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Hi Jianghai Zhu,<br>
<br>
thanks for your questions!<br>
<br>
<blockquote
cite="mid17BBFAB7-7101-4243-B1BD-2D1AC411F74F@cbr.med.harvard.edu"
type="cite"><>I have a structure refined to 2.5 A. After simulated
annealing (start temp = 5000, cool rate = 25, final temp = 100, include
TLS refinement and NCS restraint), my R and Rfree are 24.6% and 28.7%
respectively. I then turned off the SA in the generated def file and
carried on the combined refinement. My R and Rfree went up to 25% and
29.2% respectively. Why did the Rfree go up after refinement?</></blockquote>
<br>
The difference between 28.7% and 29.2% is not large (=0.5%). If you run
a set of identical refinement jobs with different random seed you will
get the distribution of final R-factors ranging within 0.5%. So I would
not worry too much about this.<br>
However, I would try different refinement strategy, for example: <br>
1) you do SA refinement first;<br>
2) then you do regular refinement + TLS.<br>
<br>
<blockquote
cite="mid17BBFAB7-7101-4243-B1BD-2D1AC411F74F@cbr.med.harvard.edu"
type="cite">
<div>The RMSD of bonds and angles after either SA or combined
refinement are about 0.006 and 0.851 respectively. Don't you guys
think the geometry restraints are too tight? </div>
</blockquote>
<br>
At 2.5A resolution I wouldn't worry about these values. The resolution
is low enough to keep the geometry tight.<br>
<br>
<blockquote
cite="mid17BBFAB7-7101-4243-B1BD-2D1AC411F74F@cbr.med.harvard.edu"
type="cite">
<div>How do I change the weight in PHENIX?</div>
</blockquote>
<br>
However, if you want you can play with the target weights. The total
target function in phenix.refine for the coordinates refinement is :<br>
T = wxc_scale * wxc * Exray + wc * Egeom, where wxc is determined
automatically and wxc_scale is a parameter that the user can modify.
So, if you want to make the X-ray term stronger, then obviously you
need to increase the wxc_scale value. By default it is 0.5 (see
parameters file under the scope refinement.target_weights). Try
several wxc_scale and pick the refinement outcome you like best.<br>
<br>
Let us know if you have more problems / questions.<br>
<br>
Cheers,<br>
Pavel.<br>
<br>
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