Hi everyone,<div><br></div><div>I am getting following error while running phenix refinement for a protein cocrystalized with a metal chelator complex. What could be the problem.</div><div><br></div><div>














<p class="MsoNormal"><span style="font-family:Courier">AssertionError : </span></p>

<p class="MsoNormal"><span style="font-family:Courier">Traceback:</span></p>

<p class="MsoNormal"><span style="font-family:Courier"> 
File
&quot;/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/libtbx/thread_utils.py&quot;,
line 229, in run</span></p>

<p class="MsoNormal"><span style="font-family:Courier">    return_value = self._target(self._args,
self._kwargs, self._c)</span></p>

<p class="MsoNormal"><span style="font-family:Courier"> </span></p>

<p class="MsoNormal"><span style="font-family:Courier"> 
File
&quot;/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/libtbx/runtime_utils.py&quot;,
line 72, in __call__</span></p>

<p class="MsoNormal"><span style="font-family:Courier">    result = self.target()</span></p>

<p class="MsoNormal"><span style="font-family:Courier"> </span></p>

<p class="MsoNormal"><span style="font-family:Courier"> 
File
&quot;/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/runtime.py&quot;,
line 67, in __call__</span></p>

<p class="MsoNormal"><span style="font-family:Courier">    call_back_handler=callback)</span></p>

<p class="MsoNormal"><span style="font-family:Courier"> </span></p>

<p class="MsoNormal"><span style="font-family:Courier"> 
File
&quot;/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/command_line.py&quot;,
line 97, in run</span></p>

<p class="MsoNormal"><span style="font-family:Courier">    call_back_handler=call_back_handler)</span></p>

<p class="MsoNormal"><span style="font-family:Courier"> </span></p>

<p class="MsoNormal"><span style="font-family:Courier"> 
File &quot;/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/driver.py&quot;,
line 1478, in run</span></p>

<p class="MsoNormal"><span style="font-family:Courier">    ncs_manager            
= self.ncs_manager)</span></p>

<p class="MsoNormal"><span style="font-family:Courier"> </span></p>

<p class="MsoNormal"><span style="font-family:Courier"> 
File
&quot;/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/strategies.py&quot;,
line 344, in refinement_machine</span></p>

<p class="MsoNormal"><span style="font-family:Courier">    model.show_occupancy_statistics(text =
&quot;Occupancies statistics&quot;, out=log)</span></p>

<p class="MsoNormal"><span style="font-family:Courier"> </span></p>

<p class="MsoNormal"><span style="font-family:Courier"> 
File
&quot;/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/model.py&quot;,
line 868, in show_occupancy_statistics</span></p>

<p class="MsoNormal"><span style="font-family:Courier">    self.xray_structure.set_occupancies(value=0.,
selection = less_than_zero)</span></p>

<p class="MsoNormal"><span style="font-family:Courier"> </span></p>

<p class="MsoNormal"><span style="font-family:Courier"> 
File
&quot;/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/cctbx/xray/structure.py&quot;,
line 480, in set_occupancies</span></p>

<p class="MsoNormal"><span style="font-family:Courier">    assert selection.size() == s.size()</span></p>

<p class="MsoNormal"><span style="font-family:Courier"> </span></p>

<p class="MsoNormal"> Thanks</p><p class="MsoNormal">Subhani</p>

</div>