15620       0    356   2.527   2.527      18414.       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45      11     17   0.622   0.622      675.01       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      6   1.427   1.427      40.217       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      4   1.605   1.605      40.037       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      1   1.210   1.210      17.065       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      1   1.402   1.402      7.7647       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   15620       0    513   2.839   2.839      4824.3       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -454.54       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1      4 146P 147E C   N    1164 1166    1.51    1.35    0.16    5.70    1.35    0.16    5.70
    2     10 147E 147E CB  CA   1168 1167    2.05    1.54    0.52   14.18    1.54    0.52   14.18
    3     11 147E 147E CG  CB   1169 1168    1.88    1.53    0.35    9.65    1.53    0.35    9.65
    4     12 147E 147E CD  CG   1170 1169    1.75    1.52    0.22    5.83    1.52    0.22    5.83
    5     15 147E 147E N   CA   1166 1167    1.96    1.43    0.53   17.59    1.43    0.53   17.59
    6     17 147E 147E C   CA   1173 1167    2.48    1.49    0.99   28.87    1.49    0.99   28.87
    7     18 147E 148G C   N    1173 1175    1.60    1.35    0.25    8.90    1.35    0.25    8.90
    8     19 148G 148G N   CA   1175 1176    1.63    1.43    0.20    6.46    1.43    0.20    6.46
    9     21 148G 148G C   CA   1177 1176    1.72    1.49    0.23    6.83    1.49    0.23    6.83
   10     31 150Y 150Y CB  CA   1189 1188    1.70    1.54    0.17    4.57    1.54    0.17    4.57
   11     52 152K 152K CB  CA   1208 1207    1.86    1.54    0.32    8.78    1.54    0.32    8.78
   12     53 152K 152K CG  CB   1209 1208    2.30    1.53    0.77   21.03    1.53    0.77   21.03
   13     54 152K 152K CD  CG   1210 1209    2.37    1.53    0.84   23.18    1.53    0.84   23.18
   14     84 156L 156L C   CA   1238 1233    1.69    1.49    0.20    5.73    1.49    0.20    5.73
   15     85 156L 157L C   N    1238 1240    1.48    1.35    0.13    4.65    1.35    0.13    4.65
   16    254 261K 261K CB  CA   2066 2065    1.81    1.54    0.27    7.49    1.54    0.27    7.49
   17    261 261K 261K C   CA   2071 2065    2.04    1.49    0.55   15.98    1.49    0.55   15.98
   18    262 261K 262V C   N    2071 2073    2.98    1.35    1.63   57.85    1.35    1.63   57.85
   19    263 262V 262V CB  CA   2075 2074    1.92    1.50    0.42   11.40    1.50    0.42   11.40
   20    264 262V 262V CG1 CB   2076 2075    1.96    1.54    0.43   11.68    1.54    0.43   11.68
   21    265 262V 262V CG2 CB   2077 2075    1.97    1.54    0.43   11.88    1.54    0.43   11.88
   22    266 262V 262V N   CA   2073 2074    2.28    1.43    0.85   28.12    1.43    0.85   28.12
   23    268 262V 262V C   CA   2078 2074    2.57    1.49    1.08   31.30    1.49    1.08   31.30
   24    270 263K 263K CB  CA   2082 2081    1.88    1.54    0.34    9.29    1.54    0.34    9.29
   25    271 263K 263K CG  CB   2083 2082    1.82    1.53    0.29    7.94    1.53    0.29    7.94
   26    275 263K 263K N   CA   2080 2081    1.58    1.43    0.15    4.83    1.43    0.15    4.83
   27    277 263K 263K C   CA   2087 2081    3.78    1.49    2.29   66.63    1.49    2.29   66.63
   28    278 263K 264E C   N    2087 2089    1.79    1.35    0.44   15.68    1.35    0.44   15.68
   29    279 264E 264E CB  CA   2091 2090    2.74    1.54    1.20   33.07    1.54    1.20   33.07
   30    284 264E 264E N   CA   2089 2090    1.86    1.43    0.43   14.20    1.43    0.43   14.20
   31    287 264E 265Q C   N    2096 2098    1.50    1.35    0.16    5.64    1.35    0.16    5.64
   32    288 265Q 265Q CB  CA   2100 2099    2.88    1.54    1.35   36.98    1.54    1.35   36.98
   33    289 265Q 265Q CG  CB   2101 2100    2.01    1.53    0.48   13.30    1.53    0.48   13.30
   34    291 265Q 265Q OE1 CD   2103 2102    1.84    1.23    0.61   28.49    1.23    0.61   28.49
   35    293 265Q 265Q N   CA   2098 2099    1.68    1.43    0.25    8.24    1.43    0.25    8.24
   36    294 265Q 265Q O   C    2106 2105    2.13    1.23    0.90   41.27    1.23    0.90   41.27
   37    297 266Y 266Y CB  CA   2109 2108    1.93    1.54    0.39   10.77    1.54    0.39   10.77
   38    306 266Y 266Y N   CA   2107 2108    3.35    1.43    1.92   63.35    1.43    1.92   63.35
   39    308 266Y 266Y C   CA   2117 2108    2.81    1.49    1.32   38.43    1.49    1.32   38.43
   40    309 266Y 267Q C   N    2117 2119    1.56    1.35    0.22    7.77    1.35    0.22    7.77
   41    315 267Q 267Q N   CA   2119 2120    1.59    1.43    0.16    5.13    1.43    0.16    5.13
   42    323 268D 268D N   CA   2128 2129    1.57    1.43    0.14    4.55    1.43    0.14    4.55
   43    326 268D 269V C   N    2134 2136    1.54    1.35    0.20    6.92    1.35    0.20    6.92
   44    330 269V 269V N   CA   2136 2137    1.63    1.43    0.20    6.49    1.43    0.20    6.49
   45    332 269V 269V C   CA   2141 2137    1.77    1.49    0.28    8.05    1.49    0.28    8.05

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    351 145W 146P C   N    1157 1159  137.26  117.00   20.26    5.04  117.00   20.26    5.04
    2    355 146P 146P N   CA   1159 1160  129.45  110.80   18.65    5.01  110.80   18.65    5.01
    3    363 146P 147E C   N    1164 1166  179.97  120.00   59.97   13.62  120.00   59.97   13.62
    4    370 147E 147E CB  CG   1168 1169  136.86  108.00   28.86    6.69  108.00   28.86    6.69
    5    375 147E 148G C   N    1173 1175  143.09  120.00   23.09    5.25  120.00   23.09    5.25
    6    377 148G 148G N   CA   1175 1176  131.10  107.00   24.10    6.92  107.00   24.10    6.92
    7    380 148G 149D C   N    1177 1179  160.18  120.00   40.18    9.13  120.00   40.18    9.13
    8    382 149D 149D N   CA   1179 1180  143.26  113.50   29.76    8.00  113.50   29.76    8.00
    9    393 150Y 150Y N   CA   1187 1188  135.96  113.50   22.46    6.04  113.50   22.46    6.04
   10    395 150Y 150Y CA  CB   1188 1189  130.00  107.50   22.50    5.20  107.50   22.50    5.20
   11    412 151P 151P N   CA   1199 1200  130.40  108.20   22.20    5.04  108.20   22.20    5.04
   12    423 152K 152K N   CA   1206 1207  130.69  113.50   17.19    4.62  113.50   17.19    4.62
   13    425 152K 152K CA  CB   1207 1208  145.76  113.50   32.26    7.92  113.50   32.26    7.92
   14    430 152K 152K CD  CE   1210 1211  133.01  110.00   23.01    6.08  110.00   23.01    6.08
   15    432 152K 153A C   N    1213 1215  142.23  120.00   22.23    5.05  120.00   22.23    5.05
   16    461 156L 156L CA  C    1233 1238  137.45  116.50   20.95    6.02  116.50   20.95    6.02
   17    694 261K 261K N   CA   2064 2065  137.29  107.00   30.29    8.70  107.00   30.29    8.70
   18    697 261K 261K CA  C    2065 2071  138.61  116.50   22.11    6.35  116.50   22.11    6.35
   19    704 262V 262V N   CA   2073 2074  136.52  113.50   23.02    6.19  113.50   23.02    6.19
   20    706 262V 262V CA  CB   2074 2075  137.31  108.50   28.81    6.76  108.50   28.81    6.76
   21    707 262V 262V CA  CB   2074 2075  137.39  108.50   28.89    6.78  108.50   28.89    6.78
   22    712 262V 263K C   N    2078 2080  143.26  120.00   23.26    5.29  120.00   23.26    5.29
   23    714 263K 263K N   CA   2080 2081  132.74  113.50   19.24    5.17  113.50   19.24    5.17
   24    715 263K 263K N   CA   2080 2081  124.90  107.00   17.90    5.14  107.00   17.90    5.14
   25    719 263K 263K CB  CG   2082 2083  134.63  113.60   21.03    5.16  113.60   21.03    5.16
   26    724 264E 263K N   C    2089 2087  145.69  122.50   23.19    6.66  122.50   23.19    6.66
   27    725 264E 264E N   CA   2089 2090  147.19  113.50   33.69    9.06  113.50   33.69    9.06
   28    727 264E 264E CA  CB   2090 2091  139.27  113.50   25.77    6.32  113.50   25.77    6.32
   29    728 264E 264E CA  C    2090 2096  143.14  121.00   22.14    6.36  121.00   22.14    6.36
   30    731 264E 264E CG  CD   2092 2093  142.60  118.00   24.60    5.00  118.00   24.60    5.00
   31    736 265Q 264E N   C    2098 2096  145.56  122.50   23.06    6.63  122.50   23.06    6.63
   32    737 265Q 265Q N   CA   2098 2099  158.29  113.50   44.79   12.04  113.50   44.79   12.04
   33    742 265Q 265Q CB  CG   2100 2101  132.26  108.00   24.26    5.62  108.00   24.26    5.62
   34    751 266Y 266Y CA  CB   2108 2109  136.72  107.50   29.22    6.76  107.50   29.22    6.76
   35    768 267Q 267Q N   CA   2119 2120  134.17  107.00   27.17    7.81  107.00   27.17    7.81
   36    777 267Q 268D C   N    2126 2128  146.77  120.00   26.77    6.08  120.00   26.77    6.08
   37    781 268D 268D CA  CB   2129 2130  127.74  108.00   19.74    4.57  108.00   19.74    4.57
   38    786 268D 268D OD2 CG   2133 2131  144.54  124.00   20.54    6.60  124.00   20.54    6.60
   39    791 269V 269V N   CA   2136 2137  136.21  107.00   29.21    8.39  107.00   29.21    8.39
   40    792 269V 269V CA  CB   2137 2138  150.16  108.50   41.66    9.78  108.50   41.66    9.78
   41    798 269V 270P C   N    2141 2143  145.02  117.00   28.02    6.97  117.00   28.02    6.97
   42    817 271M 271M CB  CG   2152 2153  133.50  114.50   19.00    4.65  114.50   19.00    4.65
   43    818 271M 271M CG  SD   2153 2154  122.54   95.00   27.54    5.16   95.00   27.54    5.16

-------------------------------------------------------------------------------------------------

Feature  3                           : Stereochemical cosine torsion potential 
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1238 265Q 265Q O   C    2106 2105   72.04    0.00   72.04    4.52    0.00   72.04    4.52

-------------------------------------------------------------------------------------------------

Feature  4                           : Stereochemical improper torsion potentia
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    849 154N 154N C   CA   1226 1221   16.49    0.00   16.49    5.81    0.00   16.49    5.81
    2    930 264E 264E C   CA   2096 2090   15.41    0.00   15.41    5.43    0.00   15.41    5.43
    3    933 265Q 265Q C   CA   2105 2099   16.26    0.00   16.26    5.72    0.00   16.26    5.72
    4    935 265Q 265Q CD  CG   2102 2101   48.60    0.00   48.60   10.48    0.00   48.60   10.48

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1303 147E 147E CA  C    1167 1173 -154.28  180.00   25.72    5.14  180.00   25.72    5.14
    2   1334 260R 260R CA  C    2054 2062 -151.57  180.00   28.43    5.69  180.00   28.43    5.69
    3   1335 261K 261K CA  C    2065 2071  -89.99  180.00   90.01   18.00  180.00   90.01   18.00
    4   1337 263K 263K CA  C    2081 2087  -49.95  180.00  130.05   26.01  180.00  130.05   26.01
    5   1339 265Q 265Q CA  C    2099 2105  -85.09  180.00   94.91   18.98  180.00   94.91   18.98


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1100 1210   2.256
  serious non-bonded atom clash:  1100 1211   2.287
  serious non-bonded atom clash:  1108 1212   2.041
  serious non-bonded atom clash:  1116 1166   2.250
  serious non-bonded atom clash:  1124 1209   2.275
  serious non-bonded atom clash:  1126 1210   2.264
  serious non-bonded atom clash:  1138 1173   2.124
  serious non-bonded atom clash:  1145 1166   2.150
  serious non-bonded atom clash:  1212 1287   2.264
  serious non-bonded atom clash:  1496 2082   2.224
  serious non-bonded atom clash:  2065 2239   2.269
  serious non-bonded atom clash:  2071 2233   2.238
  serious non-bonded atom clash:  2071 2275   2.131
  serious non-bonded atom clash:  2072 2229   2.102
  serious non-bonded atom clash:  2072 2233   2.272
  serious non-bonded atom clash:  2072 2236   2.208
  serious non-bonded atom clash:  2072 2239   2.124
  serious non-bonded atom clash:  2073 2232   1.940
  serious non-bonded atom clash:  2073 2234   2.292
  serious non-bonded atom clash:  2073 2268   2.167
  serious non-bonded atom clash:  2073 2271   2.210
  serious non-bonded atom clash:  2073 2272   2.256
  serious non-bonded atom clash:  2074 2232   2.060
  serious non-bonded atom clash:  2075 2258   2.300
  serious non-bonded atom clash:  2078 2232   2.095
  serious non-bonded atom clash:  2078 2259   2.288
  serious non-bonded atom clash:  2081 2225   2.062
  serious non-bonded atom clash:  2081 2244   2.155
  serious non-bonded atom clash:  2082 2244   2.257
  serious non-bonded atom clash:  2087 2242   2.198
  serious non-bonded atom clash:  2087 2243   2.289
  serious non-bonded atom clash:  2087 2245   2.137
  serious non-bonded atom clash:  2089 2243   2.292
  serious non-bonded atom clash:  2090 2250   2.187
  serious non-bonded atom clash:  2091 2250   2.262
  serious non-bonded atom clash:  2098 2282   2.298
  serious non-bonded atom clash:  2099 2287   2.156
  serious non-bonded atom clash:  2099 2306   2.296
  serious non-bonded atom clash:  2100 2287   1.878
  serious non-bonded atom clash:  2100 2292   1.967
  serious non-bonded atom clash:  2100 2293   2.238
  serious non-bonded atom clash:  2100 2302   2.048
  serious non-bonded atom clash:  2100 2309   1.910
  serious non-bonded atom clash:  2101 2106   2.150
  serious non-bonded atom clash:  2101 2293   1.969
  serious non-bonded atom clash:  2101 2300   2.010
  serious non-bonded atom clash:  2101 2301   2.039
  serious non-bonded atom clash:  2101 2309   2.085
  serious non-bonded atom clash:  2101 2317   1.956
  serious non-bonded atom clash:  2102 2293   1.841
  serious non-bonded atom clash:  2102 2300   2.272
  serious non-bonded atom clash:  2102 2301   2.015
  serious non-bonded atom clash:  2102 2317   2.011
  serious non-bonded atom clash:  2102 2320   2.026
  serious non-bonded atom clash:  2103 2293   1.845
  serious non-bonded atom clash:  2103 2319   2.101
  serious non-bonded atom clash:  2103 2320   2.297
  serious non-bonded atom clash:  2103 2321   2.234
  serious non-bonded atom clash:  2104 2293   1.803
  serious non-bonded atom clash:  2104 2295   2.075
  serious non-bonded atom clash:  2104 2300   2.059
  serious non-bonded atom clash:  2104 2301   2.002
  serious non-bonded atom clash:  2104 2320   2.002
  serious non-bonded atom clash:  2104 2321   2.046
  serious non-bonded atom clash:  2105 2286   2.175
  serious non-bonded atom clash:  2105 2287   2.013
  serious non-bonded atom clash:  2105 2302   2.046
  serious non-bonded atom clash:  2106 2287   1.754
  serious non-bonded atom clash:  2106 2292   1.973
  serious non-bonded atom clash:  2106 2294   2.243
  serious non-bonded atom clash:  2106 2302   1.903
  serious non-bonded atom clash:  2106 2309   2.081
  serious non-bonded atom clash:  2107 2280   2.251
  serious non-bonded atom clash:  2107 2282   2.058
  serious non-bonded atom clash:  2107 2286   2.191
  serious non-bonded atom clash:  2107 2294   2.123
  serious non-bonded atom clash:  2107 2298   2.193
  serious non-bonded atom clash:  2108 2180   1.998
  serious non-bonded atom clash:  2108 2280   2.299
  serious non-bonded atom clash:  2108 2281   1.946
  serious non-bonded atom clash:  2117 2178   2.282
  serious non-bonded atom clash:  2117 2285   2.141
  serious non-bonded atom clash:  2118 2285   2.259

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:    34   18   31   36   32   80  128  358  389  461  502  567  654  653  756


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   758627
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -46751.5625




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -46751.562500
>> Normalized DOPE z score: -0.191
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.128613
Native energy (pair)     :  -238.806784
Native energy (surface)  :    -3.877279
Native energy (combined) :    -5.477388
Z score (pair)           :    -9.632731
Z score (surface)        :    -6.389026
Z score (combined)       :   -10.741996
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    87585
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         900.0026




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               :   900.002563
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    87585
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        7485.3853




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :  7485.385254
readlinef__W> File: pkp2a.B99990002.pdb, Line: 5
              Modeller will only read the first 80 characters of this line.

iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
readlinef__W> File: pkp2a.B99990002.pdb, Line: 5
              Modeller will only read the first 80 characters of this line.

  #      ALGNMT CODE

  1  pkp2a
  2  pkp2a
341 atoms selected for loop refinement
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:     1640     1438
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    14309
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        3312.0112





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      15     23   0.047   0.047      223.39       1.000
 2 Bond angle potential               :     473      15     25   0.105   0.105      325.95       1.000
 3 Stereochemical cosine torsion poten:     340       0      8   1.045   1.045      116.40       1.000
 4 Stereochemical improper torsion pot:     138       2      2   0.063   0.063      32.981       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   14309       0    151   2.540   2.540      527.75       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       0      6   0.123   0.123      26.206       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      3   1.468   1.468      17.795       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      0   1.376   1.376      19.097       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      0   1.633   1.633      14.014       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.708   1.708      4.5445       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   14284       0    290   2.755   2.755      2445.3       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -441.37       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    286 264E 264E C   CA   2096 2090    1.65    1.49    0.16    4.66    1.49    0.16    4.66
    2    295 265Q 265Q C   CA   2105 2099    1.67    1.49    0.18    5.25    1.49    0.18    5.25
    3    308 266Y 266Y C   CA   2117 2108    1.66    1.49    0.17    4.83    1.49    0.17    4.83
    4    315 267Q 267Q N   CA   2119 2120    1.58    1.43    0.15    4.95    1.43    0.15    4.95
    5    317 267Q 267Q C   CA   2126 2120    1.65    1.49    0.16    4.77    1.49    0.16    4.77
    6    323 268D 268D N   CA   2128 2129    1.60    1.43    0.17    5.62    1.43    0.17    5.62
    7    326 268D 269V C   N    2134 2136    1.51    1.35    0.17    6.02    1.35    0.17    6.02
    8    330 269V 269V N   CA   2136 2137    1.65    1.43    0.22    7.13    1.43    0.22    7.13
    9    332 269V 269V C   CA   2141 2137    1.77    1.49    0.28    8.08    1.49    0.28    8.08
   10    333 269V 270P C   N    2141 2143    1.56    1.30    0.26    7.63    1.30    0.26    7.63
   11    335 270P 270P C   CA   2148 2144    1.78    1.49    0.29    8.36    1.49    0.29    8.36
   12    336 270P 271M C   N    2148 2150    1.52    1.35    0.17    6.06    1.35    0.17    6.06
   13    337 270P 270P N   CA   2143 2144    1.66    1.43    0.23    7.59    1.43    0.23    7.59
   14    346 271M 271M N   CA   2150 2151    1.62    1.43    0.19    6.24    1.43    0.19    6.24
   15    348 271M 271M C   CA   2156 2151    1.67    1.49    0.18    5.27    1.49    0.18    5.27

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    738 265Q 265Q N   CA   2098 2099  128.83  107.00   21.83    6.27  107.00   21.83    6.27
    2    747 265Q 266Y C   N    2105 2107  150.65  120.00   30.65    6.96  120.00   30.65    6.96
    3    750 266Y 266Y N   CA   2107 2108  139.53  107.00   32.53    9.35  107.00   32.53    9.35
    4    765 266Y 267Q C   N    2117 2119  145.72  120.00   25.72    5.84  120.00   25.72    5.84
    5    768 267Q 267Q N   CA   2119 2120  136.25  107.00   29.25    8.41  107.00   29.25    8.41
    6    777 267Q 268D C   N    2126 2128  155.76  120.00   35.76    8.12  120.00   35.76    8.12
    7    780 268D 268D N   CA   2128 2129  132.73  107.00   25.73    7.39  107.00   25.73    7.39
    8    788 268D 269V C   N    2134 2136  158.51  120.00   38.51    8.75  120.00   38.51    8.75
    9    791 269V 269V N   CA   2136 2137  140.58  107.00   33.58    9.65  107.00   33.58    9.65
   10    798 269V 270P C   N    2141 2143  144.97  117.00   27.97    6.96  117.00   27.97    6.96
   11    801 270P 270P N   CA   2143 2144  151.32  108.20   43.12    9.80  108.20   43.12    9.80
   12    805 270P 270P CA  C    2144 2148  135.95  116.50   19.45    5.59  116.50   19.45    5.59
   13    813 271M 271M N   CA   2150 2151  127.60  107.00   20.60    5.92  107.00   20.60    5.92
   14    820 271M 272P C   N    2156 2158  135.19  117.00   18.19    4.53  117.00   18.19    4.53


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    1   36   85  318  321  431  451  506  630  662  694


<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    15016
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       22408.4766





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      42     61   0.254   0.254      8891.4       1.000
 2 Bond angle potential               :     473      47    112   0.203   0.203      1213.4       1.000
 3 Stereochemical cosine torsion poten:     340       0     31   1.248   1.248      183.69       1.000
 4 Stereochemical improper torsion pot:     138       6     19   0.119   0.119      134.49       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   15016       0    218   2.568   2.568      9974.0       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       7     12   0.297   0.297      154.00       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0     12   1.497   1.497      60.208       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      7   1.387   1.387      42.560       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      0   1.441   1.441      16.223       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.483   1.483      5.5237       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   15016       0    281   2.828   2.828      2225.3       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -492.24       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1     20 148G 148G O   C    1178 1177    3.22    1.23    1.99   91.35    1.23    1.99   91.35
    2     22 148G 149D C   N    1177 1179    1.50    1.35    0.15    5.35    1.35    0.15    5.35
    3    180 251S 251S CB  CA   1993 1992    3.59    1.54    2.05   56.29    1.54    2.05   56.29
    4    182 251S 251S N   CA   1991 1992    1.60    1.43    0.17    5.68    1.43    0.17    5.68
    5    184 251S 251S C   CA   1995 1992    1.76    1.49    0.27    7.93    1.49    0.27    7.93
    6    193 252I 253G C   N    2003 2005    1.63    1.35    0.29   10.10    1.35    0.29   10.10
    7    194 253G 253G N   CA   2005 2006    3.06    1.43    1.63   53.84    1.43    1.63   53.84
    8    196 253G 253G C   CA   2007 2006    3.15    1.49    1.66   48.40    1.49    1.66   48.40
    9    197 253G 254C C   N    2007 2009    1.88    1.35    0.53   18.80    1.35    0.53   18.80
   10    200 254C 254C N   CA   2009 2010    1.72    1.43    0.29    9.60    1.43    0.29    9.60
   11    202 254C 254C C   CA   2013 2010    1.76    1.49    0.27    7.97    1.49    0.27    7.97
   12    203 254C 255F C   N    2013 2015    1.52    1.35    0.18    6.28    1.35    0.18    6.28
   13    212 255F 255F N   CA   2015 2016    1.67    1.43    0.24    8.06    1.43    0.24    8.06
   14    214 255F 255F C   CA   2024 2016    1.81    1.49    0.32    9.19    1.49    0.32    9.19
   15    215 255F 256G C   N    2024 2026    1.48    1.35    0.14    4.84    1.35    0.14    4.84
   16    216 256G 256G N   CA   2026 2027    1.60    1.43    0.17    5.65    1.43    0.17    5.65
   17    218 256G 256G C   CA   2028 2027    1.71    1.49    0.22    6.55    1.49    0.22    6.55
   18    219 256G 257S C   N    2028 2030    1.50    1.35    0.15    5.43    1.35    0.15    5.43
   19    222 257S 257S N   CA   2030 2031    1.59    1.43    0.16    5.30    1.43    0.16    5.30
   20    224 257S 257S C   CA   2034 2031    1.70    1.49    0.21    6.20    1.49    0.21    6.20
   21    225 257S 258R C   N    2034 2036    1.50    1.35    0.16    5.51    1.35    0.16    5.51
   22    233 258R 258R N   CA   2036 2037    1.61    1.43    0.18    5.87    1.43    0.18    5.87
   23    235 258R 258R C   CA   2045 2037    1.73    1.49    0.24    7.03    1.49    0.24    7.03
   24    239 259S 259S N   CA   2047 2048    1.59    1.43    0.16    5.11    1.43    0.16    5.11
   25    240 259S 259S O   C    2052 2051    3.26    1.23    2.03   93.00    1.23    2.03   93.00
   26    241 259S 259S C   CA   2051 2048    1.83    1.49    0.34    9.99    1.49    0.34    9.99
   27    242 259S 260R C   N    2051 2053    1.62    1.35    0.28    9.78    1.35    0.28    9.78
   28    243 260R 260R CB  CA   2055 2054    1.98    1.54    0.44   12.20    1.54    0.44   12.20
   29    250 260R 260R N   CA   2053 2054    2.26    1.43    0.83   27.43    1.43    0.83   27.43
   30    252 260R 260R C   CA   2062 2054    2.55    1.49    1.06   30.92    1.49    1.06   30.92
   31    253 260R 261K C   N    2062 2064    1.50    1.35    0.15    5.40    1.35    0.15    5.40
   32    259 261K 261K N   CA   2064 2065    1.60    1.43    0.17    5.53    1.43    0.17    5.53
   33    261 261K 261K C   CA   2071 2065    1.92    1.49    0.43   12.62    1.49    0.43   12.62
   34    262 261K 262V C   N    2071 2073    1.65    1.35    0.30   10.71    1.35    0.30   10.71
   35    263 262V 262V CB  CA   2075 2074    1.73    1.50    0.23    6.29    1.50    0.23    6.29
   36    266 262V 262V N   CA   2073 2074    1.84    1.43    0.41   13.66    1.43    0.41   13.66
   37    326 268D 269V C   N    2134 2136    1.55    1.35    0.20    7.23    1.35    0.20    7.23
   38    327 269V 269V CB  CA   2138 2137    1.66    1.50    0.16    4.51    1.50    0.16    4.51
   39    330 269V 269V N   CA   2136 2137    1.93    1.43    0.50   16.42    1.43    0.50   16.42

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    380 148G 149D C   N    1177 1179  145.59  120.00   25.59    5.81  120.00   25.59    5.81
    2    381 149D 148G N   C    1179 1177  145.28  122.50   22.78    6.55  122.50   22.78    6.55
    3    412 151P 151P N   CA   1199 1200  133.12  108.20   24.92    5.66  108.20   24.92    5.66
    4    528 244I 245Q C   N    1940 1942  139.85  120.00   19.85    4.51  120.00   19.85    4.51
    5    594 250K 251S C   N    1989 1991  152.86  120.00   32.86    7.47  120.00   32.86    7.47
    6    596 251S 251S N   CA   1991 1992  146.47  113.50   32.97    8.86  113.50   32.97    8.86
    7    602 251S 252I C   N    1995 1997  141.97  120.00   21.97    4.99  120.00   21.97    4.99
    8    613 252I 253G C   N    2003 2005  140.31  120.00   20.31    4.61  120.00   20.31    4.61
    9    615 253G 253G N   CA   2005 2006  157.99  107.00   50.99   14.65  107.00   50.99   14.65
   10    616 253G 253G CA  C    2006 2007  141.16  121.00   20.16    5.79  121.00   20.16    5.79
   11    618 253G 254C C   N    2007 2009  161.61  120.00   41.61    9.45  120.00   41.61    9.45
   12    626 254C 255F C   N    2013 2015  155.94  120.00   35.94    8.16  120.00   35.94    8.16
   13    629 255F 255F N   CA   2015 2016  144.28  107.00   37.28   10.71  107.00   37.28   10.71
   14    642 255F 256G C   N    2024 2026  162.20  120.00   42.20    9.59  120.00   42.20    9.59
   15    644 256G 256G N   CA   2026 2027  129.09  107.00   22.09    6.35  107.00   22.09    6.35
   16    647 256G 257S C   N    2028 2030  140.17  120.00   20.17    4.58  120.00   20.17    4.58
   17    658 258R 258R N   CA   2036 2037  128.47  107.00   21.47    6.17  107.00   21.47    6.17
   18    669 258R 259S C   N    2045 2047  173.80  120.00   53.80   12.22  120.00   53.80   12.22
   19    672 259S 259S N   CA   2047 2048  127.60  107.00   20.60    5.92  107.00   20.60    5.92
   20    679 260R 260R N   CA   2053 2054  130.98  113.50   17.48    4.70  113.50   17.48    4.70
   21    681 260R 260R CA  CB   2054 2055  144.58  113.50   31.08    7.63  113.50   31.08    7.63
   22    683 260R 260R CA  C    2054 2062  152.19  116.50   35.69   10.26  116.50   35.69   10.26
   23    691 260R 261K C   N    2062 2064  158.65  120.00   38.65    8.78  120.00   38.65    8.78
   24    694 261K 261K N   CA   2064 2065  128.65  107.00   21.65    6.22  107.00   21.65    6.22
   25    697 261K 261K CA  C    2065 2071  140.77  116.50   24.27    6.97  116.50   24.27    6.97
   26    701 261K 261K C   CA   2071 2065  135.94  108.00   27.94    6.47  108.00   27.94    6.47
   27    702 261K 262V C   N    2071 2073  169.91  120.00   49.91   11.34  120.00   49.91   11.34
   28    704 262V 262V N   CA   2073 2074  132.08  113.50   18.58    5.00  113.50   18.58    5.00
   29    788 268D 269V C   N    2134 2136  160.08  120.00   40.08    9.11  120.00   40.08    9.11
   30    790 269V 269V N   CA   2136 2137  148.75  113.50   35.25    9.48  113.50   35.25    9.48
   31    791 269V 269V N   CA   2136 2137  130.38  107.00   23.38    6.72  107.00   23.38    6.72
   32    801 270P 270P N   CA   2143 2144  140.52  108.20   32.32    7.34  108.20   32.32    7.34
   33    818 271M 271M CG  SD   2153 2154  129.49   95.00   34.49    6.46   95.00   34.49    6.46
   34    819 271M 271M C   CA   2156 2151  131.38  108.00   23.38    5.42  108.00   23.38    5.42

-------------------------------------------------------------------------------------------------

Feature  4                           : Stereochemical improper torsion potentia
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    829 148G 148G C   CA   1177 1176   18.65    0.00   18.65    6.57    0.00   18.65    6.57
    2    923 261K 261K C   CA   2071 2065   13.68    0.00   13.68    4.82    0.00   13.68    4.82
    3    954 269V 269V C   CA   2141 2137   13.33    0.00   13.33    4.69    0.00   13.33    4.69

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1304 148G 148G CA  C    1176 1177 -132.55  180.00   47.45    9.49  180.00   47.45    9.49
    2   1306 150Y 150Y CA  C    1188 1197 -156.42  180.00   23.58    4.72  180.00   23.58    4.72
    3   1333 259S 259S CA  C    2048 2051 -146.58  180.00   33.42    6.68  180.00   33.42    6.68


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1149 1177   2.203
  serious non-bonded atom clash:  1149 1178   1.973
  serious non-bonded atom clash:  1152 1177   2.185
  serious non-bonded atom clash:  1152 1178   1.988
  serious non-bonded atom clash:  1153 1177   2.250
  serious non-bonded atom clash:  1153 1178   2.037
  serious non-bonded atom clash:  1154 1177   2.213
  serious non-bonded atom clash:  1154 1178   2.063
  serious non-bonded atom clash:  1155 1177   2.230
  serious non-bonded atom clash:  1155 1178   2.045
  serious non-bonded atom clash:  1156 1177   2.210
  serious non-bonded atom clash:  1156 1178   2.058
  serious non-bonded atom clash:  1823 2063   2.112
  serious non-bonded atom clash:  1825 2006   1.850
  serious non-bonded atom clash:  1833 2006   2.013
  serious non-bonded atom clash:  1834 2005   2.049
  serious non-bonded atom clash:  1834 2006   2.103
  serious non-bonded atom clash:  1838 2051   2.221
  serious non-bonded atom clash:  1838 2052   2.036
  serious non-bonded atom clash:  1839 2051   2.233
  serious non-bonded atom clash:  1839 2052   2.045
  serious non-bonded atom clash:  1840 2051   2.213
  serious non-bonded atom clash:  1840 2052   2.025
  serious non-bonded atom clash:  1841 2051   2.249
  serious non-bonded atom clash:  1841 2052   2.062
  serious non-bonded atom clash:  1842 2051   2.204
  serious non-bonded atom clash:  1842 2052   2.016
  serious non-bonded atom clash:  1843 2051   2.222
  serious non-bonded atom clash:  1843 2052   2.037
  serious non-bonded atom clash:  1847 2006   2.091
  serious non-bonded atom clash:  1847 2007   2.198
  serious non-bonded atom clash:  1852 1993   1.844
  serious non-bonded atom clash:  1852 1994   1.893
  serious non-bonded atom clash:  1853 2006   1.968
  serious non-bonded atom clash:  1855 2005   2.297
  serious non-bonded atom clash:  1858 2005   2.200
  serious non-bonded atom clash:  1860 1993   2.011
  serious non-bonded atom clash:  1860 1994   2.251
  serious non-bonded atom clash:  1861 1992   2.118
  serious non-bonded atom clash:  1861 1993   2.002
  serious non-bonded atom clash:  1861 1994   1.934
  serious non-bonded atom clash:  1870 1993   1.980
  serious non-bonded atom clash:  1878 1993   1.957
  serious non-bonded atom clash:  1878 1994   1.986
  serious non-bonded atom clash:  1883 1994   1.982
  serious non-bonded atom clash:  2052 2553   2.279
  serious non-bonded atom clash:  2052 2554   2.145
  serious non-bonded atom clash:  2136 2191   2.286
  serious non-bonded atom clash:  2149 2277   2.202

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:    26    6   17   12   17   56   95  308  316  404  456  508  635  691  691


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   749853
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -48897.7109




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -48897.710938
>> Normalized DOPE z score: -0.520
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.134144
Native energy (pair)     :  -215.484682
Native energy (surface)  :    -6.434251
Native energy (combined) :    -5.476992
Z score (pair)           :    -9.731018
Z score (surface)        :    -6.249813
Z score (combined)       :   -10.432925
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    81436
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        -440.7022




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               :  -440.702179
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    81436
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        3929.8945




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :  3929.894531
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    11076
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        2996.0593





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349       9     11   0.089   0.089      662.13       1.000
 2 Bond angle potential               :     473       9     28   0.094   0.094      258.60       1.000
 3 Stereochemical cosine torsion poten:     340       0     16   1.138   1.138      145.14       1.000
 4 Stereochemical improper torsion pot:     138       0      4   0.056   0.056      30.313       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   11076       0     89   2.539   2.539      1794.2       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       0      3   0.133   0.133      30.934       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      4   1.461   1.461      31.620       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      2   1.528   1.528      27.488       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      0   1.963   1.963      15.505       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.130   1.130      4.5937       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   11076       0    119   2.814   2.814      429.26       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -433.71       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1     53 152K 152K CG  CB   1209 1208    1.76    1.53    0.23    6.40    1.53    0.23    6.40
    2     54 152K 152K CD  CG   1210 1209    2.45    1.53    0.92   25.26    1.53    0.92   25.26
    3     55 152K 152K CE  CD   1211 1210    2.53    1.53    1.00   27.58    1.53    1.00   27.58
    4     56 152K 152K NZ  CE   1212 1211    1.70    1.48    0.22    5.63    1.48    0.22    5.63
    5     60 152K 153A C   N    1213 1215    1.69    1.35    0.35   12.39    1.35    0.35   12.39
    6     61 153A 153A CB  CA   1217 1216    1.75    1.54    0.22    5.93    1.54    0.22    5.93
    7     64 153A 153A C   CA   1218 1216    2.12    1.49    0.63   18.23    1.49    0.63   18.23

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    421 151P 152K C   N    1204 1206  140.01  120.00   20.01    4.55  120.00   20.01    4.55
    2    423 152K 152K N   CA   1206 1207  138.17  113.50   24.67    6.63  113.50   24.67    6.63
    3    425 152K 152K CA  CB   1207 1208  136.00  113.50   22.50    5.52  113.50   22.50    5.52
    4    435 153A 153A N   CA   1215 1216  126.06  107.00   19.06    5.48  107.00   19.06    5.48
    5    788 268D 269V C   N    2134 2136  140.40  120.00   20.40    4.63  120.00   20.40    4.63


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1100 1210   2.220
  serious non-bonded atom clash:  1108 1210   2.296
  serious non-bonded atom clash:  1108 1211   2.178
  serious non-bonded atom clash:  1126 1210   2.267
  serious non-bonded atom clash:  1128 1213   2.288
  serious non-bonded atom clash:  1128 1215   2.188
  serious non-bonded atom clash:  1130 1216   2.203
  serious non-bonded atom clash:  1210 1288   2.266
  serious non-bonded atom clash:  1211 1290   2.236
  serious non-bonded atom clash:  1215 1247   2.245
  serious non-bonded atom clash:  1216 1247   2.231
  serious non-bonded atom clash:  1216 1255   2.253

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    2   10    8    8   42   94  279  308  392  430  484  592  645  660


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90:       90.3425
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   732106
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50108.1641




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -50108.164062
>> Normalized DOPE z score: -0.705
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.134144
Native energy (pair)     :  -336.085816
Native energy (surface)  :    -9.069734
Native energy (combined) :    -8.832131
Z score (pair)           :   -10.550459
Z score (surface)        :    -6.760520
Z score (combined)       :   -11.084059
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    63689
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -1651.5753




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -1651.575317
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    63689
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         -69.0709




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :   -69.070854
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     9969
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        4236.1113





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      12     27   0.085   0.085      638.59       1.000
 2 Bond angle potential               :     473      47     99   0.219   0.219      1322.9       1.000
 3 Stereochemical cosine torsion poten:     340       3     27   1.256   1.256      198.07       1.000
 4 Stereochemical improper torsion pot:     138       9     28   0.175   0.175      280.47       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :    9969       0     62   2.533   2.533      1574.7       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       8     13   0.333   0.333      193.14       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0     15   1.414   1.414      79.545       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      8   1.657   1.657      50.268       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      1   1.505   1.505      16.241       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      2   2.008   2.008      10.238       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :    9969       0     96   2.675   2.675      324.44       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -452.52       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    235 258R 258R C   CA   2045 2037    1.65    1.49    0.16    4.71    1.49    0.16    4.71
    2    268 262V 262V C   CA   2078 2074    1.66    1.49    0.17    5.06    1.49    0.17    5.06
    3    306 266Y 266Y N   CA   2107 2108    1.57    1.43    0.14    4.54    1.43    0.14    4.54
    4    310 267Q 267Q CB  CA   2121 2120    1.85    1.54    0.31    8.63    1.54    0.31    8.63
    5    311 267Q 267Q CG  CB   2122 2121    2.80    1.53    1.27   34.74    1.53    1.27   34.74
    6    312 267Q 267Q CD  CG   2123 2122    1.69    1.52    0.17    4.50    1.52    0.17    4.50
    7    335 270P 270P C   CA   2148 2144    1.67    1.49    0.18    5.24    1.49    0.18    5.24
    8    343 271M 271M CG  CB   2153 2152    1.72    1.53    0.19    5.12    1.53    0.19    5.12
    9    346 271M 271M N   CA   2150 2151    1.58    1.43    0.15    4.89    1.43    0.15    4.89

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    576 249N 249N CA  CB   1975 1976  131.86  108.00   23.86    5.53  108.00   23.86    5.53
    2    585 250K 250K N   CA   1982 1983  138.56  113.50   25.06    6.74  113.50   25.06    6.74
    3    587 250K 250K CA  CB   1983 1984  135.26  113.50   21.76    5.34  113.50   21.76    5.34
    4    598 251S 251S CA  CB   1992 1993  126.27  110.10   16.17    4.52  110.10   16.17    4.52
    5    606 252I 252I CA  CB   1998 1999  130.62  111.00   19.62    4.61  111.00   19.62    4.61
    6    615 253G 253G N   CA   2005 2006  123.20  107.00   16.20    4.65  107.00   16.20    4.65
    7    621 254C 254C N   CA   2009 2010  129.52  107.00   22.52    6.47  107.00   22.52    6.47
    8    630 255F 255F CA  CB   2016 2017  146.62  107.50   39.12    9.05  107.50   39.12    9.05
    9    638 255F 255F CD2 CG   2020 2018  145.17  120.00   25.17    5.11  120.00   25.17    5.11
   10    668 258R 258R C   CA   2045 2037  131.88  108.00   23.88    5.53  108.00   23.88    5.53
   11    706 262V 262V CA  CB   2074 2075  128.91  108.50   20.41    4.79  108.50   20.41    4.79
   12    727 264E 264E CA  CB   2090 2091  134.78  113.50   21.28    5.22  113.50   21.28    5.22
   13    741 265Q 265Q CA  C    2099 2105  135.13  116.50   18.63    5.35  116.50   18.63    5.35
   14    750 266Y 266Y N   CA   2107 2108  129.69  107.00   22.69    6.52  107.00   22.69    6.52
   15    765 266Y 267Q C   N    2117 2119  141.42  120.00   21.42    4.87  120.00   21.42    4.87
   16    767 267Q 267Q N   CA   2119 2120  149.36  113.50   35.86    9.64  113.50   35.86    9.64
   17    769 267Q 267Q CA  CB   2120 2121  153.02  113.50   39.52    9.70  113.50   39.52    9.70
   18    772 267Q 267Q CB  CG   2121 2122  134.29  108.00   26.29    6.09  108.00   26.29    6.09
   19    776 267Q 267Q C   CA   2126 2120  136.69  108.00   28.69    6.65  108.00   28.69    6.65
   20    777 267Q 268D C   N    2126 2128  148.28  120.00   28.28    6.43  120.00   28.28    6.43
   21    781 268D 268D CA  CB   2129 2130  132.31  108.00   24.31    5.63  108.00   24.31    5.63
   22    789 269V 268D N   C    2136 2134  138.63  122.50   16.13    4.63  122.50   16.13    4.63
   23    810 270P 271M C   N    2148 2150  149.61  120.00   29.61    6.73  120.00   29.61    6.73
   24    812 271M 271M N   CA   2150 2151  139.52  113.50   26.02    6.99  113.50   26.02    6.99
   25    818 271M 271M CG  SD   2153 2154  119.39   95.00   24.39    4.57   95.00   24.39    4.57
   26    820 271M 272P C   N    2156 2158  146.31  117.00   29.31    7.29  117.00   29.31    7.29

-------------------------------------------------------------------------------------------------

Feature  3                           : Stereochemical cosine torsion potential 
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1162 255F 255F CE1 CD1  2021 2019   67.65    0.00   67.65    5.30    0.00   67.65    5.30
    2   1164 255F 255F CE2 CD2  2022 2020  -65.14    0.00  -65.14    5.10    0.00  -65.14    5.10
    3   1173 255F 255F O   C    2025 2024  -75.69    0.00  -75.69    4.69    0.00  -75.69    4.69

-------------------------------------------------------------------------------------------------

Feature  4                           : Stereochemical improper torsion potentia
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    904 255F 255F C   CA   2024 2016   16.91    0.00   16.91    5.95    0.00   16.91    5.95
    2    906 255F 255F CB  CG   2017 2018 -153.10  180.00   26.90    8.20  180.00   26.90    8.20
    3    959 271M 271M C   CA   2156 2151   16.71    0.00   16.71    5.88    0.00   16.71    5.88

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1322 248N 248N CA  C    1967 1972 -149.12  180.00   30.88    6.18  180.00   30.88    6.18
    2   1327 253G 253G CA  C    2006 2007 -152.90  180.00   27.10    5.42  180.00   27.10    5.42
    3   1336 262V 262V CA  C    2074 2078 -149.23  180.00   30.77    6.15  180.00   30.77    6.15


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  2122 2603   2.271
  serious non-bonded atom clash:  2122 2609   2.300
  serious non-bonded atom clash:  2122 2610   2.045
  serious non-bonded atom clash:  2122 2625   2.130
  serious non-bonded atom clash:  2122 2634   2.199
  serious non-bonded atom clash:  2123 2625   2.236
  serious non-bonded atom clash:  2123 2632   2.268
  serious non-bonded atom clash:  2123 2652   2.230
  serious non-bonded atom clash:  2124 2610   2.271
  serious non-bonded atom clash:  2124 2617   1.994
  serious non-bonded atom clash:  2124 2643   2.272
  serious non-bonded atom clash:  2125 2610   2.031
  serious non-bonded atom clash:  2125 2625   2.279

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     3    2    8    5    4   38   86  281  282  394  423  487  592  637  665


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   720351
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50148.8828




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -50148.882812
>> Normalized DOPE z score: -0.711
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.129627
Native energy (pair)     :  -376.812078
Native energy (surface)  :   -10.876715
Native energy (combined) :   -10.123073
Z score (pair)           :   -11.193134
Z score (surface)        :    -7.101693
Z score (combined)       :   -11.974830
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    51934
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -1692.2545




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -1692.254517
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    51934
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         355.5964




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :   355.596405
readlinef__W> File: pkp2a.B99990003.pdb, Line: 5
              Modeller will only read the first 80 characters of this line.

iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
readlinef__W> File: pkp2a.B99990003.pdb, Line: 5
              Modeller will only read the first 80 characters of this line.

  #      ALGNMT CODE

  1  pkp2a
  2  pkp2a
341 atoms selected for loop refinement
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:     1640     1438
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    15590
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        2153.7961





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349       0      0   0.010   0.010      9.0540       1.000
 2 Bond angle potential               :     473       1      6   0.046   0.046      58.327       1.000
 3 Stereochemical cosine torsion poten:     340       0     14   1.126   1.126      132.29       1.000
 4 Stereochemical improper torsion pot:     138       0      1   0.026   0.026      6.0003       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   15590       0    126   2.547   2.547      344.68       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       0      2   0.081   0.081      11.553       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      0   1.378   1.378      12.303       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      1   1.144   1.144      18.557       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      0   1.754   1.754      12.068       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.861   1.861      4.2905       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   15580       0    256   2.838   2.838      2041.1       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -496.39       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    751 266Y 266Y CA  CB   2108 2109  132.77  107.50   25.27    5.84  107.50   25.27    5.84


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    1   45   87  363  335  485  459  502  604  676  724


<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     8513
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         821.2953





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349       5      5   0.064   0.064      372.44       1.000
 2 Bond angle potential               :     473      12     44   0.117   0.117      400.91       1.000
 3 Stereochemical cosine torsion poten:     340       0     32   1.263   1.263      175.03       1.000
 4 Stereochemical improper torsion pot:     138       2      6   0.083   0.083      55.490       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :    8513       0     36   2.522   2.522      409.94       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       2     10   0.183   0.183      58.499       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0     10   1.491   1.491      64.740       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      5   1.470   1.470      34.916       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      1   1.468   1.468      15.576       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.678   1.678      6.8525       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :    8513       0     49   2.733   2.733     -280.96       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -492.14       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    262 261K 262V C   N    2071 2073    1.52    1.35    0.18    6.26    1.35    0.18    6.26
    2    263 262V 262V CB  CA   2075 2074    2.15    1.50    0.65   17.90    1.50    0.65   17.90
    3    266 262V 262V N   CA   2073 2074    1.87    1.43    0.44   14.43    1.43    0.44   14.43
    4    268 262V 262V C   CA   2078 2074    2.28    1.49    0.79   22.98    1.49    0.79   22.98
    5    269 262V 263K C   N    2078 2080    1.56    1.35    0.21    7.45    1.35    0.21    7.45

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    528 244I 245Q C   N    1940 1942  146.81  120.00   26.81    6.09  120.00   26.81    6.09
    2    702 261K 262V C   N    2071 2073  148.13  120.00   28.13    6.39  120.00   28.13    6.39
    3    709 262V 262V CA  C    2074 2078  140.91  116.50   24.41    7.02  116.50   24.41    7.02
    4    781 268D 268D CA  CB   2129 2130  129.01  108.00   21.01    4.87  108.00   21.01    4.87
    5    810 270P 271M C   N    2148 2150  141.64  120.00   21.64    4.92  120.00   21.64    4.92
    6    813 271M 271M N   CA   2150 2151  130.76  107.00   23.76    6.83  107.00   23.76    6.83
    7    816 271M 271M CA  C    2151 2156  149.31  112.50   36.81    5.29  112.50   36.81    5.29
    8    821 271M 272P C   N    2156 2158  141.00  117.00   24.00    5.97  117.00   24.00    5.97

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1314 240Q 240Q CA  C    1899 1905 -155.79  180.00   24.21    4.84  180.00   24.21    4.84
    2   1335 261K 261K CA  C    2065 2071 -154.02  180.00   25.98    5.20  180.00   25.98    5.20


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1831 2074   2.225

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    1    1    2   41   86  323  313  433  433  485  591  629  680


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   718241
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -49557.6016




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -49557.601562
>> Normalized DOPE z score: -0.621
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.129563
Native energy (pair)     :  -362.336614
Native energy (surface)  :   -11.299583
Native energy (combined) :    -9.820402
Z score (pair)           :   -10.383564
Z score (surface)        :    -7.414037
Z score (combined)       :   -11.560751
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    48630
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -1615.7263




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -1615.726318
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    48630
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        -564.8653




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :  -564.865295
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    10186
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        9784.4570





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      17     26   0.154   0.154      2335.6       1.000
 2 Bond angle potential               :     473      19     82   0.145   0.145      638.96       1.000
 3 Stereochemical cosine torsion poten:     340       2     31   1.230   1.230      185.89       1.000
 4 Stereochemical improper torsion pot:     138       4     13   0.132   0.132      156.45       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   10186       0    109   2.581   2.581      5533.3       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       7     21   0.355   0.355      219.36       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      9   1.498   1.498      55.936       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      5   1.322   1.322      40.721       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      1   1.916   1.916      17.237       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.658   1.658      9.1402       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   10186       0    148   2.784   2.784      1067.0       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -475.13       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    146 246T 247D C   N    1956 1958    1.54    1.35    0.20    6.93    1.35    0.20    6.93
    2    147 247D 247D CB  CA   1960 1959    1.81    1.54    0.27    7.44    1.54    0.27    7.44
    3    151 247D 247D N   CA   1958 1959    1.66    1.43    0.23    7.45    1.43    0.23    7.45
    4    153 247D 247D C   CA   1964 1959    2.38    1.49    0.89   25.89    1.49    0.89   25.89
    5    154 247D 248N C   N    1964 1966    1.55    1.35    0.21    7.27    1.35    0.21    7.27
    6    159 248N 248N N   CA   1966 1967    1.75    1.43    0.32   10.64    1.43    0.32   10.64
    7    161 248N 248N C   CA   1972 1967    1.93    1.49    0.44   12.76    1.49    0.44   12.76
    8    162 248N 249N C   N    1972 1974    1.85    1.35    0.51   17.91    1.35    0.51   17.91
    9    163 249N 249N CB  CA   1976 1975    1.75    1.54    0.21    5.73    1.54    0.21    5.73
   10    167 249N 249N N   CA   1974 1975    3.45    1.43    2.02   66.40    1.43    2.02   66.40
   11    169 249N 249N C   CA   1980 1975    1.73    1.49    0.24    7.07    1.49    0.24    7.07
   12    245 260R 260R CD  CG   2057 2056    1.99    1.53    0.46   12.53    1.53    0.46   12.53
   13    246 260R 260R NE  CD   2058 2057    1.90    1.49    0.41   12.33    1.49    0.41   12.33
   14    256 261K 261K CD  CG   2068 2067    2.45    1.53    0.92   25.30    1.53    0.92   25.30
   15    257 261K 261K CE  CD   2069 2068    1.77    1.53    0.24    6.54    1.53    0.24    6.54
   16    258 261K 261K NZ  CE   2070 2069    2.46    1.48    0.98   25.58    1.48    0.98   25.58
   17    346 271M 271M N   CA   2150 2151    1.57    1.43    0.14    4.74    1.43    0.14    4.74

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    469 239I 240Q C   N    1896 1898  144.38  120.00   24.38    5.54  120.00   24.38    5.54
    2    553 247D 247D N   CA   1958 1959  138.99  107.00   31.99    9.19  107.00   31.99    9.19
    3    554 247D 247D CA  CB   1959 1960  150.93  108.00   42.93    9.95  108.00   42.93    9.95
    4    556 247D 247D CA  C    1959 1964  139.25  116.50   22.75    6.54  116.50   22.75    6.54
    5    564 248N 248N N   CA   1966 1967  124.63  107.00   17.63    5.07  107.00   17.63    5.07
    6    572 248N 249N C   N    1972 1974  143.11  120.00   23.11    5.25  120.00   23.11    5.25
    7    574 249N 249N N   CA   1974 1975  138.75  113.50   25.25    6.79  113.50   25.25    6.79
    8    620 254C 254C N   CA   2009 2010  136.43  113.50   22.93    6.16  113.50   22.93    6.16
    9    680 260R 260R N   CA   2053 2054  124.63  107.00   17.63    5.07  107.00   17.63    5.07
   10    685 260R 260R CG  CD   2056 2057  127.60  107.50   20.10    5.31  107.50   20.10    5.31
   11    686 260R 260R CD  NE   2057 2058  141.27  120.00   21.27    5.39  120.00   21.27    5.39
   12    698 261K 261K CB  CG   2066 2067  137.06  113.60   23.46    5.76  113.60   23.46    5.76
   13    700 261K 261K CD  CE   2068 2069  133.76  110.00   23.76    6.28  110.00   23.76    6.28
   14    791 269V 269V N   CA   2136 2137  125.32  107.00   18.32    5.26  107.00   18.32    5.26
   15    813 271M 271M N   CA   2150 2151  125.07  107.00   18.07    5.19  107.00   18.07    5.19

-------------------------------------------------------------------------------------------------

Feature  3                           : Stereochemical cosine torsion potential 
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1114 247D 247D O   C    1965 1964   76.51    0.00   76.51    4.73    0.00   76.51    4.73
    2   1121 248N 248N O   C    1973 1972  105.98  180.00  -74.02    4.62  180.00  -74.02    4.62

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1305 149D 149D CA  C    1180 1185 -154.64  180.00   25.36    5.07  180.00   25.36    5.07
    2   1308 152K 152K CA  C    1207 1213 -156.33  180.00   23.67    4.73  180.00   23.67    4.73
    3   1309 153A 153A CA  C    1216 1218 -152.44  180.00   27.56    5.51  180.00   27.56    5.51
    4   1321 247D 247D CA  C    1959 1964 -121.57  180.00   58.43   11.69  180.00   58.43   11.69
    5   1322 248N 248N CA  C    1967 1972 -126.38  180.00   53.62   10.72  180.00   53.62   10.72


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1785 1965   2.259
  serious non-bonded atom clash:  1825 2068   2.076
  serious non-bonded atom clash:  1825 2069   1.813
  serious non-bonded atom clash:  1827 2068   2.118
  serious non-bonded atom clash:  1833 2068   2.209
  serious non-bonded atom clash:  1833 2069   1.995
  serious non-bonded atom clash:  1834 2068   2.155
  serious non-bonded atom clash:  1834 2069   2.147
  serious non-bonded atom clash:  1847 2069   1.970
  serious non-bonded atom clash:  1847 2070   2.272
  serious non-bonded atom clash:  1852 1974   2.044
  serious non-bonded atom clash:  1853 2069   1.966
  serious non-bonded atom clash:  1855 2068   2.185
  serious non-bonded atom clash:  1856 2068   2.125
  serious non-bonded atom clash:  1861 1975   2.109
  serious non-bonded atom clash:  1874 1974   2.221
  serious non-bonded atom clash:  1881 1974   2.181
  serious non-bonded atom clash:  1883 1974   2.160
  serious non-bonded atom clash:  1883 1975   2.066

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     7    8    4    7   12   47   97  335  319  436  453  491  588  645  690


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   731415
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -48598.2930




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -48598.292969
>> Normalized DOPE z score: -0.474
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.129563
Native energy (pair)     :  -354.326292
Native energy (surface)  :    -9.197321
Native energy (combined) :    -9.009773
Z score (pair)           :   -10.156830
Z score (surface)        :    -7.146453
Z score (combined)       :   -11.386456
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    61804
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        -656.7945




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               :  -656.794495
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    61804
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        1990.2979




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :  1990.297852
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    10485
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       15566.9316





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      19     28   0.230   0.230      5526.4       1.000
 2 Bond angle potential               :     473      33     77   0.178   0.178      915.38       1.000
 3 Stereochemical cosine torsion poten:     340       0     27   1.310   1.310      197.03       1.000
 4 Stereochemical improper torsion pot:     138       6     13   0.160   0.160      252.45       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   10485       0    155   2.541   2.541      7571.0       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       9     14   0.302   0.302      159.44       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      7   1.433   1.433      43.904       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      6   1.453   1.453      39.197       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      2   1.572   1.572      19.446       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      1   1.747   1.747      7.6311       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   10485       0    194   2.734   2.734      1294.0       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -458.84       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1     22 148G 149D C   N    1177 1179    1.65    1.35    0.31   10.83    1.35    0.31   10.83
    2     27 149D 149D N   CA   1179 1180    1.99    1.43    0.56   18.30    1.43    0.56   18.30
    3     29 149D 149D C   CA   1185 1180    3.01    1.49    1.52   44.31    1.49    1.52   44.31
    4     30 149D 150Y C   N    1185 1187    1.83    1.35    0.48   17.13    1.35    0.48   17.13
    5     43 150Y 151P C   N    1197 1199    1.97    1.30    0.67   19.75    1.30    0.67   19.75
    6     47 151P 151P N   CA   1199 1200    2.80    1.43    1.36   44.94    1.43    1.36   44.94
    7     48 151P 151P CA  CB   1200 1202    2.75    1.53    1.23   33.67    1.53    1.23   33.67
    8     49 151P 151P CB  CG   1202 1203    3.12    1.54    1.58   43.34    1.54    1.58   43.34
    9     50 151P 151P CG  CD   1203 1201    3.00    1.54    1.46   40.14    1.54    1.46   40.14
   10     51 151P 151P N   CD   1199 1201    3.26    1.46    1.80   59.38    1.46    1.80   59.38
   11    171 250K 250K CB  CA   1984 1983    2.06    1.54    0.52   14.29    1.54    0.52   14.29
   12    172 250K 250K CG  CB   1985 1984    2.48    1.53    0.95   26.06    1.53    0.95   26.06
   13    173 250K 250K CD  CG   1986 1985    1.84    1.53    0.31    8.53    1.53    0.31    8.53
   14    174 250K 250K CE  CD   1987 1986    1.76    1.53    0.23    6.37    1.53    0.23    6.37
   15    177 250K 250K O   C    1990 1989    2.53    1.23    1.30   59.55    1.23    1.30   59.55
   16    178 250K 250K C   CA   1989 1983    2.06    1.49    0.57   16.63    1.49    0.57   16.63
   17    179 250K 251S C   N    1989 1991    1.61    1.35    0.26    9.30    1.35    0.26    9.30
   18    182 251S 251S N   CA   1991 1992    1.60    1.43    0.17    5.69    1.43    0.17    5.69

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    380 148G 149D C   N    1177 1179  168.57  120.00   48.57   11.04  120.00   48.57   11.04
    2    383 149D 149D N   CA   1179 1180  124.17  107.00   17.17    4.93  107.00   17.17    4.93
    3    388 149D 149D CB  CG   1181 1182  142.58  118.00   24.58    4.99  118.00   24.58    4.99
    4    389 149D 149D OD2 CG   1184 1182  139.65  124.00   15.65    5.03  124.00   15.65    5.03
    5    390 149D 149D C   CA   1185 1180  147.55  108.00   39.55    9.16  108.00   39.55    9.16
    6    391 149D 150Y C   N    1185 1187  153.04  120.00   33.04    7.51  120.00   33.04    7.51
    7    395 150Y 150Y CA  CB   1188 1189  129.42  107.50   21.92    5.07  107.50   21.92    5.07
    8    420 151P 151P C   CA   1204 1200  135.49  112.30   23.19    5.37  112.30   23.19    5.37
    9    469 239I 240Q C   N    1896 1898  142.21  120.00   22.21    5.05  120.00   22.21    5.05
   10    509 243N 243N N   CA   1926 1927  122.81  107.00   15.81    4.54  107.00   15.81    4.54
   11    583 249N 250K C   N    1980 1982  158.98  120.00   38.98    8.86  120.00   38.98    8.86
   12    587 250K 250K CA  CB   1983 1984  152.28  113.50   38.78    9.52  113.50   38.78    9.52
   13    590 250K 250K CB  CG   1984 1985  149.00  113.60   35.40    8.69  113.60   35.40    8.69
   14    591 250K 250K CG  CD   1985 1986  132.53  113.60   18.93    4.65  113.60   18.93    4.65
   15    593 250K 250K C   CA   1989 1983  137.65  108.00   29.65    6.87  108.00   29.65    6.87
   16    594 250K 251S C   N    1989 1991  157.50  120.00   37.50    8.52  120.00   37.50    8.52
   17    595 251S 250K N   C    1991 1989  141.94  122.50   19.44    5.59  122.50   19.44    5.59
   18    596 251S 251S N   CA   1991 1992  135.26  113.50   21.76    5.85  113.50   21.76    5.85
   19    615 253G 253G N   CA   2005 2006  122.93  107.00   15.93    4.58  107.00   15.93    4.58
   20    642 255F 256G C   N    2024 2026  143.01  120.00   23.01    5.23  120.00   23.01    5.23
   21    777 267Q 268D C   N    2126 2128  142.02  120.00   22.02    5.00  120.00   22.02    5.00
   22    819 271M 271M C   CA   2156 2151  128.82  108.00   20.82    4.82  108.00   20.82    4.82
   23    821 271M 272P C   N    2156 2158  148.15  117.00   31.15    7.75  117.00   31.15    7.75

-------------------------------------------------------------------------------------------------

Feature  4                           : Stereochemical improper torsion potentia
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    830 149D 149D C   CA   1185 1180   48.04    0.00   48.04   16.91    0.00   48.04   16.91

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1305 149D 149D CA  C    1180 1185 -115.60  180.00   64.40   12.88  180.00   64.40   12.88
    2   1306 150Y 150Y CA  C    1188 1197 -139.85  180.00   40.15    8.03  180.00   40.15    8.03
    3   1312 156L 156L CA  C    1233 1238 -154.36  180.00   25.64    5.13  180.00   25.64    5.13
    4   1316 242R 242R CA  C    1916 1924 -150.30  180.00   29.70    5.94  180.00   29.70    5.94
    5   1320 246T 246T CA  C    1952 1956 -151.91  180.00   28.09    5.62  180.00   28.09    5.62
    6   1324 250K 250K CA  C    1983 1989 -152.68  180.00   27.32    5.46  180.00   27.32    5.46
    7   1344 270P 270P CA  C    2144 2148 -149.33  180.00   30.67    6.13  180.00   30.67    6.13


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1100 1203   1.872
  serious non-bonded atom clash:  1107 1203   2.187
  serious non-bonded atom clash:  1108 1201   2.013
  serious non-bonded atom clash:  1108 1203   1.991
  serious non-bonded atom clash:  1114 1185   2.222
  serious non-bonded atom clash:  1116 1185   2.096
  serious non-bonded atom clash:  1116 1186   1.875
  serious non-bonded atom clash:  1116 1187   2.277
  serious non-bonded atom clash:  1116 1201   2.006
  serious non-bonded atom clash:  1117 1203   2.056
  serious non-bonded atom clash:  1122 1199   2.063
  serious non-bonded atom clash:  1123 1199   1.969
  serious non-bonded atom clash:  1123 1200   2.066
  serious non-bonded atom clash:  1124 1202   2.299
  serious non-bonded atom clash:  1124 1203   1.987
  serious non-bonded atom clash:  1125 1200   2.251
  serious non-bonded atom clash:  1133 1199   2.128
  serious non-bonded atom clash:  1135 1199   2.297
  serious non-bonded atom clash:  1135 1201   2.086
  serious non-bonded atom clash:  1138 1185   2.085
  serious non-bonded atom clash:  1138 1186   2.054
  serious non-bonded atom clash:  1140 1183   2.269
  serious non-bonded atom clash:  1141 1186   2.198
  serious non-bonded atom clash:  1141 1199   1.993
  serious non-bonded atom clash:  1145 1185   2.106
  serious non-bonded atom clash:  1145 1186   2.021
  serious non-bonded atom clash:  1145 1187   2.289
  serious non-bonded atom clash:  1146 1180   2.285
  serious non-bonded atom clash:  1846 1989   1.997
  serious non-bonded atom clash:  1846 1990   1.737
  serious non-bonded atom clash:  1851 1990   2.014
  serious non-bonded atom clash:  1852 1990   2.181
  serious non-bonded atom clash:  1862 1990   1.940
  serious non-bonded atom clash:  1870 1989   2.223
  serious non-bonded atom clash:  1870 1990   1.877

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:    21    5    9   12   10   47   96  339  339  453  449  490  596  630  704


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   727908
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -48879.3398




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -48879.339844
>> Normalized DOPE z score: -0.517
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.123108
Native energy (pair)     :  -342.596892
Native energy (surface)  :    -9.659218
Native energy (combined) :    -9.025208
Z score (pair)           :   -10.933599
Z score (surface)        :    -7.227985
Z score (combined)       :   -11.965166
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    58297
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        -937.4592




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               :  -937.459229
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    58297
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        2085.8542




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :  2085.854248
readlinef__W> File: pkp2a.B99990004.pdb, Line: 5
              Modeller will only read the first 80 characters of this line.

iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
readlinef__W> File: pkp2a.B99990004.pdb, Line: 5
              Modeller will only read the first 80 characters of this line.

  #      ALGNMT CODE

  1  pkp2a
  2  pkp2a
341 atoms selected for loop refinement
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:     1640     1438
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    16902
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        2675.2695





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349       0      0   0.015   0.015      21.424       1.000
 2 Bond angle potential               :     473       0      6   0.048   0.048      68.381       1.000
 3 Stereochemical cosine torsion poten:     340       0      6   1.075   1.075      120.92       1.000
 4 Stereochemical improper torsion pot:     138       0      0   0.024   0.024      4.9270       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   16902       0    148   2.589   2.589      407.85       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       1      4   0.123   0.123      26.490       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      2   1.247   1.247      19.140       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      2   1.400   1.400      17.560       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      0   1.804   1.804      14.800       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   0.939   0.939      4.1342       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   16876       0    286   2.833   2.833      2405.8       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -436.20       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1338 264E 264E CA  C    2090 2096 -151.41  180.00   28.59    5.72  180.00   28.59    5.72


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0   38   57  305  321  467  437  513  565  650  694


<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    20341
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       28405.1309





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      45     66   0.330   0.330      9064.2       1.000
 2 Bond angle potential               :     473      75    138   0.261   0.261      2005.3       1.000
 3 Stereochemical cosine torsion poten:     340       2     31   1.304   1.304      201.23       1.000
 4 Stereochemical improper torsion pot:     138      13     20   0.228   0.228      480.40       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   20341       0    310   2.557   2.557      12604.       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45      11     16   0.419   0.419      305.48       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0     15   1.562   1.562      74.616       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      9   1.728   1.728      49.490       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      1   1.288   1.288      17.304       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      2   1.547   1.547      9.6357       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   20341       0    446   2.891   2.891      4024.5       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -430.48       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1      3 146P 146P C   CA   1164 1160    1.68    1.49    0.19    5.63    1.49    0.19    5.63
    2      4 146P 147E C   N    1164 1166    1.74    1.35    0.40   14.00    1.35    0.40   14.00
    3     11 147E 147E CG  CB   1169 1168    1.84    1.53    0.31    8.51    1.53    0.31    8.51
    4     12 147E 147E CD  CG   1170 1169    2.00    1.52    0.47   12.37    1.52    0.47   12.37
    5     15 147E 147E N   CA   1166 1167    2.11    1.43    0.68   22.43    1.43    0.68   22.43
    6     17 147E 147E C   CA   1173 1167    3.60    1.49    2.11   61.53    1.49    2.11   61.53
    7     53 152K 152K CG  CB   1209 1208    1.95    1.53    0.42   11.40    1.53    0.42   11.40
    8     54 152K 152K CD  CG   1210 1209    2.95    1.53    1.42   39.01    1.53    1.42   39.01
    9     55 152K 152K CE  CD   1211 1210    2.51    1.53    0.98   26.90    1.53    0.98   26.90
   10    163 249N 249N CB  CA   1976 1975    2.18    1.54    0.64   17.55    1.54    0.64   17.55
   11    164 249N 249N CG  CB   1977 1976    2.81    1.52    1.29   33.55    1.52    1.29   33.55
   12    185 251S 252I C   N    1995 1997    1.48    1.35    0.13    4.62    1.35    0.13    4.62
   13    186 252I 252I CB  CA   1999 1998    3.70    1.50    2.20   60.43    1.50    2.20   60.43
   14    187 252I 252I CG1 CB   2000 1999    2.18    1.54    0.65   17.73    1.54    0.65   17.73
   15    188 252I 252I CG2 CB   2001 1999    2.84    1.54    1.31   35.89    1.54    1.31   35.89
   16    189 252I 252I CD1 CG1  2002 2000    2.16    1.53    0.63   17.42    1.53    0.63   17.42
   17    190 252I 252I N   CA   1997 1998    1.73    1.43    0.30    9.97    1.43    0.30    9.97
   18    252 260R 260R C   CA   2062 2054    1.69    1.49    0.20    5.78    1.49    0.20    5.78
   19    259 261K 261K N   CA   2064 2065    1.66    1.43    0.23    7.66    1.43    0.23    7.66
   20    261 261K 261K C   CA   2071 2065    2.68    1.49    1.19   34.56    1.49    1.19   34.56
   21    262 261K 262V C   N    2071 2073    1.57    1.35    0.23    8.06    1.35    0.23    8.06
   22    263 262V 262V CB  CA   2075 2074    4.65    1.50    3.15   86.61    1.50    3.15   86.61
   23    267 262V 262V O   C    2079 2078    1.59    1.23    0.36   16.58    1.23    0.36   16.58
   24    268 262V 262V C   CA   2078 2074    3.17    1.49    1.68   48.84    1.49    1.68   48.84
   25    269 262V 263K C   N    2078 2080    1.95    1.35    0.61   21.50    1.35    0.61   21.50
   26    271 263K 263K CG  CB   2083 2082    1.71    1.53    0.18    4.92    1.53    0.18    4.92
   27    275 263K 263K N   CA   2080 2081    1.88    1.43    0.45   14.85    1.43    0.45   14.85
   28    277 263K 263K C   CA   2087 2081    1.77    1.49    0.28    8.09    1.49    0.28    8.09
   29    284 264E 264E N   CA   2089 2090    1.58    1.43    0.15    4.82    1.43    0.15    4.82
   30    296 265Q 266Y C   N    2105 2107    1.72    1.35    0.38   13.42    1.35    0.38   13.42
   31    297 266Y 266Y CB  CA   2109 2108    2.68    1.54    1.15   31.49    1.54    1.15   31.49
   32    298 266Y 266Y CG  CB   2110 2109    1.66    1.49    0.17    4.61    1.49    0.17    4.61
   33    306 266Y 266Y N   CA   2107 2108    2.16    1.43    0.73   23.93    1.43    0.73   23.93
   34    308 266Y 266Y C   CA   2117 2108    2.41    1.49    0.92   26.84    1.49    0.92   26.84
   35    309 266Y 267Q C   N    2117 2119    1.88    1.35    0.54   18.95    1.35    0.54   18.95
   36    310 267Q 267Q CB  CA   2121 2120    1.98    1.54    0.44   12.18    1.54    0.44   12.18
   37    311 267Q 267Q CG  CB   2122 2121    1.92    1.53    0.39   10.59    1.53    0.39   10.59
   38    312 267Q 267Q CD  CG   2123 2122    1.84    1.52    0.32    8.36    1.52    0.32    8.36
   39    315 267Q 267Q N   CA   2119 2120    1.94    1.43    0.51   16.89    1.43    0.51   16.89
   40    317 267Q 267Q C   CA   2126 2120    1.67    1.49    0.18    5.15    1.49    0.18    5.15
   41    320 268D 268D CG  CB   2131 2130    1.92    1.52    0.40   10.48    1.52    0.40   10.48

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    351 145W 146P C   N    1157 1159  147.09  117.00   30.09    7.49  117.00   30.09    7.49
    2    362 146P 146P C   CA   1164 1160  134.90  112.30   22.60    5.24  112.30   22.60    5.24
    3    367 147E 147E CA  CB   1167 1168  150.20  113.50   36.70    9.01  113.50   36.70    9.01
    4    370 147E 147E CB  CG   1168 1169  156.14  108.00   48.14   11.15  108.00   48.14   11.15
    5    374 147E 147E C   CA   1173 1167  128.14  108.00   20.14    4.67  108.00   20.14    4.67
    6    395 150Y 150Y CA  CB   1188 1189  129.60  107.50   22.10    5.11  107.50   22.10    5.11
    7    425 152K 152K CA  CB   1207 1208  152.06  113.50   38.56    9.46  113.50   38.56    9.46
    8    428 152K 152K CB  CG   1208 1209  147.88  113.60   34.28    8.41  113.60   34.28    8.41
    9    458 156L 156L N   CA   1232 1233  123.47  107.00   16.47    4.73  107.00   16.47    4.73
   10    517 243N 244I C   N    1932 1934  141.41  120.00   21.41    4.86  120.00   21.41    4.86
   11    540 245Q 246T C   N    1949 1951  140.74  120.00   20.74    4.71  120.00   20.74    4.71
   12    572 248N 249N C   N    1972 1974  141.80  120.00   21.80    4.95  120.00   21.80    4.95
   13    576 249N 249N CA  CB   1975 1976  164.83  108.00   56.83   13.17  108.00   56.83   13.17
   14    582 249N 249N C   CA   1980 1975  131.07  108.00   23.07    5.34  108.00   23.07    5.34
   15    583 249N 250K C   N    1980 1982  140.55  120.00   20.55    4.67  120.00   20.55    4.67
   16    602 251S 252I C   N    1995 1997  147.63  120.00   27.63    6.28  120.00   27.63    6.28
   17    612 252I 252I C   CA   2003 1998  143.40  108.00   35.40    8.20  108.00   35.40    8.20
   18    615 253G 253G N   CA   2005 2006  123.12  107.00   16.12    4.63  107.00   16.12    4.63
   19    691 260R 261K C   N    2062 2064  156.50  120.00   36.50    8.29  120.00   36.50    8.29
   20    694 261K 261K N   CA   2064 2065  135.16  107.00   28.16    8.09  107.00   28.16    8.09
   21    696 261K 261K CA  C    2065 2071  136.91  121.00   15.91    4.57  121.00   15.91    4.57
   22    701 261K 261K C   CA   2071 2065  135.43  108.00   27.43    6.36  108.00   27.43    6.36
   23    704 262V 262V N   CA   2073 2074  132.99  113.50   19.49    5.24  113.50   19.49    5.24
   24    705 262V 262V N   CA   2073 2074  125.63  107.00   18.63    5.35  107.00   18.63    5.35
   25    706 262V 262V CA  CB   2074 2075  131.00  108.50   22.50    5.28  108.50   22.50    5.28
   26    707 262V 262V CA  CB   2074 2075  132.61  108.50   24.11    5.66  108.50   24.11    5.66
   27    709 262V 262V CA  C    2074 2078  137.63  116.50   21.13    6.07  116.50   21.13    6.07
   28    714 263K 263K N   CA   2080 2081  145.09  113.50   31.59    8.49  113.50   31.59    8.49
   29    715 263K 263K N   CA   2080 2081  129.15  107.00   22.15    6.37  107.00   22.15    6.37
   30    716 263K 263K CA  CB   2081 2082  135.12  113.50   21.62    5.31  113.50   21.62    5.31
   31    718 263K 263K CA  C    2081 2087  145.28  116.50   28.78    8.27  116.50   28.78    8.27
   32    725 264E 264E N   CA   2089 2090  130.28  113.50   16.78    4.51  113.50   16.78    4.51
   33    727 264E 264E CA  CB   2090 2091  146.94  113.50   33.44    8.21  113.50   33.44    8.21
   34    738 265Q 265Q N   CA   2098 2099  123.25  107.00   16.25    4.67  107.00   16.25    4.67
   35    739 265Q 265Q CA  CB   2099 2100  133.13  113.50   19.63    4.82  113.50   19.63    4.82
   36    741 265Q 265Q CA  C    2099 2105  148.39  116.50   31.89    9.16  116.50   31.89    9.16
   37    751 266Y 266Y CA  CB   2108 2109  137.74  107.50   30.24    6.99  107.50   30.24    6.99
   38    753 266Y 266Y CA  C    2108 2117  163.06  116.50   46.56   13.38  116.50   46.56   13.38
   39    765 266Y 267Q C   N    2117 2119  160.38  120.00   40.38    9.18  120.00   40.38    9.18
   40    767 267Q 267Q N   CA   2119 2120  146.78  113.50   33.28    8.95  113.50   33.28    8.95
   41    769 267Q 267Q CA  CB   2120 2121  143.97  113.50   30.47    7.48  113.50   30.47    7.48
   42    772 267Q 267Q CB  CG   2121 2122  148.68  108.00   40.68    9.43  108.00   40.68    9.43
   43    785 268D 268D CB  CG   2130 2131  150.99  118.00   32.99    6.70  118.00   32.99    6.70
   44    787 268D 268D C   CA   2134 2129  131.73  108.00   23.73    5.50  108.00   23.73    5.50
   45    790 269V 269V N   CA   2136 2137  150.17  113.50   36.67    9.86  113.50   36.67    9.86
   46    793 269V 269V CA  CB   2137 2138  133.30  108.50   24.80    5.82  108.50   24.80    5.82
   47    818 271M 271M CG  SD   2153 2154  126.69   95.00   31.69    5.94   95.00   31.69    5.94
   48    820 271M 272P C   N    2156 2158  179.95  117.00   62.95   15.67  117.00   62.95   15.67

-------------------------------------------------------------------------------------------------

Feature  3                           : Stereochemical cosine torsion potential 
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    969 146P 146P O   C    1165 1164  -96.96  180.00   83.04    4.93  180.00   83.04    4.93
    2   1210 261K 261K O   C    2072 2071  -92.65  180.00   87.35    4.99  180.00   87.35    4.99

-------------------------------------------------------------------------------------------------

Feature  4                           : Stereochemical improper torsion potentia
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    857 239I 239I C   CA   1896 1891   26.70    0.00   26.70    9.40    0.00   26.70    9.40
    2    891 249N 249N CG  ND2  1977 1979   24.05    0.00   24.05    5.18    0.00   24.05    5.18
    3    959 271M 271M C   CA   2156 2151   22.90    0.00   22.90    8.06    0.00   22.90    8.06

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1305 149D 149D CA  C    1180 1185 -145.96  180.00   34.04    6.81  180.00   34.04    6.81
    2   1334 260R 260R CA  C    2054 2062 -153.02  180.00   26.98    5.40  180.00   26.98    5.40


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1100 1209   2.226
  serious non-bonded atom clash:  1100 1210   2.168
  serious non-bonded atom clash:  1108 1210   2.297
  serious non-bonded atom clash:  1108 1211   2.230
  serious non-bonded atom clash:  1126 1210   2.238
  serious non-bonded atom clash:  1147 1167   2.183
  serious non-bonded atom clash:  1147 1173   2.253
  serious non-bonded atom clash:  1173 1511   2.189
  serious non-bonded atom clash:  1825 2000   1.878
  serious non-bonded atom clash:  1825 2002   2.247
  serious non-bonded atom clash:  1833 2000   2.080
  serious non-bonded atom clash:  1834 1999   1.813
  serious non-bonded atom clash:  1834 2000   2.048
  serious non-bonded atom clash:  1834 2001   2.190
  serious non-bonded atom clash:  1845 1999   1.884
  serious non-bonded atom clash:  1846 1998   2.254
  serious non-bonded atom clash:  1846 1999   1.854
  serious non-bonded atom clash:  1847 2000   2.204
  serious non-bonded atom clash:  1851 1999   2.232
  serious non-bonded atom clash:  1853 1999   1.928
  serious non-bonded atom clash:  1853 2000   1.977
  serious non-bonded atom clash:  1861 1977   2.116
  serious non-bonded atom clash:  1861 1978   2.249
  serious non-bonded atom clash:  1862 1999   1.861
  serious non-bonded atom clash:  2074 2851   2.222
  serious non-bonded atom clash:  2074 2871   2.002
  serious non-bonded atom clash:  2074 2874   2.099
  serious non-bonded atom clash:  2075 2869   2.248
  serious non-bonded atom clash:  2075 2872   2.257
  serious non-bonded atom clash:  2075 2873   2.099
  serious non-bonded atom clash:  2078 2840   1.930
  serious non-bonded atom clash:  2078 2851   2.033
  serious non-bonded atom clash:  2078 2868   2.278
  serious non-bonded atom clash:  2078 2870   2.155
  serious non-bonded atom clash:  2078 2871   2.076
  serious non-bonded atom clash:  2079 2840   1.765
  serious non-bonded atom clash:  2079 2850   2.009
  serious non-bonded atom clash:  2079 2851   1.859
  serious non-bonded atom clash:  2079 2860   2.002
  serious non-bonded atom clash:  2079 2868   1.900
  serious non-bonded atom clash:  2080 2840   2.234
  serious non-bonded atom clash:  2107 2614   2.259
  serious non-bonded atom clash:  2108 2352   2.163
  serious non-bonded atom clash:  2108 2617   2.229
  serious non-bonded atom clash:  2109 2651   2.269
  serious non-bonded atom clash:  2118 2615   2.300

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:    20    7   19   22   33   63  106  316  329  467  470  520  632  710  723


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90:      -93.0232
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90:       91.1624
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   771187
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -48515.9805




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -48515.980469
>> Normalized DOPE z score: -0.461
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.129334
Native energy (pair)     :  -160.765842
Native energy (surface)  :     3.941612
Native energy (combined) :    -2.838298
Z score (pair)           :    -9.966698
Z score (surface)        :    -5.868055
Z score (combined)       :   -10.434247
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   107948
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         402.4987




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               :   402.498718
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   107948
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        6301.3086




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :  6301.308594
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     8464
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         455.5571





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349       3      4   0.067   0.067      349.66       1.000
 2 Bond angle potential               :     473       7     35   0.100   0.100      276.77       1.000
 3 Stereochemical cosine torsion poten:     340       0     26   1.167   1.167      151.08       1.000
 4 Stereochemical improper torsion pot:     138       1      2   0.073   0.073      45.020       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :    8464       0     23   2.564   2.564      397.61       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       1      4   0.128   0.128      28.534       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      6   1.409   1.409      47.797       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      3   1.602   1.602      34.936       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      1   1.616   1.616      16.530       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.431   1.431      6.1828       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :    8464       0     31   2.643   2.643     -437.26       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -461.30       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    174 250K 250K CE  CD   1987 1986    2.64    1.53    1.11   30.49    1.53    1.11   30.49
    2    175 250K 250K NZ  CE   1988 1987    1.87    1.48    0.39   10.23    1.48    0.39   10.23
    3    349 271M 272P C   N    2156 2158    1.53    1.30    0.23    6.96    1.30    0.23    6.96

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    591 250K 250K CG  CD   1985 1986  147.01  113.60   33.41    8.20  113.60   33.41    8.20
    2    592 250K 250K CD  CE   1986 1987  136.80  110.00   26.80    7.09  110.00   26.80    7.09
    3    751 266Y 266Y CA  CB   2108 2109  127.93  107.50   20.43    4.72  107.50   20.43    4.72
    4    801 270P 270P N   CA   2143 2144  130.14  108.20   21.94    4.98  108.20   21.94    4.98
    5    819 271M 271M C   CA   2156 2151  127.73  108.00   19.73    4.57  108.00   19.73    4.57


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1861 1987   2.272

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    1    5    0   35   56  266  302  402  403  459  549  626  652


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   711767
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50922.7188




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -50922.718750
>> Normalized DOPE z score: -0.830
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.125232
Native energy (pair)     :  -411.797976
Native energy (surface)  :    -8.493133
Native energy (combined) :   -10.355921
Z score (pair)           :   -10.412482
Z score (surface)        :    -6.842856
Z score (combined)       :   -11.056307
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    48528
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -2004.0265




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -2004.026489
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    48528
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -1388.9222




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               : -1388.922241
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    16726
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       14504.8857





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      37     59   0.219   0.219      4153.2       1.000
 2 Bond angle potential               :     473      63    107   0.235   0.235      1481.9       1.000
 3 Stereochemical cosine torsion poten:     340       3     35   1.198   1.198      198.94       1.000
 4 Stereochemical improper torsion pot:     138      17     24   0.259   0.259      641.98       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   16726       0    240   2.572   2.572      5558.8       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       7     13   0.347   0.347      210.22       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0     12   1.397   1.397      67.158       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      7   1.510   1.510      47.542       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      3   1.980   1.980      23.307       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.255   1.255      5.4827       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   16726       0    332   2.809   2.809      2600.1       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -483.77       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    222 257S 257S N   CA   2030 2031    1.58    1.43    0.15    5.04    1.43    0.15    5.04
    2    224 257S 257S C   CA   2034 2031    2.24    1.49    0.75   21.85    1.49    0.75   21.85
    3    226 258R 258R CB  CA   2038 2037    1.97    1.54    0.43   11.87    1.54    0.43   11.87
    4    227 258R 258R CG  CB   2039 2038    3.31    1.53    1.78   48.91    1.53    1.78   48.91
    5    228 258R 258R CD  CG   2040 2039    1.80    1.53    0.27    7.47    1.53    0.27    7.47
    6    233 258R 258R N   CA   2036 2037    1.66    1.43    0.23    7.70    1.43    0.23    7.70
    7    235 258R 258R C   CA   2045 2037    1.71    1.49    0.22    6.44    1.49    0.22    6.44
    8    241 259S 259S C   CA   2051 2048    1.70    1.49    0.21    5.97    1.49    0.21    5.97
    9    252 260R 260R C   CA   2062 2054    1.70    1.49    0.21    6.10    1.49    0.21    6.10
   10    259 261K 261K N   CA   2064 2065    1.59    1.43    0.16    5.15    1.43    0.16    5.15
   11    261 261K 261K C   CA   2071 2065    1.69    1.49    0.20    5.73    1.49    0.20    5.73
   12    268 262V 262V C   CA   2078 2074    1.81    1.49    0.32    9.32    1.49    0.32    9.32
   13    269 262V 263K C   N    2078 2080    1.67    1.35    0.32   11.34    1.35    0.32   11.34
   14    271 263K 263K CG  CB   2083 2082    1.78    1.53    0.25    6.99    1.53    0.25    6.99
   15    272 263K 263K CD  CG   2084 2083    2.47    1.53    0.94   25.88    1.53    0.94   25.88
   16    275 263K 263K N   CA   2080 2081    1.99    1.43    0.56   18.31    1.43    0.56   18.31
   17    277 263K 263K C   CA   2087 2081    2.34    1.49    0.85   24.73    1.49    0.85   24.73
   18    278 263K 264E C   N    2087 2089    1.91    1.35    0.56   19.84    1.35    0.56   19.84
   19    279 264E 264E CB  CA   2091 2090    3.47    1.54    1.93   53.01    1.54    1.93   53.01
   20    280 264E 264E CG  CB   2092 2091    1.73    1.53    0.20    5.58    1.53    0.20    5.58
   21    281 264E 264E CD  CG   2093 2092    2.12    1.52    0.60   15.50    1.52    0.60   15.50
   22    284 264E 264E N   CA   2089 2090    2.01    1.43    0.58   19.05    1.43    0.58   19.05
   23    286 264E 264E C   CA   2096 2090    2.71    1.49    1.22   35.45    1.49    1.22   35.45
   24    287 264E 265Q C   N    2096 2098    1.71    1.35    0.36   12.76    1.35    0.36   12.76
   25    293 265Q 265Q N   CA   2098 2099    1.75    1.43    0.32   10.50    1.43    0.32   10.50
   26    295 265Q 265Q C   CA   2105 2099    2.28    1.49    0.79   23.11    1.49    0.79   23.11
   27    296 265Q 266Y C   N    2105 2107    1.98    1.35    0.63   22.44    1.35    0.63   22.44
   28    297 266Y 266Y CB  CA   2109 2108    2.11    1.54    0.57   15.63    1.54    0.57   15.63
   29    298 266Y 266Y CG  CB   2110 2109    2.13    1.49    0.64   17.74    1.49    0.64   17.74
   30    308 266Y 266Y C   CA   2117 2108    2.55    1.49    1.06   30.77    1.49    1.06   30.77
   31    333 269V 270P C   N    2141 2143    1.50    1.30    0.20    6.04    1.30    0.20    6.04
   32    335 270P 270P C   CA   2148 2144    1.71    1.49    0.22    6.55    1.49    0.22    6.55
   33    336 270P 271M C   N    2148 2150    1.52    1.35    0.18    6.37    1.35    0.18    6.37
   34    346 271M 271M N   CA   2150 2151    1.71    1.43    0.28    9.29    1.43    0.28    9.29
   35    348 271M 271M C   CA   2156 2151    1.95    1.49    0.46   13.44    1.49    0.46   13.44
   36    349 271M 272P C   N    2156 2158    1.49    1.30    0.19    5.55    1.30    0.19    5.55

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    354 146P 146P N   CA   1159 1160  128.36  108.20   20.16    4.58  108.20   20.16    4.58
    2    492 241N 242R C   N    1913 1915  148.48  120.00   28.48    6.47  120.00   28.48    6.47
    3    543 246T 246T N   CA   1951 1952  125.32  107.00   18.32    5.26  107.00   18.32    5.26
    4    647 256G 257S C   N    2028 2030  144.77  120.00   24.77    5.63  120.00   24.77    5.63
    5    650 257S 257S N   CA   2030 2031  142.28  107.00   35.28   10.14  107.00   35.28   10.14
    6    653 257S 257S CA  C    2031 2034  143.13  116.50   26.63    7.65  116.50   26.63    7.65
    7    654 257S 257S C   CA   2034 2031  128.77  108.00   20.77    4.81  108.00   20.77    4.81
    8    659 258R 258R CA  CB   2037 2038  146.08  113.50   32.58    8.00  113.50   32.58    8.00
    9    661 258R 258R CA  C    2037 2045  134.66  116.50   18.16    5.22  116.50   18.16    5.22
   10    662 258R 258R CB  CG   2038 2039  135.06  113.60   21.46    5.27  113.60   21.46    5.27
   11    663 258R 258R CG  CD   2039 2040  125.54  107.50   18.04    4.77  107.50   18.04    4.77
   12    672 259S 259S N   CA   2047 2048  132.33  107.00   25.33    7.28  107.00   25.33    7.28
   13    680 260R 260R N   CA   2053 2054  122.78  107.00   15.78    4.53  107.00   15.78    4.53
   14    683 260R 260R CA  C    2054 2062  133.06  116.50   16.56    4.76  116.50   16.56    4.76
   15    694 261K 261K N   CA   2064 2065  127.25  107.00   20.25    5.82  107.00   20.25    5.82
   16    705 262V 262V N   CA   2073 2074  139.42  107.00   32.42    9.32  107.00   32.42    9.32
   17    706 262V 262V CA  CB   2074 2075  139.90  108.50   31.40    7.37  108.50   31.40    7.37
   18    709 262V 262V CA  C    2074 2078  145.00  116.50   28.50    8.19  116.50   28.50    8.19
   19    712 262V 263K C   N    2078 2080  144.71  120.00   24.71    5.61  120.00   24.71    5.61
   20    714 263K 263K N   CA   2080 2081  141.74  113.50   28.24    7.59  113.50   28.24    7.59
   21    716 263K 263K CA  CB   2081 2082  154.33  113.50   40.83   10.02  113.50   40.83   10.02
   22    718 263K 263K CA  C    2081 2087  147.52  116.50   31.02    8.92  116.50   31.02    8.92
   23    719 263K 263K CB  CG   2082 2083  138.61  113.60   25.01    6.14  113.60   25.01    6.14
   24    720 263K 263K CG  CD   2083 2084  134.92  113.60   21.32    5.23  113.60   21.32    5.23
   25    726 264E 264E N   CA   2089 2090  123.21  107.00   16.21    4.66  107.00   16.21    4.66
   26    735 264E 265Q C   N    2096 2098  140.56  120.00   20.56    4.67  120.00   20.56    4.67
   27    738 265Q 265Q N   CA   2098 2099  128.92  107.00   21.92    6.30  107.00   21.92    6.30
   28    748 266Y 265Q N   C    2107 2105  140.92  122.50   18.42    5.29  122.50   18.42    5.29
   29    751 266Y 266Y CA  CB   2108 2109  146.42  107.50   38.92    9.00  107.50   38.92    9.00
   30    753 266Y 266Y CA  C    2108 2117  139.04  116.50   22.54    6.48  116.50   22.54    6.48
   31    754 266Y 266Y CB  CG   2109 2110  154.82  122.30   32.52    7.07  122.30   32.52    7.07
   32    755 266Y 266Y CB  CG   2109 2110  166.40  122.30   44.10    9.59  122.30   44.10    9.59
   33    758 266Y 266Y CD1 CE1  2111 2113  150.89  120.00   30.89    6.28  120.00   30.89    6.28
   34    760 266Y 266Y CD2 CE2  2112 2114  161.82  120.00   41.82    8.50  120.00   41.82    8.50
   35    761 266Y 266Y CE1 CZ   2113 2115  157.38  120.00   37.38    8.07  120.00   37.38    8.07
   36    763 266Y 266Y CE2 CZ   2114 2115  162.64  120.00   42.64    9.21  120.00   42.64    9.21
   37    795 269V 269V CA  C    2137 2141  151.58  112.50   39.08    5.62  112.50   39.08    5.62
   38    797 269V 269V C   CA   2141 2137  130.76  108.00   22.76    5.27  108.00   22.76    5.27
   39    801 270P 270P N   CA   2143 2144  128.09  108.20   19.89    4.52  108.20   19.89    4.52
   40    805 270P 270P CA  C    2144 2148  132.66  116.50   16.16    4.64  116.50   16.16    4.64
   41    813 271M 271M N   CA   2150 2151  127.01  107.00   20.01    5.75  107.00   20.01    5.75
   42    820 271M 272P C   N    2156 2158  161.86  117.00   44.86   11.17  117.00   44.86   11.17

-------------------------------------------------------------------------------------------------

Feature  3                           : Stereochemical cosine torsion potential 
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1231 264E 264E O   C    2097 2096  -97.04  180.00   82.96    4.92  180.00   82.96    4.92
    2   1242 266Y 266Y CE1 CD1  2113 2111   87.57    0.00   87.57    6.19    0.00   87.57    6.19
    3   1244 266Y 266Y CE2 CD2  2114 2112  -76.92    0.00  -76.92    5.88    0.00  -76.92    5.88

-------------------------------------------------------------------------------------------------

Feature  4                           : Stereochemical improper torsion potentia
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    939 266Y 266Y CB  CG   2109 2110 -124.23  180.00   55.77   17.00  180.00   55.77   17.00
    2    942 266Y 266Y CE1 CZ   2113 2115   45.65    0.00   45.65   13.91    0.00   45.65   13.91
    3    943 266Y 266Y CZ  CE2  2115 2114   41.99    0.00   41.99   12.80    0.00   41.99   12.80
    4    958 270P 270P CA  N    2144 2143   67.72   35.26   32.45    7.73   35.26   32.45    7.73

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1331 257S 257S CA  C    2031 2034 -137.11  180.00   42.89    8.58  180.00   42.89    8.58
    2   1343 269V 269V CA  C    2137 2141 -153.42  180.00   26.58    5.32  180.00   26.58    5.32


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1446 2105   2.173
  serious non-bonded atom clash:  1448 2105   2.248
  serious non-bonded atom clash:  1448 2107   2.269
  serious non-bonded atom clash:  1451 2090   2.196
  serious non-bonded atom clash:  1451 2091   2.194
  serious non-bonded atom clash:  1451 2096   2.296
  serious non-bonded atom clash:  1743 2083   2.212
  serious non-bonded atom clash:  1749 2080   2.291
  serious non-bonded atom clash:  1749 2081   2.259
  serious non-bonded atom clash:  1761 2088   2.133
  serious non-bonded atom clash:  1762 2079   2.281
  serious non-bonded atom clash:  1798 2091   2.200
  serious non-bonded atom clash:  1798 2092   2.213
  serious non-bonded atom clash:  1798 2093   2.299
  serious non-bonded atom clash:  1799 2090   2.214
  serious non-bonded atom clash:  1807 2105   2.113
  serious non-bonded atom clash:  2039 2547   1.973
  serious non-bonded atom clash:  2039 2566   2.234
  serious non-bonded atom clash:  2105 2230   2.206
  serious non-bonded atom clash:  2107 2230   2.259
  serious non-bonded atom clash:  2108 2230   2.221
  serious non-bonded atom clash:  2110 2232   2.125
  serious non-bonded atom clash:  2110 2259   2.225

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     1    7   15   21   30   62   96  294  327  433  451  500  589  692  721


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   754426
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -49377.4844




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -49377.484375
>> Normalized DOPE z score: -0.593
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.129334
Native energy (pair)     :  -256.152916
Native energy (surface)  :    -1.060233
Native energy (combined) :    -5.314602
Z score (pair)           :    -9.580110
Z score (surface)        :    -5.900834
Z score (combined)       :   -10.082388
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    91187
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        -458.8964




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               :  -458.896423
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    91187
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        4130.0410




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :  4130.041016
readlinef__W> File: pkp2a.B99990005.pdb, Line: 5
              Modeller will only read the first 80 characters of this line.

iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
readlinef__W> File: pkp2a.B99990005.pdb, Line: 5
              Modeller will only read the first 80 characters of this line.

  #      ALGNMT CODE

  1  pkp2a
  2  pkp2a
341 atoms selected for loop refinement
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:     1640     1438
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     9604
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         900.7162





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349       0      0   0.006   0.006      3.7348       1.000
 2 Bond angle potential               :     473       0      0   0.034   0.034      32.967       1.000
 3 Stereochemical cosine torsion poten:     340       0     11   1.080   1.080      118.24       1.000
 4 Stereochemical improper torsion pot:     138       0      0   0.018   0.018      3.7284       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :    9604       0     74   2.556   2.556      207.57       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       0      0   0.069   0.069      8.2462       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      0   1.483   1.483      12.170       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      0   1.278   1.278      10.608       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      0   1.526   1.526      12.631       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.603   1.603      5.9521       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :    9601       0    159   2.677   2.677      958.78       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -473.92       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.



report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    3   43   89  325  320  441  460  471  588  635  688


<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    12120
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        6423.7256





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      18     25   0.137   0.137      3311.4       1.000
 2 Bond angle potential               :     473      18     48   0.155   0.155      736.61       1.000
 3 Stereochemical cosine torsion poten:     340       1     24   1.130   1.130      164.54       1.000
 4 Stereochemical improper torsion pot:     138       2      7   0.109   0.109      141.49       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   12120       0     76   2.534   2.534      2067.0       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       5      9   0.369   0.369      237.22       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0      2   1.473   1.473      30.786       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      1   1.643   1.643      23.117       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      1   1.792   1.792      14.561       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.159   1.159      4.1035       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   12120       0    106   2.787   2.787      192.93       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -500.02       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1     45 151P 151P C   CA   1204 1200    2.05    1.49    0.56   16.26    1.49    0.56   16.26
    2     46 151P 152K C   N    1204 1206    1.81    1.35    0.47   16.63    1.35    0.47   16.63
    3     47 151P 151P N   CA   1199 1200    1.65    1.43    0.21    7.04    1.43    0.21    7.04
    4     52 152K 152K CB  CA   1208 1207    2.03    1.54    0.49   13.44    1.54    0.49   13.44
    5     53 152K 152K CG  CB   1209 1208    1.84    1.53    0.31    8.57    1.53    0.31    8.57
    6     54 152K 152K CD  CG   1210 1209    1.80    1.53    0.27    7.48    1.53    0.27    7.48
    7     57 152K 152K N   CA   1206 1207    2.05    1.43    0.62   20.35    1.43    0.62   20.35
    8     58 152K 152K O   C    1214 1213    3.29    1.23    2.06   94.31    1.23    2.06   94.31
    9     59 152K 152K C   CA   1213 1207    1.82    1.49    0.33    9.47    1.49    0.33    9.47
   10     60 152K 153A C   N    1213 1215    1.87    1.35    0.52   18.45    1.35    0.52   18.45
   11     62 153A 153A N   CA   1215 1216    1.80    1.43    0.37   12.07    1.43    0.37   12.07
   12     64 153A 153A C   CA   1218 1216    1.77    1.49    0.28    8.03    1.49    0.28    8.03
   13     72 154N 154N C   CA   1226 1221    1.72    1.49    0.23    6.75    1.49    0.23    6.75
   14     74 155G 155G N   CA   1228 1229    1.59    1.43    0.16    5.15    1.43    0.16    5.15
   15     76 155G 155G C   CA   1230 1229    1.65    1.49    0.16    4.52    1.49    0.16    4.52
   16     82 156L 156L N   CA   1232 1233    1.58    1.43    0.15    4.99    1.43    0.15    4.99
   17     85 156L 157L C   N    1238 1240    1.54    1.35    0.20    7.07    1.35    0.20    7.07

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    394 150Y 150Y N   CA   1187 1188  125.19  107.00   18.19    5.23  107.00   18.19    5.23
    2    395 150Y 150Y CA  CB   1188 1189  128.36  107.50   20.86    4.82  107.50   20.86    4.82
    3    409 150Y 151P C   N    1197 1199  150.74  117.00   33.74    8.40  117.00   33.74    8.40
    4    412 151P 151P N   CA   1199 1200  152.02  108.20   43.82    9.96  108.20   43.82    9.96
    5    423 152K 152K N   CA   1206 1207  153.08  113.50   39.58   10.64  113.50   39.58   10.64
    6    428 152K 152K CB  CG   1208 1209  142.70  113.60   29.10    7.14  113.60   29.10    7.14
    7    429 152K 152K CG  CD   1209 1210  138.83  113.60   25.23    6.19  113.60   25.23    6.19
    8    435 153A 153A N   CA   1215 1216  135.81  107.00   28.81    8.28  107.00   28.81    8.28
    9    445 154N 154N CA  C    1221 1226  142.88  116.50   26.38    7.58  116.50   26.38    7.58
   10    449 154N 154N C   CA   1226 1221  143.47  108.00   35.47    8.22  108.00   35.47    8.22
   11    452 155G 155G N   CA   1228 1229  132.45  107.00   25.45    7.31  107.00   25.45    7.31

-------------------------------------------------------------------------------------------------

Feature  3                           : Stereochemical cosine torsion potential 
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1016 151P 151P O   C    1205 1204  -97.57  180.00   82.43    4.91  180.00   82.43    4.91

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1312 156L 156L CA  C    1233 1238 -117.41  180.00   62.59   12.52  180.00   62.59   12.52


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1127 1214   2.080
  serious non-bonded atom clash:  1128 1214   2.074
  serious non-bonded atom clash:  1129 1204   2.281
  serious non-bonded atom clash:  1129 1213   2.241
  serious non-bonded atom clash:  1129 1214   2.060
  serious non-bonded atom clash:  1130 1213   2.236
  serious non-bonded atom clash:  1130 1214   2.054
  serious non-bonded atom clash:  1131 1213   2.090
  serious non-bonded atom clash:  1131 1214   2.037
  serious non-bonded atom clash:  1132 1213   2.093
  serious non-bonded atom clash:  1132 1214   2.035
  serious non-bonded atom clash:  1207 1287   2.255

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     8    0    4    9    6   50   86  314  316  431  464  464  604  635  693


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90:       90.1819
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   736919
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50082.6602




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -50082.660156
>> Normalized DOPE z score: -0.701
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.129826
Native energy (pair)     :  -387.695701
Native energy (surface)  :   -11.777630
Native energy (combined) :   -10.201741
Z score (pair)           :   -10.467671
Z score (surface)        :    -7.438528
Z score (combined)       :   -11.487861
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    67930
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -1813.8494




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -1813.849365
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    67930
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         -36.5236




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :   -36.523579
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    13222
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       16089.3613





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      15     29   0.124   0.124      1840.2       1.000
 2 Bond angle potential               :     473      24     82   0.150   0.150      685.37       1.000
 3 Stereochemical cosine torsion poten:     340       0     29   1.256   1.256      189.69       1.000
 4 Stereochemical improper torsion pot:     138      12     21   0.213   0.213      490.39       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   13222       0    140   2.578   2.578      11732.       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45       5     11   0.504   0.504      442.33       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0     12   1.486   1.486      63.162       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0      2   1.609   1.609      26.897       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      1   2.007   2.007      17.677       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   1.785   1.785      6.1778       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   13222       0    190   2.736   2.736      1057.4       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -461.83       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    184 251S 251S C   CA   1995 1992    1.78    1.49    0.29    8.32    1.49    0.29    8.32
    2    186 252I 252I CB  CA   1999 1998    2.18    1.50    0.68   18.54    1.50    0.68   18.54
    3    187 252I 252I CG1 CB   2000 1999    1.70    1.54    0.17    4.57    1.54    0.17    4.57
    4    190 252I 252I N   CA   1997 1998    2.03    1.43    0.60   19.73    1.43    0.60   19.73
    5    191 252I 252I O   C    2004 2003    1.69    1.23    0.46   20.87    1.23    0.46   20.87
    6    192 252I 252I C   CA   2003 1998    2.48    1.49    0.99   28.82    1.49    0.99   28.82
    7    194 253G 253G N   CA   2005 2006    2.31    1.43    0.88   28.98    1.43    0.88   28.98
    8    195 253G 253G O   C    2008 2007    1.90    1.23    0.67   30.51    1.23    0.67   30.51
    9    196 253G 253G C   CA   2007 2006    1.89    1.49    0.40   11.60    1.49    0.40   11.60
   10    197 253G 254C C   N    2007 2009    2.49    1.35    1.15   40.64    1.35    1.15   40.64
   11    200 254C 254C N   CA   2009 2010    1.73    1.43    0.30    9.83    1.43    0.30    9.83

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    354 146P 146P N   CA   1159 1160  128.32  108.20   20.12    4.57  108.20   20.12    4.57
    2    471 240Q 240Q N   CA   1898 1899  132.44  113.50   18.94    5.09  113.50   18.94    5.09
    3    543 246T 246T N   CA   1951 1952  123.30  107.00   16.30    4.68  107.00   16.30    4.68
    4    601 251S 251S C   CA   1995 1992  139.97  108.00   31.97    7.41  108.00   31.97    7.41
    5    602 251S 252I C   N    1995 1997  160.74  120.00   40.74    9.26  120.00   40.74    9.26
    6    604 252I 252I N   CA   1997 1998  141.54  113.50   28.04    7.54  113.50   28.04    7.54
    7    605 252I 252I N   CA   1997 1998  127.20  107.00   20.20    5.81  107.00   20.20    5.81
    8    606 252I 252I CA  CB   1998 1999  136.21  111.00   25.21    5.92  111.00   25.21    5.92
    9    614 253G 252I N   C    2005 2003  141.10  122.50   18.60    5.34  122.50   18.60    5.34
   10    617 253G 253G CA  C    2006 2007  142.62  116.50   26.12    7.51  116.50   26.12    7.51
   11    621 254C 254C N   CA   2009 2010  124.46  107.00   17.46    5.02  107.00   17.46    5.02
   12    649 257S 257S N   CA   2030 2031  138.42  113.50   24.92    6.70  113.50   24.92    6.70
   13    702 261K 262V C   N    2071 2073  141.13  120.00   21.13    4.80  120.00   21.13    4.80
   14    705 262V 262V N   CA   2073 2074  127.81  107.00   20.81    5.98  107.00   20.81    5.98
   15    712 262V 263K C   N    2078 2080  150.87  120.00   30.87    7.01  120.00   30.87    7.01
   16    738 265Q 265Q N   CA   2098 2099  126.29  107.00   19.29    5.54  107.00   19.29    5.54
   17    742 265Q 265Q CB  CG   2100 2101  132.64  108.00   24.64    5.71  108.00   24.64    5.71
   18    751 266Y 266Y CA  CB   2108 2109  127.77  107.50   20.27    4.69  107.50   20.27    4.69

-------------------------------------------------------------------------------------------------

Feature  4                           : Stereochemical improper torsion potentia
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    898 252I 252I C   CA   2003 1998   25.84    0.00   25.84    9.10    0.00   25.84    9.10
    2    906 255F 255F CB  CG   2017 2018 -164.23  180.00   15.77    4.81  180.00   15.77    4.81


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1998 2593   2.188
  serious non-bonded atom clash:  1998 2594   2.109
  serious non-bonded atom clash:  1998 2621   2.212
  serious non-bonded atom clash:  1998 2912   2.099
  serious non-bonded atom clash:  2003 2594   2.025
  serious non-bonded atom clash:  2003 2602   2.180
  serious non-bonded atom clash:  2003 2603   1.950
  serious non-bonded atom clash:  2003 2618   2.167
  serious non-bonded atom clash:  2003 2621   2.008
  serious non-bonded atom clash:  2004 2603   1.904
  serious non-bonded atom clash:  2004 2621   2.042
  serious non-bonded atom clash:  2004 2625   2.288
  serious non-bonded atom clash:  2005 2594   1.935
  serious non-bonded atom clash:  2005 2602   2.056
  serious non-bonded atom clash:  2005 2603   2.024
  serious non-bonded atom clash:  2005 2611   2.044
  serious non-bonded atom clash:  2005 2618   2.015
  serious non-bonded atom clash:  2006 2589   1.832
  serious non-bonded atom clash:  2006 2593   2.267
  serious non-bonded atom clash:  2006 2594   1.886
  serious non-bonded atom clash:  2006 2611   1.978
  serious non-bonded atom clash:  2006 2614   1.999
  serious non-bonded atom clash:  2007 2589   1.677
  serious non-bonded atom clash:  2007 2604   1.831
  serious non-bonded atom clash:  2007 2605   2.114
  serious non-bonded atom clash:  2007 2608   1.891
  serious non-bonded atom clash:  2007 2609   2.282
  serious non-bonded atom clash:  2007 2611   1.861
  serious non-bonded atom clash:  2008 2589   1.983
  serious non-bonded atom clash:  2008 2608   2.107
  serious non-bonded atom clash:  2008 2611   2.085
  serious non-bonded atom clash:  2009 2582   2.038
  serious non-bonded atom clash:  2009 2608   2.184

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:    22    7    4    9   13   53   92  318  331  431  458  474  611  651  706


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90:      106.5818
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90:       90.1819
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   745364
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -50271.1758




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -50271.175781
>> Normalized DOPE z score: -0.730
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.129826
Native energy (pair)     :  -357.232008
Native energy (surface)  :   -10.172256
Native energy (combined) :    -8.971391
Z score (pair)           :   -10.803310
Z score (surface)        :    -7.118988
Z score (combined)       :   -11.883506
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    76375
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       -2002.0349




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -2002.034912
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    76375
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         970.7230




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :   970.723022
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    14079
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    8.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       T       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :       43659.5781





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     349      46     63   0.330   0.330      11520.       1.000
 2 Bond angle potential               :     473      70    138   0.259   0.259      2188.3       1.000
 3 Stereochemical cosine torsion poten:     340       1     37   1.275   1.275      208.41       1.000
 4 Stereochemical improper torsion pot:     138      13     20   0.224   0.224      476.49       1.000
 5 Soft-sphere overlap restraints     :       0       0      0   0.000   0.000      0.0000       1.000
 6 Lennard-Jones 6-12 potential       :   14079       0    335   2.534   2.534      25211.       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000      0.0000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000      0.0000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      45      13     16   0.624   0.624      678.12       1.000
14 Sidechain Chi_1 dihedral restraints:      38       0     12   1.353   1.353      60.758       1.000
15 Sidechain Chi_2 dihedral restraints:      31       0     12   1.503   1.503      51.697       1.000
16 Sidechain Chi_3 dihedral restraints:      17       0      3   1.802   1.802      37.402       1.000
17 Sidechain Chi_4 dihedral restraints:       7       0      0   0.911   0.911      5.8639       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000      0.0000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000      0.0000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :   14079       0    411   2.672   2.672      3673.8       0.600
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000     -452.31       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1     40 150Y 150Y N   CA   1187 1188    1.67    1.43    0.24    7.88    1.43    0.24    7.88
    2     42 150Y 150Y C   CA   1197 1188    1.94    1.49    0.45   12.97    1.49    0.45   12.97
    3     43 150Y 151P C   N    1197 1199    2.39    1.30    1.09   32.28    1.30    1.09   32.28
    4     45 151P 151P C   CA   1204 1200    1.76    1.49    0.27    7.83    1.49    0.27    7.83
    5     46 151P 152K C   N    1204 1206    3.14    1.35    1.80   63.73    1.35    1.80   63.73
    6     47 151P 151P N   CA   1199 1200    1.67    1.43    0.24    7.92    1.43    0.24    7.92
    7     48 151P 151P CA  CB   1200 1202    1.93    1.53    0.41   11.14    1.53    0.41   11.14
    8     50 151P 151P CG  CD   1203 1201    1.84    1.54    0.30    8.32    1.54    0.30    8.32
    9     51 151P 151P N   CD   1199 1201    2.18    1.46    0.73   24.04    1.46    0.73   24.04
   10     52 152K 152K CB  CA   1208 1207    2.08    1.54    0.54   14.93    1.54    0.54   14.93
   11     54 152K 152K CD  CG   1210 1209    3.07    1.53    1.54   42.19    1.53    1.54   42.19
   12     57 152K 152K N   CA   1206 1207    2.04    1.43    0.61   20.20    1.43    0.61   20.20
   13     59 152K 152K C   CA   1213 1207    3.83    1.49    2.34   68.11    1.49    2.34   68.11
   14     60 152K 153A C   N    1213 1215    3.77    1.35    2.42   85.74    1.35    2.42   85.74
   15     62 153A 153A N   CA   1215 1216    2.46    1.43    1.03   33.87    1.43    1.03   33.87
   16     64 153A 153A C   CA   1218 1216    1.68    1.49    0.19    5.50    1.49    0.19    5.50
   17    268 262V 262V C   CA   2078 2074    1.73    1.49    0.24    6.87    1.49    0.24    6.87
   18    269 262V 263K C   N    2078 2080    1.72    1.35    0.38   13.38    1.35    0.38   13.38
   19    270 263K 263K CB  CA   2082 2081    2.43    1.54    0.89   24.45    1.54    0.89   24.45
   20    271 263K 263K CG  CB   2083 2082    3.03    1.53    1.50   41.11    1.53    1.50   41.11
   21    275 263K 263K N   CA   2080 2081    2.81    1.43    1.38   45.51    1.43    1.38   45.51
   22    277 263K 263K C   CA   2087 2081    2.94    1.49    1.45   42.12    1.49    1.45   42.12
   23    279 264E 264E CB  CA   2091 2090    2.16    1.54    0.63   17.16    1.54    0.63   17.16
   24    280 264E 264E CG  CB   2092 2091    1.84    1.53    0.31    8.57    1.53    0.31    8.57
   25    284 264E 264E N   CA   2089 2090    1.64    1.43    0.21    6.77    1.43    0.21    6.77
   26    286 264E 264E C   CA   2096 2090    2.82    1.49    1.33   38.78    1.49    1.33   38.78
   27    287 264E 265Q C   N    2096 2098    1.78    1.35    0.43   15.40    1.35    0.43   15.40
   28    290 265Q 265Q CD  CG   2102 2101    1.70    1.52    0.18    4.71    1.52    0.18    4.71
   29    293 265Q 265Q N   CA   2098 2099    2.05    1.43    0.62   20.28    1.43    0.62   20.28
   30    294 265Q 265Q O   C    2106 2105    2.34    1.23    1.11   51.10    1.23    1.11   51.10
   31    295 265Q 265Q C   CA   2105 2099    2.52    1.49    1.03   30.07    1.49    1.03   30.07
   32    297 266Y 266Y CB  CA   2109 2108    1.83    1.54    0.29    7.92    1.54    0.29    7.92
   33    308 266Y 266Y C   CA   2117 2108    1.84    1.49    0.35   10.20    1.49    0.35   10.20
   34    309 266Y 267Q C   N    2117 2119    2.34    1.35    0.99   35.13    1.35    0.99   35.13
   35    310 267Q 267Q CB  CA   2121 2120    2.29    1.54    0.75   20.72    1.54    0.75   20.72
   36    311 267Q 267Q CG  CB   2122 2121    2.37    1.53    0.84   23.08    1.53    0.84   23.08
   37    316 267Q 267Q O   C    2127 2126    1.73    1.23    0.50   22.82    1.23    0.50   22.82
   38    317 267Q 267Q C   CA   2126 2120    1.73    1.49    0.24    7.12    1.49    0.24    7.12
   39    318 267Q 268D C   N    2126 2128    2.24    1.35    0.89   31.65    1.35    0.89   31.65
   40    323 268D 268D N   CA   2128 2129    1.62    1.43    0.19    6.36    1.43    0.19    6.36
   41    325 268D 268D C   CA   2134 2129    1.73    1.49    0.24    7.04    1.49    0.24    7.04

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    354 146P 146P N   CA   1159 1160  130.17  108.20   21.97    4.99  108.20   21.97    4.99
    2    380 148G 149D C   N    1177 1179  141.99  120.00   21.99    5.00  120.00   21.99    5.00
    3    394 150Y 150Y N   CA   1187 1188  130.27  107.00   23.27    6.69  107.00   23.27    6.69
    4    395 150Y 150Y CA  CB   1188 1189  148.08  107.50   40.58    9.38  107.50   40.58    9.38
    5    397 150Y 150Y CA  C    1188 1197  146.21  112.50   33.71    4.84  112.50   33.71    4.84
    6    409 150Y 151P C   N    1197 1199  150.51  117.00   33.51    8.34  117.00   33.51    8.34
    7    410 150Y 151P C   N    1197 1199  153.61  117.00   36.61    9.11  117.00   36.61    9.11
    8    413 151P 151P N   CA   1199 1200  148.82  110.80   38.02   10.22  110.80   38.02   10.22
    9    414 151P 151P N   CD   1199 1201  138.32  110.50   27.82    7.48  110.50   27.82    7.48
   10    420 151P 151P C   CA   1204 1200  137.90  112.30   25.60    5.93  112.30   25.60    5.93
   11    422 152K 151P N   C    1206 1204  148.62  122.50   26.12    7.51  122.50   26.12    7.51
   12    424 152K 152K N   CA   1206 1207  130.15  107.00   23.15    6.65  107.00   23.15    6.65
   13    425 152K 152K CA  CB   1207 1208  135.07  113.50   21.57    5.29  113.50   21.57    5.29
   14    430 152K 152K CD  CE   1210 1211  135.60  110.00   25.60    6.77  110.00   25.60    6.77
   15    434 153A 153A N   CA   1215 1216  139.26  113.50   25.76    6.93  113.50   25.76    6.93
   16    435 153A 153A N   CA   1215 1216  144.90  107.00   37.90   10.89  107.00   37.90   10.89
   17    469 239I 240Q C   N    1896 1898  149.37  120.00   29.37    6.67  120.00   29.37    6.67
   18    481 240Q 241N C   N    1905 1907  140.18  120.00   20.18    4.58  120.00   20.18    4.58
   19    628 255F 255F N   CA   2015 2016  133.64  113.50   20.14    5.41  113.50   20.14    5.41
   20    655 257S 258R C   N    2034 2036  142.99  120.00   22.99    5.22  120.00   22.99    5.22
   21    705 262V 262V N   CA   2073 2074  125.59  107.00   18.59    5.34  107.00   18.59    5.34
   22    709 262V 262V CA  C    2074 2078  136.82  116.50   20.32    5.84  116.50   20.32    5.84
   23    712 262V 263K C   N    2078 2080  160.63  120.00   40.63    9.23  120.00   40.63    9.23
   24    714 263K 263K N   CA   2080 2081  133.46  113.50   19.96    5.37  113.50   19.96    5.37
   25    719 263K 263K CB  CG   2082 2083  140.12  113.60   26.52    6.51  113.60   26.52    6.51
   26    723 263K 264E C   N    2087 2089  141.76  120.00   21.76    4.94  120.00   21.76    4.94
   27    726 264E 264E N   CA   2089 2090  138.26  107.00   31.26    8.98  107.00   31.26    8.98
   28    727 264E 264E CA  CB   2090 2091  134.67  113.50   21.17    5.20  113.50   21.17    5.20
   29    729 264E 264E CA  C    2090 2096  140.32  116.50   23.82    6.85  116.50   23.82    6.85
   30    730 264E 264E CB  CG   2091 2092  138.59  108.00   30.59    7.09  108.00   30.59    7.09
   31    734 264E 264E C   CA   2096 2090  140.03  108.00   32.03    7.42  108.00   32.03    7.42
   32    742 265Q 265Q CB  CG   2100 2101  139.11  108.00   31.11    7.21  108.00   31.11    7.21
   33    748 266Y 265Q N   C    2107 2105  141.65  122.50   19.15    5.50  122.50   19.15    5.50
   34    751 266Y 266Y CA  CB   2108 2109  135.18  107.50   27.68    6.40  107.50   27.68    6.40
   35    754 266Y 266Y CB  CG   2109 2110  148.71  122.30   26.41    5.74  122.30   26.41    5.74
   36    764 266Y 266Y C   CA   2117 2108  142.84  108.00   34.84    8.07  108.00   34.84    8.07
   37    766 267Q 266Y N   C    2119 2117  145.45  122.50   22.95    6.59  122.50   22.95    6.59
   38    768 267Q 267Q N   CA   2119 2120  138.27  107.00   31.27    8.99  107.00   31.27    8.99
   39    772 267Q 267Q CB  CG   2121 2122  130.20  108.00   22.20    5.14  108.00   22.20    5.14
   40    777 267Q 268D C   N    2126 2128  149.93  120.00   29.93    6.80  120.00   29.93    6.80
   41    779 268D 268D N   CA   2128 2129  134.67  113.50   21.17    5.69  113.50   21.17    5.69
   42    783 268D 268D CA  C    2129 2134  133.88  116.50   17.38    5.00  116.50   17.38    5.00
   43    791 269V 269V N   CA   2136 2137  126.81  107.00   19.81    5.69  107.00   19.81    5.69
   44    821 271M 272P C   N    2156 2158  135.48  117.00   18.48    4.60  117.00   18.48    4.60

-------------------------------------------------------------------------------------------------

Feature  3                           : Stereochemical cosine torsion potential 
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1028 152K 152K O   C    1214 1213  -74.24    0.00  -74.24    4.63    0.00  -74.24    4.63

-------------------------------------------------------------------------------------------------

Feature  4                           : Stereochemical improper torsion potentia
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    843 151P 151P C   CA   1204 1200   19.34    0.00   19.34    6.81    0.00   19.34    6.81
    2    947 267Q 267Q C   CA   2126 2120   58.84    0.00   58.84   20.71    0.00   58.84   20.71
    3    948 267Q 267Q CD  NE2  2123 2125   21.94    0.00   21.94    4.73    0.00   21.94    4.73

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1301 145W 145W CA  C    1146 1157 -157.01  180.00   22.99    4.60  180.00   22.99    4.60
    2   1307 151P 151P CA  C    1200 1204 -116.75  180.00   63.25   12.65  180.00   63.25   12.65
    3   1337 263K 263K CA  C    2081 2087  -53.23  180.00  126.77   25.35  180.00  126.77   25.35
    4   1339 265Q 265Q CA  C    2099 2105 -150.55  180.00   29.45    5.89  180.00   29.45    5.89
    5   1340 266Y 266Y CA  C    2108 2117  -96.45  180.00   83.55   16.71  180.00   83.55   16.71


report______> Distribution of short non-bonded contacts:

  serious non-bonded atom clash:  1084 1209   2.092
  serious non-bonded atom clash:  1084 1210   2.207
  serious non-bonded atom clash:  1092 1208   2.286
  serious non-bonded atom clash:  1099 1208   2.142
  serious non-bonded atom clash:  1100 1206   1.891
  serious non-bonded atom clash:  1100 1207   1.986
  serious non-bonded atom clash:  1100 1208   2.235
  serious non-bonded atom clash:  1108 1200   2.228
  serious non-bonded atom clash:  1108 1204   1.944
  serious non-bonded atom clash:  1108 1206   1.844
  serious non-bonded atom clash:  1116 1204   2.259
  serious non-bonded atom clash:  1116 1205   2.098
  serious non-bonded atom clash:  1117 1207   2.133
  serious non-bonded atom clash:  1117 1213   2.250
  serious non-bonded atom clash:  1117 1215   2.237
  serious non-bonded atom clash:  1118 1213   2.222
  serious non-bonded atom clash:  1118 1215   2.239
  serious non-bonded atom clash:  1119 1207   2.288
  serious non-bonded atom clash:  1119 1208   2.241
  serious non-bonded atom clash:  1119 1213   2.168
  serious non-bonded atom clash:  1120 1213   2.165
  serious non-bonded atom clash:  1121 1207   2.191
  serious non-bonded atom clash:  1121 1208   2.177
  serious non-bonded atom clash:  1121 1215   2.106
  serious non-bonded atom clash:  1122 1215   2.270
  serious non-bonded atom clash:  1124 1206   1.991
  serious non-bonded atom clash:  1124 1207   2.217
  serious non-bonded atom clash:  1124 1215   2.128
  serious non-bonded atom clash:  1126 1206   2.110
  serious non-bonded atom clash:  1135 1204   2.259
  serious non-bonded atom clash:  1138 1201   2.274
  serious non-bonded atom clash:  1215 1244   2.134
  serious non-bonded atom clash:  1216 1244   2.293
  serious non-bonded atom clash:  1822 2099   2.246
  serious non-bonded atom clash:  1834 2080   2.154
  serious non-bonded atom clash:  1834 2081   1.792
  serious non-bonded atom clash:  1834 2087   2.285
  serious non-bonded atom clash:  1837 2106   2.022
  serious non-bonded atom clash:  1838 2106   1.964
  serious non-bonded atom clash:  1839 2106   2.027
  serious non-bonded atom clash:  1840 2105   2.299
  serious non-bonded atom clash:  1841 2118   2.241
  serious non-bonded atom clash:  1842 2096   2.291
  serious non-bonded atom clash:  1842 2099   2.278
  serious non-bonded atom clash:  1845 2081   2.020
  serious non-bonded atom clash:  1846 2081   1.880
  serious non-bonded atom clash:  1846 2082   1.737
  serious non-bonded atom clash:  1851 2082   1.929
  serious non-bonded atom clash:  1852 2082   1.766
  serious non-bonded atom clash:  1852 2083   2.233
  serious non-bonded atom clash:  1853 2081   1.974
  serious non-bonded atom clash:  1862 2080   2.288
  serious non-bonded atom clash:  1862 2081   1.908
  serious non-bonded atom clash:  1870 2082   1.830
  serious non-bonded atom clash:  1873 2082   1.918
  serious non-bonded atom clash:  2105 2557   2.148
  serious non-bonded atom clash:  2106 2555   2.125
  serious non-bonded atom clash:  2106 2556   1.948
  serious non-bonded atom clash:  2106 2557   2.051
  serious non-bonded atom clash:  2117 2562   2.013
  serious non-bonded atom clash:  2117 2577   2.237
  serious non-bonded atom clash:  2117 2579   2.262
  serious non-bonded atom clash:  2118 2554   2.021
  serious non-bonded atom clash:  2118 2580   2.259
  serious non-bonded atom clash:  2119 2562   1.872
  serious non-bonded atom clash:  2119 2568   2.015
  serious non-bonded atom clash:  2119 2569   2.211
  serious non-bonded atom clash:  2119 2577   2.004
  serious non-bonded atom clash:  2119 2583   1.961
  serious non-bonded atom clash:  2120 2569   1.888
  serious non-bonded atom clash:  2120 2575   1.992
  serious non-bonded atom clash:  2120 2576   2.193
  serious non-bonded atom clash:  2120 2583   2.029
  serious non-bonded atom clash:  2120 2590   1.988
  serious non-bonded atom clash:  2121 2569   2.115
  serious non-bonded atom clash:  2121 2576   2.225
  serious non-bonded atom clash:  2121 2592   2.174
  serious non-bonded atom clash:  2121 2890   2.248
  serious non-bonded atom clash:  2124 2859   2.173
  serious non-bonded atom clash:  2126 2576   1.818
  serious non-bonded atom clash:  2126 2581   2.022
  serious non-bonded atom clash:  2126 2582   2.081
  serious non-bonded atom clash:  2126 2590   1.989
  serious non-bonded atom clash:  2126 2595   1.960
  serious non-bonded atom clash:  2127 2569   2.161
  serious non-bonded atom clash:  2127 2575   2.262
  serious non-bonded atom clash:  2127 2576   1.842
  serious non-bonded atom clash:  2127 2590   1.991
  serious non-bonded atom clash:  2127 2592   2.078
  serious non-bonded atom clash:  2128 2576   2.135
  serious non-bonded atom clash:  2128 2578   2.249
  serious non-bonded atom clash:  2128 2582   2.282
  serious non-bonded atom clash:  2128 2597   2.269

DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:    40   19   34   33   51   65  108  336  346  440  489  506  640  666  733


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90:       90.1819
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620    3620
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):   741643
Dynamic pairs routine                             : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :      -47936.6602




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               : -47936.660156
>> Normalized DOPE z score: -0.372
>> Model assessment by GA341 potential

Surface library          : C:\Program Files\Modeller9.25/modlib/surf5.de
Pair library             : C:\Program Files\Modeller9.25/modlib/pair9.de
Chain identifier         : _
% sequence identity      :    42.856998
Sequence length          :          462
Compactness              :     0.115404
Native energy (pair)     :  -196.927839
Native energy (surface)  :    -6.952645
Native energy (combined) :    -4.992986
Z score (pair)           :    -9.734612
Z score (surface)        :    -6.887545
Z score (combined)       :   -10.795849
GA341 score              :     1.000000

>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    72654
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         332.4448




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE score               :   332.444763
>> Model assessment by DOPE-HR potential
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      462
Number of all, selected real atoms                :     3620     341
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     1438    1438
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):    72654
Dynamic pairs routine                             : 5, NATM_SEL x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        1    9999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :   15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       F       F       F       T
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        6132.3550




<< end of ENERGY.
iatmcls_286W> MODEL atom not classified:  HIS:OXT  HIS
DOPE-HR score               :  6132.354980

>> Summary of successfully produced models:
Filename                          molpdf     DOPE score  DOPE-HR score    GA341 score Normalized DOPE score
-----------------------------------------------------------------------------------------------------------
pkp2a.B99990001.pdb           2795.26489   -49628.08984   -39483.81250        1.00000       -0.63150
pkp2a.B99990002.pdb           3874.63525   -49846.62500   -37652.26172        1.00000       -0.66500
pkp2a.B99990003.pdb           3048.55371   -50001.34766   -37202.75391        1.00000       -0.68871
pkp2a.B99990004.pdb           2926.77344   -50752.70703   -39683.59766        1.00000       -0.80389
pkp2a.B99990005.pdb           3074.65894   -50274.00391   -39426.53516        1.00000       -0.73051


>> Summary of successfully produced loop models:
Filename                          molpdf     DOPE score  DOPE-HR score    GA341 score Normalized DOPE score
-----------------------------------------------------------------------------------------------------------
pkp2a.BL00010001.pdb         -1682.73450    -3652.28979    -3640.06470        1.00000       -0.88842
pkp2a.BL00020001.pdb         12422.82617    -1182.12671     1565.64111        1.00000       -0.50980
pkp2a.BL00030001.pdb         33962.43750      900.00256     7485.38525        1.00000       -0.19054
pkp2a.BL00010002.pdb         22408.47656     -440.70218     3929.89453        1.00000       -0.51953
pkp2a.BL00020002.pdb          2996.05933    -1651.57532      -69.07085        1.00000       -0.70509
pkp2a.BL00030002.pdb          4236.11133    -1692.25452      355.59641        1.00000       -0.71133
pkp2a.BL00010003.pdb           821.29529    -1615.72632     -564.86530        1.00000       -0.62069
pkp2a.BL00020003.pdb          9784.45703     -656.79449     1990.29785        1.00000       -0.47363
pkp2a.BL00030003.pdb         15566.93164     -937.45923     2085.85425        1.00000       -0.51672
pkp2a.BL00010004.pdb         28405.13086      402.49872     6301.30859        1.00000       -0.46102
pkp2a.BL00020004.pdb           455.55713    -2004.02649    -1388.92224        1.00000       -0.82995
pkp2a.BL00030004.pdb         14504.88574     -458.89642     4130.04102        1.00000       -0.59308
pkp2a.BL00010005.pdb          6423.72559    -1813.84937      -36.52358        1.00000       -0.70118
pkp2a.BL00020005.pdb         16089.36133    -2002.03491      970.72302        1.00000       -0.73008
pkp2a.BL00030005.pdb         43659.57812      332.44476     6132.35498        1.00000       -0.37221


The final winner: pkp2a.BL00010001.pdb
