[phenixbb] Real-space refinement fails to restrain CYS SG ZN properly

[Nigel Moriarty]

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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Mon, Mar 2, 2020 at 3:23 PM Aaron Oakley <aarono at uow.edu.au> 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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