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    Hi Morten,<br>
    <br>
    sorry for the trouble once again.<br>
    <br>
    Hm.. this seems like a case where I need the data to be able to
    reproduce the problem myself and fix it. Could you please send me
    all inputs so I can do it? I'll need data and model, and tell what
    exactly did you do, or just .eff file. Please send files off-list:
    directly to my email.<br>
    <br>
    I'm traveling right now so I might not be able to look right away,
    though I will do my best to address this problem asap (once I get
    the files).<br>
    <br>
    Thanks,<br>
    Pavel<br>
    <br>
    On 5/29/12 7:39 AM, Morten Groftehauge wrote:
    <blockquote
cite="mid:CAEAG6YS1kzbg9-y1g2qkv=q_bC2v+y2=cgYPbsx-Q6AcV9L2kA@mail.gmail.com"
      type="cite">I like the new version but it does not seem to have
      helped much. Before it shot up by 3%, this time by 2.5%.
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                  <div class="gmail_quote">On 29 May 2012 12:23, Pavel
                    Afonine <span dir="ltr">&lt;<a
                        moz-do-not-send="true"
                        href="mailto:pafonine@lbl.gov" target="_blank">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">Hi
                      Morten,<br>
                      <br>
                      I'm sorry about the problem.<br>
                      <br>
                      Are you using the latest Phenix? There was a bug
                      in phenix.refine that I fixed a while ago, and the
                      bug behavior was very similar to what I see
                      happening in your case.<br>
                      <br>
                      Could you please try the latest version and see if
                      the problem goes away? Please let me know.<br>
                      <br>
                      Pavel
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                        <br>
                        On 5/29/12 3:56 AM, Morten Groftehauge wrote:<br>
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                          Hi Phenixbb,<br>
                          <br>
                          3.2A data, 110 Wilson B, I41, twinned.
                          Imperfect inverted repeat dsDNA with 4 protein
                          monomers, NCS not used in refinement.<br>
                          If I don't include TLS I get a nice stable
                          R-factor while RMS goes down.<br>
                          If I include TLS (whether as one group per
                          chain or as chosen by Phenix) this happens:<br>
                          <br>
                          <br>
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                          Density disappears around some of the DNA
                          bases as an obvious difference. If I run
                          Refmac with TLS it just never finishes.<br>
                          <br>
                          While I could just refine without TLS this
                          does make me worried that there is something
                          wrong with my model or my data (besides being
                          terrible).<br>
                          <br>
                          Cheers,<br>
                          Morten<br>
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