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Hi,<br>
<br>
One way of dealing with this is to place a (symmetry) unique copy of
the ligand , which may be its part. <br>
Alternatively it's possible to disable nonbonded repulsion forces
for selected atoms.<br>
<br>
Send me model and data files if still need help with this.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 5/20/20 01:01, Tom Vanmarcke wrote:<br>
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<p class="MsoNormal">Dear,</p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">We are trying to solve a protein structure
that contains a ligand (polyoxometalate). We found the ligand
in the electron density but through the middle of the ligand
goes a 2 fold axis. For this reason, we placed the
occupendency of the ligand on 0.50. When we try to refine the
structure using phenix.refine, the ligand breaks down even
when adding a cif restrain file.</p>
<p class="MsoNormal">The cif restrain file contains information
about atoms, angles and bond lengths.</p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">Is there a way to fix this problem?</p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">Greetings</p>
<p class="MsoNormal"><o:p>�</o:p><br>
</p>
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