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Hi Tongqin,<br>
<br>
I second Dorothee's point that we need more information to resolve
this problem. If you still have this problem please send me inputs
files (data, model, .eff from last refinement, as well as ligand
.CIF files if any) and I will look into this once I have files.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 8/31/16 09:29, Dorothee Liebschner
wrote:<br>
</div>
<blockquote
cite="mid:CAAA+Ob=VWfUJRuMqAza19DaGResKt8twKD6renBnGxRT5ov-vA@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Tongqin,
<div><br>
</div>
<div>It is a bit difficult to diagnose with the information you
provided. Could you please answer the following questions?<br>
<div><br>
</div>
<div>- Did you also try to reset the B-factors to similar
values than neighboring atoms?</div>
<div>F.ex. the average B-factor in the model could be 50 A**2,
but in the ligand region, it could be lower, let's say 20
A**2. Then the starting value using average B is quite far
from the likely B-factor of the ligand.</div>
<div><br>
</div>
<div>- What refinement strategy do you apply? How many
macro-cycles? Do you use any non-default parameters for
B-factor refinement?</div>
</div>
<div><br>
</div>
<div>- Which Phenix version are you using?</div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Dorothee</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Aug 31, 2016 at 7:12 AM, Zhou,
Tongqing (NIH/VRC) [E] <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:tzhou@mail.nih.gov"
target="_blank">tzhou@mail.nih.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div link="#0563C1" vlink="#954F72" lang="EN-US">
<div>
<p class="MsoNormal">Dear All,</p>
<p class="MsoNormal">�</p>
<p class="MsoNormal">I am refining a structure with
diffraction to 2.2A resolution and 95 % overall
completeness. Now the Rs are at 18% and 23%,
respectively. But the program failed to refine B
factors for several ligands, atoms had high B factors
while showing positive Fo-Fc map around them.
Occupancy was set to 1 and I also tried to reset B to
mean B of the whole PDB. Any of you seeing this
phenomenon? Thanks!</p>
<p class="MsoNormal">�</p>
<p class="MsoNormal">Shown below is HEPES that has high
B factor and positive density around it after
refinement:<br>
</p>
</div>
</div>
</blockquote>
</div>
</div>
</blockquote>
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