In some of the cases discussed in the thread, a less biased Rfree could be calculated by procedures discussed in the paper below. Felcy, a post-doc of mine, followed ideas discussed by several at conferences and examined systematically the impact of NCS on Rfree, and how to mitigate the effect. She put together procedures that excluded correlated reflections that I think would eliminate the challenges of cross-validation in the pathological cases. (I also think that her discussion will address some of the concerns in the thread about the independence of reflections etc.).
Michael. Fabiola, F., A. Korostelev, et al. (2006). "Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry." Acta Crystallogr D Biol Crystallogr 62(Pt 3): 227-38. Current methods of free R factor cross-validation assume that the structure factors of the test and working sets are independent of one another. This assumption is only an approximation when the modeled structure occupies anything less than the full asymmetric unit. Through progressive elimination of reflections from the working set, starting with those expected to be most correlated to the test set, small biases in free R can be measured, presumably because of over-sampling of the Fourier transform owing to bulk solvent in the crystal. This level of bias may be of little practical importance, but it rises to significant levels with increasing non-crystallographic symmetry owing to wider correlations between structure factors than hitherto appreciated. In the presence of 15-fold non-crystallographic symmetry, with resolutions commonly attainable in macromolecular crystallography, it may not be possible to calculate an unbiased free R factor. Methods are developed for the calculation of reduced-bias free R factors through elimination of the strongest correlations between test and working sets. With 180-fold non-crystallographic symmetry they may not be an accurate indicator of absolute quality, but they do yield the correct optimal weighting for stereochemical restraints. Michael S. Chapman, R.T. Jones Professor of Structural Biology Dept. Biochemistry & Molecular Biology; School of Medicine, Mail Code L224 Oregon Health & Science University 3181 Sam Jackson Park Road; Portland, OR 97239-3098 [EMAIL PROTECTED] / (503) 494-1025; http://xtal.ohsu.edu/