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

Pavel Afonine pafonine at lbl.gov
Mon Mar 2 16:57:44 PST 2020


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.
>

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