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Dear phenix users,
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<div class="">I’m refining a model that has FAD and SO4 ligands. Phenix makes a covalent bond between the N3 of the FAD and an O atom of SO4 during the automatic linking stage, even though the distance between the atoms is larger than the automatic link distance.
The covalent bond yanks the ligands out of their density. I suppose I could disable automatic linking, but I’ve never seen this happen. I note that we recently upgraded to phenix-1.11.1-2575, and this may be my first refinement calculation with the new version.
Output is shown below.
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<div class="">I welcome any suggestions.
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<div class="">Thanks, </div>
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<div class="">Jack </div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">-------------------------------------------------------------------------------</span></div>
<div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> Version: 1.11.1</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> Release tag: 2575</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> Platform: intel-linux-2.6-x86_64</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> User: tannerjj</span></div>
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<div class="">From the phenix.refine log file:</div>
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<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Automatic linking</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Parameters for automatic linking</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Linking & cutoffs</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Metal : False - 3.50</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Amimo acid : False - 1.90</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Carbohydrate : True - 1.99</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Ligands : True - 1.99</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Amino acid - RNA/DNA : False</span></div>
<div style="margin: 0px; line-height: normal; min-height: 13px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class="">
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<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Number of custom bonds: simple=2, symmetry=0</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Number of additional bonds: simple=2, symmetry=0</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Coordination:</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Other bonds:</span></div>
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<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> Simple bond: pdb=</span><span style="font-variant-ligatures: no-common-ligatures" class="">" N3 FAD C 601 "</span><span style="font-variant-ligatures: no-common-ligatures; color: #000000" class="">
- pdb=</span><span style="font-variant-ligatures: no-common-ligatures" class="">" O2 SO4 F 605 "</span></div>
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<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> Simple bond: pdb=</span><span style="font-variant-ligatures: no-common-ligatures" class="">" N3 FAD D 601 "</span><span style="font-variant-ligatures: no-common-ligatures; color: #000000" class="">
- pdb=</span><span style="font-variant-ligatures: no-common-ligatures" class="">" O4 SO4 F 606 "</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Time building additional restraints: 2.29</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Conformation dependent library (CDL) restraints added in 636.6 milliseconds</span></div>
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<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">.</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">.</span></div>
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<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Bond restraints: 15971</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Sorted by residual:</span></div>
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<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> bond pdb=</span><span style="font-variant-ligatures: no-common-ligatures" class="">" N3 FAD D 601 "</span></div>
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<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> pdb=</span><span style="font-variant-ligatures: no-common-ligatures" class="">" O4 SO4 F 606 "</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ideal model delta sigma weight residual</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> 1.297 3.084 -1.787 1.00e-02 1.00e+04 3.19e+04</span></div>
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<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> bond pdb=</span><span style="font-variant-ligatures: no-common-ligatures" class="">" N3 FAD C 601 "</span></div>
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<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> pdb=</span><span style="font-variant-ligatures: no-common-ligatures" class="">" O2 SO4 F 605 "</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ideal model delta sigma weight residual</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> 1.297 2.975 -1.678 1.00e-02 1.00e+04 2.81e+04</span></div>
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<div class="">The output refined PDB file shows the links were made. The LINK lines were not in the input PDB file. </div>
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<span style="font-variant-ligatures: no-common-ligatures; background-color: #e6e600" class="">LINK</span><span style="font-variant-ligatures: no-common-ligatures" class=""> N3 FAD C
</span><span style="font-variant-ligatures: no-common-ligatures;" class="">601</span><span style="font-variant-ligatures: no-common-ligatures" class=""> O2 SO4 F
</span><span style="font-variant-ligatures: no-common-ligatures;" class="">605</span></div>
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<span style="font-variant-ligatures: no-common-ligatures; background-color: #e6e600" class="">LINK</span><span style="font-variant-ligatures: no-common-ligatures" class=""> N3 FAD D
</span><span style="font-variant-ligatures: no-common-ligatures;" class="">601</span><span style="font-variant-ligatures: no-common-ligatures" class=""> O4 SO4 F
</span><span style="font-variant-ligatures: no-common-ligatures;" class="">606</span></div>
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<div style="orphans: 2; widows: 2;" class="">John J. Tanner, PhD<br class="">
Professor of Biochemistry and Chemistry</div>
<div style="orphans: 2; widows: 2;" class="">Director, Biochemistry Graduate Admissions Committee</div>
<div style="orphans: 2; widows: 2;" class="">Department of Biochemistry</div>
<div style="orphans: 2; widows: 2;" class="">University of Missouri-Columbia<br class="">
117 Schweitzer Hall<br class="">
503 S. College Avenue<br class="">
Columbia, MO 65211<br class="">
Phone: 573-884-1280<br class="">
Fax: 573-882-2754<br class="">
Email: <a href="mailto:tannerjj@missouri.edu" class="">tannerjj@missouri.edu</a><br class="">
<a href="http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html" class="">http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html</a></div>
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