[phenixbb] a few questions

Pavel Afonine PAfonine at lbl.gov
Fri Aug 4 14:45:52 PDT 2006

Hi Jianghai Zhu,

thanks for your questions!

> <>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?

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.
However, I would  try different refinement strategy, for example:
1) you do SA refinement first;
2) then you do regular refinement + TLS.

> 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? 

At 2.5A resolution I wouldn't worry about these values. The resolution 
is low enough to keep the geometry tight.

> How do I change the weight in PHENIX?

However, if you want you can play with the target weights. The total 
target function in phenix.refine for the coordinates refinement is :
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.

Let us know if you have more problems / questions.


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