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    Ok, in this case I need to look at the files ...<br>
    <br>
    Pavel<br>
    <br>
    On 4/19/12 5:46 AM, Mario Sanches wrote:
    <blockquote
cite="mid:CAHBaby7=Z=0WGdc+5Uy5HSp_DLiJZPgtiFMOFp7R1pSu23gM+g@mail.gmail.com"
      type="cite">I am using a nightly build from around two weeks ago
      (dev-1021). &nbsp;I am sending you some files.&nbsp;
      <div>Thank you,</div>
      <div><br>
      </div>
      <div>Mario Sanches<br>
        <br>
        <div class="gmail_quote">On Thu, Apr 19, 2012 at 8:42 AM, Pavel
          Afonine <span dir="ltr">&lt;<a moz-do-not-send="true"
              href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>&gt;</span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div text="#000000" bgcolor="#FFFFFF"> Hi Mario,<br>
              <br>
              are you using the latest Phenix? If not, please update
              your version of Phenix and try again:<br>
              <br>
              <a moz-do-not-send="true"
                href="http://www.phenix-online.org/download/nightly_builds.cgi"
                target="_blank">http://www.phenix-online.org/download/nightly_builds.cgi</a><br>
              <br>
              If this doesn't help, please send me the data and model
              (offlist) and I will have a look to see what's&nbsp; going on.<br>
              <br>
              Pavel
              <div>
                <div class="h5"><br>
                  <br>
                  <br>
                  On 4/19/12 5:37 AM, Mario Sanches wrote: </div>
              </div>
              <blockquote type="cite">
                <div>
                  <div class="h5">I am refining a low resolution
                    structure (2.9A) using phenix.refine. As I continue
                    the refinement &nbsp;Rwork/Rfree are dropping but my
                    &nbsp;geometry statistics in general are very bad. My
                    clashscore is getting worst and the RMS(angle) is
                    really high. I have tried to play with the
                    "wxc_scale" &nbsp;parameter and also ran phenix selecting
                    the "Optimize X-ray/ADP weight" option. All attempts
                    end with a RMS(angle) of ~3.8 and a Clashscore of
                    ~190.&nbsp;
                    <div> <br>
                    </div>
                    <div>Is there a known procedure to deal with this? I
                      feel that my geometry weighing term is too loose
                      but I don't know exactly how to tighten it other
                      than decreasing the wxc_scale parameter. I have
                      gone and manually corrected bad positions before
                      but given the low resolution nature of the
                      structure the clashes tend to
                      be&nbsp;reestablished&nbsp;during refinement.&nbsp;</div>
                    <div><br>
                    </div>
                    <div>Thank you in advance for your help,<br
                        clear="all">
                      <div><br>
                      </div>
                      -- <br>
                      Mario Sanches<br>
                      Postdoctoral Researcher<br>
                      Samuel Lunenfeld Research Institute<br>
                      Mount Sinai Hospital<br>
                      600 University Ave<br>
                      Toronto - Ontario<br>
                      Canada<br>
                      M5G 1X5<br>
                      <a moz-do-not-send="true"
                        href="http://ca.linkedin.com/in/mariosanches"
                        target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
                    </div>
                    <br>
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          </blockquote>
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        <br>
        <br clear="all">
        <div><br>
        </div>
        -- <br>
        Mario Sanches<br>
        Postdoctoral Researcher<br>
        Samuel Lunenfeld Research Institute<br>
        Mount Sinai Hospital<br>
        600 University Ave<br>
        Toronto - Ontario<br>
        Canada<br>
        M5G 1X5<br>
        <a moz-do-not-send="true"
          href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
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