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I'm trying to refine a structure containing ZN bound to four cysteine residues.
<div class="">I have had trouble with Real-space refinement mangling the residues around this ZN.</div>
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<div class="">At first, Real-space refinement tried to turn the cysteine into disulfides.</div>
<div class="">I tried switching this off with…</div>
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<div class=""><font face="Menlo" class="">resname CYS and name SG</font></div>
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<div class="">…in the <b class="">disulphide bond exclusion selection string</b> under the
<b class="">Model interpretation</b> menu (there are no disulfides in the protein).</div>
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<div class="">But the cysteine-zinc cluster continued to be mangled. Inspection of the
<b class="">.geo file</b> shows that the SG-ZN distance is being restrained, but the CB–SG–ZN angle is not.</div>
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<div class="">I checked the relevant dictionary file...</div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">phenix-1.17.1-3660/modules/chem_data/mon_lib/list/mon_lib_list.cif</span></div>
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<div class="">And the correct bond and angle restraints do seem to be present:</div>
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ZN-CYS 1 ZN 2 SG single 2.340 0.020</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">.</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">.</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">.</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ZN-CYS 1 ZN 2 SG 2 CB 109.000 3.000</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">.</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">.</span></div>
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<div class="">Suggestions on how to fix this welcome.</div>
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<div class="">–å</div>
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