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    Hi Tobias,<br>
    <br>
    <blockquote type="cite"
      cite="mid:5053EE65-1DCA-4D46-8D74-475D834ECA51@psi.ch">
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      <div class="WordSection1">
        <p class="MsoNormal"><span style="font-size:11.0pt;color:black"
            lang="EN-US">Dear PHENIXBB community,</span><span
            style="color:black" lang="EN-US"><o:p></o:p></span></p>
        <p class="MsoNormal"><span style="font-size:11.0pt;color:black"
            lang="EN-US"> </span><span style="color:black" lang="EN-US"><o:p></o:p></span></p>
        <p class="MsoNormal"><span style="font-size:11.0pt;color:black"
            lang="EN-US">i have come across a strange behavior in
            Phenix:</span><span style="color:black" lang="EN-US"><o:p></o:p></span></p>
        <p class="MsoNormal"><span style="font-size:11.0pt;color:black"
            lang="EN-US"> </span><span style="color:black" lang="EN-US"><o:p></o:p></span></p>
        <ul style="margin-top:0cm" type="disc">
          <li class="MsoNormal" style="color:black;mso-list:l2 level1
            lfo1"><span style="font-size:11.0pt" lang="EN-US">I copied
              Rfree-flags from a dataset with very slightly different
              unit cell</span><span lang="EN-US"><o:p></o:p></span></li>
        </ul>
        <p class="MsoNormal"><span style="font-size:11.0pt;color:black"
            lang="EN-US"> </span><span style="color:black" lang="EN-US"><o:p></o:p></span></p>
        <ul style="margin-top:0cm" type="disc">
          <li class="MsoNormal" style="color:black;mso-list:l1 level1
            lfo2"><span style="font-size:11.0pt" lang="EN-US">Refined
              the previously refined model against the new data</span><span
              lang="EN-US"><o:p></o:p></span></li>
        </ul>
        <p class="MsoNormal" style="margin-left:36.0pt"><span
            style="font-size:11.0pt;color:black" lang="EN-US"> </span><span
            style="color:black" lang="EN-US"><o:p></o:p></span></p>
        <ul style="margin-top:0cm" type="disc">
          <li class="MsoNormal" style="color:black;mso-list:l4 level1
            lfo3"><span style="font-size:11.0pt" lang="EN-US">Rfactors
              in first round were good</span><span lang="EN-US"><o:p></o:p></span></li>
        </ul>
        <p class="MsoNormal" style="margin-left:36.0pt"><span
            style="font-size:11.0pt;color:black" lang="EN-US"> </span><span
            style="color:black" lang="EN-US"><o:p></o:p></span></p>
        <ul style="margin-top:0cm" type="disc">
          <li class="MsoNormal" style="color:black;mso-list:l0 level1
            lfo4"><span style="font-size:11.0pt" lang="EN-US">Second
              round in refinement Rfree was up by 10 % just from the
              start during bulk solvent modeling and scaling</span><span
              lang="EN-US"><o:p></o:p></span></li>
        </ul>
        <p class="MsoNormal" style="margin-left:36.0pt"><span
            style="font-size:11.0pt;color:black" lang="EN-US"> </span><span
            style="color:black" lang="EN-US"><o:p></o:p></span></p>
        <ul style="margin-top:0cm" type="disc">
          <li class="MsoNormal" style="color:black;mso-list:l3 level1
            lfo5"><span style="font-size:11.0pt" lang="EN-US">In another
              round Rfree was high in the beginning, and then dropped by
              those 10 % during bulk solvent modelling and scaling.</span><span
              lang="EN-US"><o:p></o:p></span></li>
        </ul>
        <p class="MsoNormal" style="margin-left:36.0pt"><span
            style="color:black" lang="EN-US"><o:p> </o:p></span></p>
        <ul style="margin-top:0cm" type="disc">
          <li class="MsoNormal" style="color:black;mso-list:l3 level1
            lfo5"><span lang="EN-US">In yet another round Rfree started
              10% lower than the previous round during bulk solvent
              modeling in the first cycle and then it jumps up again in
              the second cycle.<o:p></o:p></span></li>
        </ul>
        <p class="MsoNormal" style="margin-left:36.0pt"><span
            style="font-size:11.0pt;color:black" lang="EN-US"> </span><span
            style="color:black" lang="EN-US"><o:p></o:p></span></p>
        <p class="MsoNormal"><span style="font-size:11.0pt;color:black"
            lang="EN-US">What could be wrong?</span></p>
      </div>
    </blockquote>
    <br>
    If I take a random structure from PDB:<br>
    <br>
    phenix.fetch_pdb 1f8t --mtz<br>
    <br>
    and run a default phenix.refine job:<br>
    <br>
    phenix.refine 1f8t.{pdb,mtz}<br>
    <br>
    then look at the log file, I see:<br>
    <br>
    For the first macro-cycle:<br>
    <br>
    (...)<br>
    <tt>                   start: r(all,work,free)=0.3064 0.3018 0.3435
      n_refl.: 27466</tt><tt><br>
    </tt><tt>       re-set all scales: r(all,work,free)=0.3064 0.3018
      0.3435 n_refl.: 27466</tt><tt><br>
    </tt><tt>         remove outliers: r(all,work,free)=0.3061 0.3016
      0.3435 n_refl.: 27464</tt><tt><br>
    </tt><tt> overall B=0.38 to atoms: r(all,work,free)=0.3096 0.3050
      0.3470 n_refl.: 27464</tt><tt><br>
    </tt><tt>bulk-solvent and scaling: r(all,work,free)=0.1839 0.1798
      0.2213 n_refl.: 27464</tt><tt><br>
    </tt><tt>         remove outliers: r(all,work,free)=0.1839 0.1798
      0.2213 n_refl.: 27464</tt><tt><br>
    </tt>(..)<br>
    <br>
    Here:<br>
    - "start" means no any solvent modeling and scaling was yet done;<br>
    - last line shows R values after all corrections. <br>
    <br>
    <br>
    Now, for the second macro-cycle we see:<br>
    <br>
    ()<br>
    <tt>                   start: r(all,work,free)=0.1798 0.1754 0.2195
      n_refl.: 27464</tt><tt><br>
    </tt><tt>       re-set all scales: r(all,work,free)=0.3200 0.3151
      0.3607 n_refl.: 27464</tt><tt><br>
    </tt><tt>         remove outliers: r(all,work,free)=0.3200 0.3151
      0.3607 n_refl.: 27464</tt><tt><br>
    </tt><tt>overall B=-2.56 to atoms: r(all,work,free)=0.2961 0.2912
      0.3366 n_refl.: 27464</tt><tt><br>
    </tt><tt>bulk-solvent and scaling: r(all,work,free)=0.1783 0.1739
      0.2183 n_refl.: 27464</tt><tt><br>
    </tt><tt>         remove outliers: r(all,work,free)=0.1783 0.1739
      0.2183 n_refl.: 27464</tt><tt><br>
    </tt>()<br>
    <br>
    Here, "start" shows values obtained by the end of 1st macro-cycle,
    second line (re-set all scale) shows values after all scales were
    discarded, and the last line shows values R values after all scales
    were re-calculated again.<br>
    <br>
    So.. if this is what you observe, then there is nothing wrong.
    Otherwise, please send me the log file and I will have a closer
    look.<br>
    <br>
    Pavel<br>
    <br>
  </body>
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