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    Hi Vikram,<br>
    <br>
    you asked this or very similar question the other day and I replied
    on 1/7/17, 08:07. Repeating:<br>
    <br>
    """<br>
    set nqh_flips=False or disable real-space refinement. That will stop
    flips from happening.
    <br>
    <br>
    I'd like to address this issue in phenix.refine centrally, so these
    unwanted flips do not happen. For this it would be helpful to have
    an example. Could you please send me model files before and after
    refinement and the data file, and also tell what His flips?<br>
    """<br>
    <br>
    Excluding atoms from refinement:<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/reference/refinement.html#refinement-of-coordinates">http://phenix-online.org/documentation/reference/refinement.html#refinement-of-coordinates</a><br>
    which is really the last resort.<br>
    <br>
    Pavel<br>
    <br>
    <div class="moz-cite-prefix">On 1/19/17 02:36, Vikram Dalal wrote:<br>
    </div>
    <blockquote
cite="mid:CAJ1_RsybYjQ94sZD0GORGrT0rqcD6mmvUbkjt-npYKFneqKvtg@mail.gmail.com"
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      <div dir="ltr">Hi all,
        <div><br>
        </div>
        <div><span style="font-size:12.8px">�I have 4 Mn (2 Mn in each
            chain) in my protein structure. One Mn has 1 cordination
            with water, 1 cordination with His and 4 cordination with
            Asp. I model build the His in coot. Even this His is in bond
            range with Mn. But, when i refine this model in phenix. This
            His again flip other side (N terminal which has to cordinate
            with Mn goes to other direction). I am facing this problem
            only with His of A chain only while N of His of B chain are
            towards Mn only.�</span>
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          <div style="font-size:12.8px">Is there any option in pehnix
            refinment where we can exclude a specific residue or atom in
            refinment??�</div>
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