# [phenixbb] Optimizing the Geometry Weight for a 2.76 A structure

Sam Stampfer Samuel.Stampfer at tufts.edu
Thu Apr 1 12:57:10 PDT 2010

```Hi,

I'm refining a 2.76 A structure and need help optimizing the refinement
weight on geometry. When I refine at the default refinement weight (wxc =
0.5), phenix seems to generate a much poorer structure (both geometrically
AND by Rfree value) relative to lower wxc values which put a stronger weight
on geometry. I am trying to pick the best structure to use for my next round
of rebuilding. The R-stats and condensed molprobity stats are listed below
(at the end of this email). I have a few questions regarding this structure
and those stats:

1. What is the relevance of having a LOW difference between Rfree and
Rwork? My structure seems to have a higher than expected Rwork value
relative to Rfree (aren't they supposed to differ by 0.05 or so, instead of
the 0.03 observed in my structure?) Additionally, as I refine at lower wxc
values (more weight on geometry) I get an increased Rwork value with an
equal or decreased Rfree (relative to the refinement at a higher wxc value).
Does that mean my structure is better or worse?

2. How can I judge the output from my refinement? I have looked at Rwork,
Rfree, and the molprobity clashscore and overall score values. I included
them below, at the end of this email. How do I tell which the best
refinement is? Which one would you suggest? I thought the best was wxc = 0.1
since the R-work and Rfree aren't changed much from the start values but the
geometry is far better.

3. How do I optimize the weight on geometry in refinement? My PI said that
phenix can do it but not for twinned structures (my structure is twinned).
Can the new version of phenix do weight optimization for twinned structures?
How? If not, what's the best way for me to do it manually?

As always, thanks immensely for all your help!

-Sam

All have the same values for:

Start R-work = 0.2002, R-free = 0.2376

*wxc = 0.01 *Final R-work = 0.2104, R-free = 0.2378

Molprobity Clashscore: 19.46 Molprobity Score: 2.29

*wxc = 0.05 *Final R-work = 0.2049, R-free = 0.2377

Molprobity Clashscore: 20.96 Molprobity Score: 2.38

*wxc = 0.1 *Final R-work = 0.2010, R-free = 0.2388

Molprobity Clashscore: 23.50 Molprobity Score: 2.54

*wxc = 0.2 *Final R-work = 0.1969, R-free = 0.2399

Molprobity Clashscore: 27.15 Molprobity Score: 2.79

*wxc = 0.3 *Final R-work = 0.1945, R-free = 0.2411

Molprobity Clashscore: 30.76 Molprobity Score: 2.97

*wxc = 0.4 *Final R-work = 0.1930, R-free = 0.2420

Molprobity Clashscore: 34.54 Molprobity Score: 3.11

*wxc = default (0.5) *Final R-work = 0.1918, R-free = 0.2429

Molprobity Clashscore: 37.73 Molprobity Score: 3.22
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