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    Hi Jack,<br>
    <br>
    this is a automatic linking bug in 1.11.1_2575 Official Release. I
    checked this with the latest code and this does not happen anymore.
    <br>
    <br>
    Anyone else experiencing this problem please update to most recent
    nightly build:<br>
    <br>
    <a class="moz-txt-link-freetext" href="http://phenix-online.org/download/nightly_builds.cgi">http://phenix-online.org/download/nightly_builds.cgi</a><br>
    <br>
    Pavel<br>
    <br>
    <div class="moz-cite-prefix">On 2/5/17 09:00, Tanner, John J. wrote:<br>
    </div>
    <blockquote
      cite="mid:378C1E79-14A9-43EF-AD27-808B80D3316A@missouri.edu"
      type="cite">
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      Dear phenix users, 
      <div class=""><br class="">
      </div>
      <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.  
        <div class=""><br class="">
        </div>
        <div class="">I welcome any suggestions.  
          <div class=""><br class="">
          </div>
          <div class="">Thanks, </div>
          <div class=""><br class="">
          </div>
          <div class="">Jack </div>
          <div class=""><br class="">
          </div>
          <div class="">
            <div style="margin: 0px; font-size: 11px; line-height:
              normal; font-family: Menlo;" class="">
              <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>
            <div style="margin: 0px; font-size: 11px; line-height:
              normal; font-family: Menlo;" class="">
              <span style="font-variant-ligatures: no-common-ligatures"
                class="">  Version: 1.11.1</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="">  Release tag: 2575</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="">  Platform: intel-linux-2.6-x86_64</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="">  User: tannerjj</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="">-------------------------------------------------------------------------------</span></div>
            <div class=""><span style="font-variant-ligatures:
                no-common-ligatures" class=""><br class="">
              </span></div>
            <div class=""><br class="">
            </div>
            <div class="">---------------------------------------------------------------</div>
            <div class="">From the phenix.refine log file:</div>
            <div class=""><br class="">
            </div>
            <div class="">
              <div style="margin: 0px; font-size: 11px; line-height:
                normal; font-family: Menlo;" class="">
                <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 &amp; 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="">
                </div>
                <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>
                <div style="margin: 0px; line-height: normal; color:
                  rgb(195, 55, 32);" class="">
                  <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>
                <div style="margin: 0px; line-height: normal; color:
                  rgb(195, 55, 32);" class="">
                  <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>
                <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>
                <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=""><br
                    class="">
                </div>
                <div style="margin: 0px; line-height: normal;" class=""><span
                    style="font-variant-ligatures: no-common-ligatures"
                    class="">
                    <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>
                    <div style="margin: 0px; line-height: normal; color:
                      rgb(195, 55, 32);" class="">
                      <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>
                    <div style="margin: 0px; line-height: normal; color:
                      rgb(195, 55, 32);" class="">
                      <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>
                    <div style="margin: 0px; line-height: normal; color:
                      rgb(195, 55, 32);" class="">
                      <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>
                    <div style="margin: 0px; line-height: normal; color:
                      rgb(195, 55, 32);" class="">
                      <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>
                    <div class=""><span style="font-variant-ligatures:
                        no-common-ligatures" class=""><br class="">
                      </span></div>
                    <div class="">
                      <div style="font-family: Helvetica; font-size:
                        12px;" class="">---------------------------------------------------------------</div>
                    </div>
                    <div class=""><br class="">
                    </div>
                    <div class="">The output refined PDB file shows the
                      links were made. The LINK lines were not in the
                      input PDB file. </div>
                    <div class=""><br class="">
                    </div>
                  </span></div>
              </div>
            </div>
            <div class=""><span style="font-variant-ligatures:
                no-common-ligatures; color: #c33720" class="">
                <div style="margin: 0px; font-size: 11px; line-height:
                  normal; font-family: Menlo;" class="">
                  <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>
                <div style="margin: 0px; font-size: 11px; line-height:
                  normal; font-family: Menlo;" class="">
                  <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>
                <div style="margin: 0px; font-size: 11px; line-height:
                  normal; font-family: Menlo;" class="">
                  <br class="">
                </div>
                <div style="color: rgb(0, 0, 0); font-family: Menlo;
                  font-size: 11px;" class="">
                  <div style="font-family: Helvetica; font-size: 12px;"
                    class="">---------------------------------------------------------------</div>
                </div>
                <div style="margin: 0px; font-size: 11px; line-height:
                  normal; font-family: Menlo;" class="">
                  <span style="font-variant-ligatures:
                    no-common-ligatures;" class=""><br class="">
                  </span></div>
                <div style="margin: 0px; font-size: 11px; line-height:
                  normal; font-family: Menlo;" class="">
                  <br class="">
                </div>
              </span></div>
            <div class="">
              <div class="">
                <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 moz-do-not-send="true"
                    href="mailto:tannerjj@missouri.edu" class="">tannerjj@missouri.edu</a><br
                    class="">
                  <a moz-do-not-send="true"
                    href="http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html"
                    class="">http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html</a></div>
              </div>
              <div class=""><br class="">
              </div>
              <br class="Apple-interchange-newline">
            </div>
            <br class="">
          </div>
        </div>
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      <br>
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      <br>
      <pre wrap="">_______________________________________________
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