On Thu, Apr 1, 2010 at 12:57 PM, Sam Stampfer <span dir="ltr"><<a href="mailto:Samuel.Stampfer@tufts.edu">Samuel.Stampfer@tufts.edu</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<p>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?</p></blockquote><div>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.</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><p>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.</p></blockquote><div>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.</div>
<div><br></div><div>PS. �Use POLYGON in the GUI to get a better idea of how good these statistics are relative to other structures.</div><div><br></div><div>-Nat</div></div>