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.

-Nat