[phenixbb] Where to find optimized wxc_scale/wxu_scale weighting factors after optimization

[amadrona at uci.edu]

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