-ex1
-ex2
-use_input_sc
-extrachi_cutoff 5
-ignore_unrecognized_res
-use_occurrence_data
#-corrections::correct
#-corrections::score:no_his_his_pairE
-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
-linmem_ig 10
-ignore_zero_occupancy false
# -random_delay 400

