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Hi Carsten,<br>
<br>
please send me files off-line so that I can investigate.<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 8/10/15 11:08, Schubert, Carsten
[JRDUS] wrote:<br>
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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">I am running into some strange issues with
regards to ADP refinement especially when I am putting final
touches on a structure for PDB submission. The problem
manifests itself most prominent in the B-factor refinement of
solvent, but also maps are affected and are becoming noisier,
so I assume this problem affects the protein as well. �I
checked this against the current release 1.9 and the latest
pre1.10 dev version, both versions show the issue. Refinement
protocol includes individual_xyz, individual_adp, TLS and
weight optimization. <o:p></o:p></p>
<p class="MsoNormal">The problem I am running into is that the
ADP of waters� only changes by a global offset. The problem is
tricky to spot but more evident when looking at solvent placed
in coot with the default ADP (30). The ADP changes only by a
global offset, no individual refinement takes place. Since the
protein is refined by TLS the problem is not as evident, but
as mentioned the fofc maps get noisier from cycle to cycle
even though no manual change to the geometry was performed. To
me an indicator that the B-factors are not refined properly. <o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">The problem can be circumvented by
reverting back to isotropic B-factors and then refine with
weight refinement for 5-10 cycles. After that TLS can be
switched back on for a final polishing cycle. In stubborn
cases I had to randomly assign B-factors close to Wilson-B and
refine for more cycles to get out of the hole I refined myself
into.<o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">Another indicator that something went awry
is the weight refinement for the B-factors:<o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">���������������� ----------Individual ADP
refinement----------����������������
<o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">��� R-FACTORS����� <Bi-Bj>�
<B>�� WEIGHT������ TARGETS<o:p></o:p></p>
<p class="MsoNormal">work� free� delta����
����������������������data restr<o:p></o:p></p>
<p class="MsoNormal">20.66 26.39�� 5.73� 5.712� 67.871� 2.160���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 0.030���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 0.125���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 0.500���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 1.000���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 1.500���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 2.000���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 2.500���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 3.000���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 3.500���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 4.000���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 4.500���
5.225<o:p></o:p></p>
<p class="MsoNormal">20.66 26.38�� 5.73� 5.712� 67.871� 5.000���
5.225<o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">Essentially there is no change in R/Rfree
with regards to different weights.<o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">I have not figured out the exact time point
when this happens during the course of the refinement but it
seems to be coupled to using TLS in combination with ADP
refinement and during the final stages of the refinement.<o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">I can provide data offline to reproduce the
issue<o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">Cheers,<o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal">Carsten<o:p></o:p></p>
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