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

[Pavel Afonine]

  Hi Yarow,

> 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)

Looks ok. Did you update solvent using "ordered_solvent=true"? Did you 
remember to add have H atoms to your structure?

> 1.  I would like to find the optimized weighting factors in the log file
> but cannot.  Instead I find the following (pasted below).

I'm wondering why you are trying to find them? It is such a technical 
thing that changes from macro-cycle to macro-cycle...

> However, the
> scale here doesn't make sense to me because many our greater than 0.5.

Hm... In the text below actually none of them is equal to 0.5. May be 
you meant ADP refinement?

> How do I find the optimized values so that I can use them in further
> rounds of refinement?

See below.

> 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)

Start here ("On atomic displacement parameters (ADP)"):
http://www.phenix-online.org/newsletter/CCN_2010_07.pdf
and
http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf
then may be have a look:
http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf

> ================================ 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

The optimal wxc_scale = 10.00, that corresponds to
Final r_work= 0.1453 r_free= 0.1780 bonds= 0.016 angles= 1.60

All the best!
Pavel.