Hi Aaron, could you please send two model files: before and after refinement, and indicate problematic residues? Thanks, Pavel
I'm trying to refine a structure containing ZN bound to four cysteine residues. I have had trouble with Real-space refinement mangling the residues around this ZN.
At first, Real-space refinement tried to turn the cysteine into disulfides. I tried switching this off with…
resname CYS and name SG
…in the *disulphide bond exclusion selection string* under the *Model interpretation* menu (there are no disulfides in the protein).
But the cysteine-zinc cluster continued to be mangled. Inspection of the *.geo file* shows that the SG-ZN distance is being restrained, but the CB–SG–ZN angle is not. I checked the relevant dictionary file...
phenix-1.17.1-3660/modules/chem_data/mon_lib/list/mon_lib_list.cif
And the correct bond and angle restraints do seem to be present:
. . . ZN-CYS 1 ZN 2 SG single 2.340 0.020 . . . ZN-CYS 1 ZN 2 SG 2 CB 109.000 3.000 . . .
Suggestions on how to fix this welcome.