[phenixbb] a few questions

Jianghai Zhu jzhu at cbr.med.harvard.edu
Fri Aug 4 14:18:12 PDT 2006

Hi all,

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?

In the remarks of the output pdb file, I have one line, "REMARK     
twinned    :  True".  What does this mean?

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?  How do I change the weight in  



Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3030

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