Dear John,
And what would you use firstly to monitor success (an Rfree drop presumably but how much is of a drop is significant?) and second to guard against 'over fitting' eg (restraining the aniso Bij?).
PDB Redo use a Hamilton Rfactor test algorithm to judge if aniso can sensibly be applied. That seems to me the ideal check (Hamilton).
Rfree and other single-number quality metrics are global figures, they will not tell you if one or few refined B-factors are bad or atoms are misfit or local geometry is distorted. This is why when it comes to validation I like to think of it being applied to data, model and model-to-data fit, for each item looking at local and global metrics: http://phenix-online.org/presentations/latest/pavel_validation.pdf Specifically to B-factors: I think Ethan Merritt's tools are most comprehensive, such as http://skuld.bmsc.washington.edu/parvati/ and other. All the best, Pavel