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Hi Jianghai,<br>
<br>
Thanks for the .log file ! I looked at it and now I think I now what's
the problem: this is the bug in phenix.refine that we will fix for the
next release. The bug arises when you try to refine using TLS and NCS
at once. Sorry for this.<br>
<br>
The possible solution is to split your refinement into 2 parts:<br>
1) First, refine coordinates and isotropic B-factors. Use NCS
restraints. DO NOT refine TLS.<br>
2) At the end, as the final tune up, refine ONLY isotropic B-factors +
TLS and do not refine coordinates. For this run, please REMOVE all NCS
information (NCS selections) from the command file. This refinement run
should be the final one.<br>
<br>
Once again, sorry for the inconvenience. This will be fixed in the next
release of CCI APPS and PHENIX. Once this fixed, you will be able to
run everything in "one go" and in any combination.<br>
<br>
Please let me know if what I suggested helped you. Any further
questions are welcome!<br>
<br>
Cheers,<br>
Pavel.<br>
<br>
<br>
Jianghai Zhu wrote:
<blockquote
cite="midEDC2DE22-7449-44BA-9E68-60C72392C5E5@cbr.med.harvard.edu"
type="cite">
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<div>Here is the log file. Thanks.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Jianghai</div>
<div><br class="khtml-block-placeholder">
</div>
</span></span></span></span></span></span></span></div>
=<br>
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class="Apple-interchange-newline">
</span></span></span></span></span></span></span> </div>
<br>
<div>
<div>On Dec 14, 2006, at 12:50 PM, Pavel Afonine wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"> Hi Jianghai,<br>
<br>
could you please send us .log file from your refinement run, so we can
analyze what's going on.<br>
<br>
In general, "bad" B-factors can be:<br>
- misplaced model;<br>
- inadequate TLS model (= domains chosen for TLS do not correspond to
the reality).<br>
<br>
If you are using like 2 months old or older version of phenix.refine,
you may want to get the latest CCI APPS since we made lots of
improvements. Just goto <a class="moz-txt-link-freetext"
href="http://www.phenix-online.org/download/cci_apps/">http://www.phenix-online.org/download/cci_apps/</a><br>
<br>
Pavel.<br>
<br>
<br>
Jianghai Zhu wrote:
<blockquote
cite="mid1450356A-EEC5-48D2-9D05-C1DC3E7BD61A@cbr.med.harvard.edu"
type="cite">
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<div>The resolution is 2.5 A. The wilson B is about 50. I know
B factor of the backbone is lower than that of the sidechian. But a B
factor like 4 is definitely wrong.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Jianghai</div>
<br class="Apple-interchange-newline">
</span></span></span></span></span></span></span> </div>
<br>
<div>
<div>On Dec 14, 2006, at 12:11 PM, Peter Zwart wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<blockquote type="cite">
<blockquote type="cite">
<div style="margin: 0px;">4) The refinement (TLS + ML + B
individual) went through, I got <span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">reasonable R, Rfree, rmsdBOND,
rmsdANGLE.<span class="Apple-converted-space"> </span>But the B
factors are <span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">pretty low.<span
class="Apple-converted-space"> </span>The B factor of the backbone
is much lower than the side <span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">chain, some have numbers like 4.<span
class="Apple-converted-space"> </span>Some metal atoms also have B <span
class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">factors around 4.<span
class="Apple-converted-space"> </span>What did I do wrong?</div>
</blockquote>
</blockquote>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">What is the resolution of your data?</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">Backbone B-s usually are lower than
the main chain.</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">What is the Wilson B value reported
by phenix.refine?</div>
<div style="margin: 0px;">You could re-refine and randomize all
B-values and see what happens (I<span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">have to get back to you to to get the
exact command for this). Maybe it<span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">is useful to obtain a copy of the
latest verison of phenix.refine by<span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">downloading cci_apps from our server <a
href="http://www.phenix-online.org">http://www.phenix-online.org</a>.</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">If your B-values still come out
lowish, try growing crystals that do not<span
class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">diffract very well, that usually does
the trick.</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">HTH</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">Peter</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
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