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

Nathaniel Echols nechols at lbl.gov
Thu Apr 1 13:48:01 PDT 2010

On Thu, Apr 1, 2010 at 12:57 PM, Sam Stampfer <Samuel.Stampfer at tufts.edu>wrote:

> 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?
When the spread between R-work and R-free widens, this means that you've
optimized R-work at the expense of R-free, i.e. you're "overfitting".  If
they're too close together this can indicate that you've somehow biased your
refinement (by improper assignment of R-free flags in the presence of NCS,
accidentally switching R-free sets in the middle of refinement, or using a
very similar MR search model refined against a different set are the usual
reasons).  However, 0.03 is (usually) not a small enough difference to worry
about - on the contrary, it's very good.  Therefore, if a refinement raises
R-work and lowers R-free, this is almost always a good thing.  Anything that
raises R-free relative to the starting value is bad.

> 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.
The first one in the list, with wxc=0.01, R=0.2104, R-free=0.2378 is
definitely the best, because all of the statistics that matter are much
better than in any other refinement.

PS.  Use POLYGON in the GUI to get a better idea of how good these
statistics are relative to other structures.

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