Dear Friend, I am using command line prompt to refine protein-dna complex using phenix.refine. I used the following command: phenix.refine YCd1p3_output.mtz sep71_001.pdb_modified.pdb simulated_annealing=true main.ncs=true refinement.ncs.excessive_distance_limit=6 ncs_groups_3.params ncs.find_automatically=False ordered_solvent=true strategy=rigid_body+individual_sites+group_adp+tls individual_sites="((chain A and not "(resid 176 or resid 179 or resid 238 or resid 242)") or (chain B and not "(resid 176 or resid 179 or resid 238 or resid 242)") or (chain C and not "(resid 176 or resid 179 or resid 238 or resid 242)") or (chain D and not "(resid 176 or resid 179 or resid 238 or resid 242)")) output.write_maps=true output.prefix=sep72 --overwrite If I omit the portion [individual_sites="((chain A and not "(resid 176 or resid 179 or resid 238 or resid 242)") or .........], it is running fine. I want to exclude some residues say resid 176, 179, 238 and 242 from all four chains in the refinement. how can I incorporate that in command line promt or using a .params file? I know my msitake is in the command individual_sites="((chain A and not "(resid 176 or resid 179 or resid 238 or resid 242)") or ......... Thanking you in advance... Raja