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Hi Mark,<br>
<br>
to me statistics from both refinement runs look essentially the same
in a sense that if you run say 100 refinement jobs each one starting
with slightly perturbed structure (shake in coordinates with
rmsd~0.3-0.5A, shake in B-factor) you will get ensemble of
essentially the same but still slightly different refined models.
Variation in R-factors my be ~0.5-2% between models in the ensemble.
Geometry may vary slightly as well. With this in mind I would say
different numbers you get are within the spread and I doubt the
differences are really significant.<br>
<br>
The strangest thing to me is that you still get ~9% or rotamer
outliers: 2155 is supposed to be much better in eliminating rotamer
outliers (although it is still limited to without H included).<br>
<br>
I agree with Eckhard: we made a lot of changed recently, such as
re-do NCS how NCS works, using CDL (conformation dependent library
for restraints), etc..<br>
<br>
Of course there may be other reasons for differences between these
two runs but this is all I can tell given amount of information
provided!<br>
<br>
All the best,<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 2/9/16 13:54, Mark A Saper wrote:<br>
</div>
<blockquote
cite="mid:04158D5A-4AC5-463E-9FD0-BDDDDF2FBE9F@umich.edu"
type="cite">
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<div>Hi,�</div>
<div>I used Phenix, build 2037 to refine a a new structure. �I
reran the refinement (with the identical parameters) in build
2155 (v1.10.1) and obtained different statistics and slightly
worse geometry. �Any idea why? ��</div>
<div><br>
</div>
<div>In <b>2037</b>:</div>
<div>� <font face="Courier">� � � � � � � � �start � � � � final<br>
� ---------------------------------------<br>
� R-work: � � � � � 0.2488 � � � �0.2244<br>
� R-free: � � � � � 0.3003 � � � �0.2851<br>
� RMS(angles): � � �1.67 � � � � � 0.80<br>
� RMS(bonds): � � � 0.020 � � � � �0.004<br>
<br>
</font></div>
<div><font face="Courier">� � � � � � � �Ramachandran outliers: �
1.2% (Goal: < 0.2%)<br>
� � � � � � � � � Ramachandran favored: �94.5% (Goal: >
98%)<br>
� � � � � � � � � � � Rotamer outliers: � 8.7% (Goal: 1%)<br>
� � � � � � � � � � � �C-beta outliers: � 0 � �(Goal: 0)<br>
� � � � � � � � � � � � � � Clashscore: � 3.14<br>
� � � � � � � � � � � � �Overall score: � 2.19</font></div>
<div><br>
</div>
<div><b>2155</b></div>
<div><br>
</div>
<div>
<div><font face="Courier">� � � � � � � � � �start � � � � final</font></div>
<div><font face="Courier">�
---------------------------------------</font></div>
<div><font face="Courier">� R-work: � � � � � 0.2488 � � �
�0.2331</font></div>
<div><font face="Courier">� R-free: � � � � � 0.3003 � � �
�0.2856</font></div>
<div><font face="Courier">� RMS(angles): � � �1.77 � � � � �
0.72</font></div>
<div><font face="Courier">� RMS(bonds): � � � 0.020 � � � �
�0.004</font></div>
<div><font face="Courier"><br>
</font></div>
<div><font face="Courier">
<div>� � � � � � � � �Ramachandran outliers: � 1.4% (Goal:
< 0.2%)</div>
<div>� � � � � � � � � Ramachandran favored: �93.4% (Goal:
> 98%)</div>
<div>� � � � � � � � � � � Rotamer outliers: � 9.4% (Goal:
1%)</div>
<div>� � � � � � � � � � � �C-beta outliers: � 0 � �(Goal:
0)</div>
<div>� � � � � � � � � � � � � � Clashscore: � 4.10</div>
<div>� � � � � � � � � � � � �Overall score: � 2.36</div>
</font></div>
<div apple-content-edited="true">
<div><span style="font-family: monospace;">_________________________________</span><br
style="font-family: monospace;">
<span style="font-family: monospace;">Mark A. Saper, Ph.D.</span><span class="Apple-tab-span" style="font-family: monospace; white-space: pre;"> </span><br
style="font-family: monospace;">
<span style="font-family: monospace;">Associate Professor of
Biological Chemistry,�</span><span style="font-family:
monospace;">University of Michigan</span><br
style="font-family: monospace;">
<span style="font-family: monospace;">Ann Arbor MI
�48109-1055 U.S.A.</span><br style="font-family:
monospace;">
<span style="font-family: monospace;"><a
moz-do-not-send="true" href="mailto:saper@umich.edu"><a class="moz-txt-link-abbreviated" href="mailto:saper@umich.edu">saper@umich.edu</a></a></span><span
style="font-family: monospace;">� � �phone (734) 764-3353
� � fax (734) 764-3323</span></div>
<div><span style="font-family: monospace;"><br>
</span></div>
<br class="Apple-interchange-newline">
</div>
<br>
</div>
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