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<p class="MsoNormal"><span lang="EN-US">Dear all, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I am running phenix.ensemble_refinement on a covalent protein-ligand complex providing the same parameter-files used for phenix.refine. I also included the .def and .cif files generated by phenix.ligand_linking.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">However, in quite a few of the ensemble structures, the covalent link exceeds 5Å, which is obviously wrong. How can I obtain ensemble structures with reasonable covalent bond length?
<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE">Best, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="DE">Eike<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black;mso-fareast-language:EN-GB">————————————————————————————<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;color:#666666;mso-fareast-language:EN-GB">Dr. Eike C. Schulz </span><span lang="EN-US" style="font-size:10.5pt;color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;color:#666666;mso-fareast-language:EN-GB">Max Planck Institute for the Structure and Dynamics of Matter</span><span lang="EN-US" style="font-size:9.5pt;color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;color:#666666;mso-fareast-language:EN-GB">Luruper Chaussee 149 | 22761 Hamburg | Germany</span><span lang="EN-US" style="font-size:9.5pt;color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;color:#666666;mso-fareast-language:EN-GB">Building 99 (CFEL) | Office O2.101</span><span lang="EN-US" style="font-size:9.5pt;color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;color:#666666;mso-fareast-language:EN-GB">Phone </span><span lang="EN-US" style="font-size:9.5pt;color:black;mso-fareast-language:EN-GB"><a href="tel:%2B49%20%280%2940%208998-6264" target="_blank"><span style="color:#1155CC">+49
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(0)40 8994-6264</span></a> | </span><span lang="EN-US" style="font-size:9.5pt;color:#666666;mso-fareast-language:EN-GB">Website </span><span lang="EN-US" style="font-size:9.5pt;color:black;mso-fareast-language:EN-GB"><a href="http://www.mpsd.mpg.de/" target="_blank"><span style="color:#1155CC">www.mpsd.mpg.de</span></a><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;color:black;mso-fareast-language:EN-GB"> <o:p></o:p></span></p>
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