What version of Phenix? Can you share the model (directly) with me? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Mar 2, 2020 at 3:23 PM Aaron Oakley wrote:

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.

–å

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