<div dir="ltr"><div>Thanks for the advice Pavel!<br><br></div>I don&#39;t want to celebrate prematurely, but I just re-ran the same refinement in both the stable and in nightly 4070, and it _seems_ to be corrected in the nightly. Will let you know if it pops up again.<br></div><div dir="auto">On Thu, Dec 3, 2020 at 9:16 AM Pavel Afonine &lt;<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>&gt; wrote:<br></div><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
  
    
  
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    Hi Igor,<br>
    <br>
    please make sure to try the same refinement using the latest Phenix
    version from nightly builds first:<br>
    <br>
    <a href="http://phenix-online.org/download/nightly_builds.cgi" target="_blank">http://phenix-online.org/download/nightly_builds.cgi</a><br>
    <br>
    The latest I see here is 1.19rc7-4070.<br>
    <br>
    Chances are the version you used had a bug that we fixed by now.<br>
    <br>
    If the problem persists please go ahead and send me inputs and
    indicate residues that are bad and I will investigate right away!<br>
    <br>
    Pavel</div><div><br>
    <br>
    <div>On 12/3/20 08:42, Igor Petrik wrote:<br>
    </div>
    </div><div><blockquote type="cite"></blockquote></div><div><blockquote type="cite">
      
      <div dir="ltr">
        <div>Thanks Nigel,</div>
        <div><br>
        </div>
        <div>I will put together the input and output file from my
          latest refinement and send them to you and Pavel later today.<br>
        </div>
        <div><br>
        </div>
        <div>
          <div dir="ltr">
            <div dir="ltr">
              <div>- Igor Petrik<span>, PhD</span></div>
            </div>
          </div>
        </div>
        <br>
      </div>
      <br>
      <div class="gmail_quote">
        <div dir="ltr" class="gmail_attr">On Wed, Dec 2, 2020 at 9:46 PM
          Folmer Fredslund &lt;<a href="mailto:folmerf@gmail.com" target="_blank">folmerf@gmail.com</a>&gt; wrote:<br>
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          <div dir="auto">Dear Igor
            <div dir="auto"><br>
            </div>
            <div dir="auto">There&#39;s a phenix bulletin board for question
              like this, which is where you should post the question. (
              I crosspost here)</div>
            <div dir="auto"><br>
            </div>
            <div dir="auto"><br>
            </div>
            <div dir="auto">I would choose to not do the real space
              refinement in phenix.refine during the last rounds of
              refinement of a model, when sidechain positions are
              essentially correct. </div>
            <div dir="auto"><br>
            </div>
            <div dir="auto"><br>
            </div>
            <div dir="auto">I hope this helps</div>
            <div dir="auto"><br>
            </div>
            <div dir="auto">Folmer</div>
            <div dir="auto"><br>
            </div>
            <div dir="auto"><br>
            </div>
          </div>
          <br>
          <div class="gmail_quote">
            <div dir="ltr" class="gmail_attr">tor. 3. dec. 2020 05.48
              skrev Igor Petrik &lt;<a href="mailto:petrik1@illinois.edu" target="_blank">petrik1@illinois.edu</a>&gt;:<br>
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            <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
              <div dir="ltr">
                <div>I am refining a 1.71A X-ray structure with phenix
                  refine. I have everything modelled in - ~150 residues
                  in the ASU and a heme - and my R-work/R-free is
                  0.17/0.22. But when I went to deposit it, PDB pointed
                  out that two of my sidechains have distorted
                  geometries. One is a His, and looking at it in Coot, I
                  can clearly see the 2Fo-Fc density for the correct
                  geometry, but the actual coordinates that phenix
                  refine produce don&#39;t lie in that density; there are
                  significant difference map peaks showing that the
                  coordinates are in the wrong place. If I use real
                  space refine in Coot to put the coordinates back into
                  the correct density and refine it again in phenix,
                  they get distorted again.</div>
                <div><br>
                </div>
                <div>What settings in phenix should I check to try to
                  get it to properly refine the coordinates?<br>
                </div>
                <div><br>
                </div>
                <div>Thanks,</div>
                <div>
                  <div dir="ltr">
                    <div dir="ltr">
                      <div>- Igor Petrik<span>, PhD</span></div>
                    </div>
                  </div>
                </div>
              </div>
              <br>
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