-score::nmer_ref_energies_list ../human.reflist
-score:nmer_ref_seq_length 9
-score:nmer_svm_list ../human14.svmlist
-score:nmer_pssm_list ../human14.svmpssmlist
-ignore_unrecognized_res
-ignore_zero_occupancy false
-overwrite
-ex1
-out:file:renumber_pdb false
-extra_res_fa TAD.params

-chemical:exclude_patches LowerDNA  UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated  tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated  lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm

-detect_disulf false
