-score::nmer_ref_energies_list ../mouse.reflist
-score:nmer_svm_list ../h2iab.svmlist
-score:nmer_pssm_list ../h2iab.svmpssmlist
-score:nmer_ref_seq_length 9
-ignore_unrecognized_res
-overwrite
-ex1
-ex2
-out:file:renumber_pdb false

-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

