-use_input_sc
-extrachi_cutoff 5
-ignore_unrecognized_res
-movemap movemapfile
-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
-out:path:pdb refinement
-out:path:score refinement
-in:auto_setup_metals
-s MD86Cln4Re.pdb
-parser:protocol refine.xml
-parser:script_vars res_to_fix=129A,170A
-parser:script_vars cst_full_path=bbCA.cst