[phenixbb] Where to find optimized wxc_scale/wxu_scale weighting factors after optimization
amadrona at uci.edu
amadrona at uci.edu
Thu Aug 12 10:27:10 PDT 2010
Hello,
I ran a refinement optimizing geometry and B factor weighting factors
using optimize_wxc=true optimize_wxu=true.
I was given these statistics in the pdb header:
Rwork Rfree Bonds Angles
start .1588 .1838 .007 1.235
end .1454 .1780 .016 1.601
(1.37 A resolution)
1. I would like to find the optimized weighting factors in the log file
but cannot. Instead I find the following (pasted below). However, the
scale here doesn't make sense to me because many our greater than 0.5.
How do I find the optimized values so that I can use them in further
rounds of refinement? I'm sorry if this has been covered in previous
posts but I could not find an answer.
2. Can anyone explain the concept of optimizing the B-factor? I don't
understand how changing it brings you closer or further from an ideal
model as oppose to xray. (which is how I make sense of refining the
geometry)
Thank you
-Yarow
================================ xyz refinement
===============================
Start r_work= 0.1462 r_free= 0.1784 bonds= 0.015 angles= 1.53
r_work= 0.1492 r_free= 0.1792 bonds= 0.005 angles= 1.08 scale= 1.00
r_work= 0.1484 r_free= 0.1788 bonds= 0.006 angles= 1.14 scale= 1.40
r_work= 0.1480 r_free= 0.1787 bonds= 0.007 angles= 1.19 scale= 1.80
r_work= 0.1476 r_free= 0.1785 bonds= 0.008 angles= 1.23 scale= 2.20
r_work= 0.1473 r_free= 0.1785 bonds= 0.008 angles= 1.26 scale= 2.60
r_work= 0.1471 r_free= 0.1784 bonds= 0.009 angles= 1.29 scale= 3.00
r_work= 0.1469 r_free= 0.1784 bonds= 0.010 angles= 1.32 scale= 3.40
r_work= 0.1467 r_free= 0.1783 bonds= 0.010 angles= 1.34 scale= 3.80
r_work= 0.1465 r_free= 0.1782 bonds= 0.011 angles= 1.36 scale= 4.20
r_work= 0.1464 r_free= 0.1782 bonds= 0.011 angles= 1.39 scale= 4.60
r_work= 0.1463 r_free= 0.1782 bonds= 0.011 angles= 1.40 scale= 5.00
r_work= 0.1461 r_free= 0.1781 bonds= 0.012 angles= 1.45 scale= 6.00
r_work= 0.1458 r_free= 0.1781 bonds= 0.013 angles= 1.49 scale= 7.00
r_work= 0.1456 r_free= 0.1781 bonds= 0.014 angles= 1.53 scale= 8.00
r_work= 0.1454 r_free= 0.1781 bonds= 0.015 angles= 1.57 scale= 9.00
r_work= 0.1453 r_free= 0.1780 bonds= 0.016 angles= 1.60 scale= 10.00
r_work= 0.1495 r_free= 0.1794 bonds= 0.005 angles= 1.05 scale= 0.85
r_work= 0.1501 r_free= 0.1797 bonds= 0.005 angles= 1.02 scale= 0.70
r_work= 0.1507 r_free= 0.1800 bonds= 0.004 angles= 0.98 scale= 0.55
Final r_work= 0.1453 r_free= 0.1780 bonds= 0.016 angles= 1.60
More information about the phenixbb
mailing list