I am using a nightly build from around two weeks ago (dev-1021).  I am sending you some files. <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 href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>&gt;</span> wrote:<br>
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    Hi Mario,<br>
    <br>
    are you using the latest Phenix? If not, please update your version
    of Phenix and try again:<br>
    <br>
    <a 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&#39;t help, please send me the data and model (offlist)
    and I will have a look to see what&#39;s  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  Rwork/Rfree are
      dropping but my  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 &quot;wxc_scale&quot;  parameter and also ran
      phenix selecting the &quot;Optimize X-ray/ADP weight&quot; option. All
      attempts end with a RMS(angle) of ~3.8 and a Clashscore of ~190. 
      <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&#39;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 reestablished during refinement. </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 href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
      </div></div><pre>_______________________________________________
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<br></blockquote></div><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 href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
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