More pertinent to this example is the s.d. of the R-free itself, i.e. sigma(Rfree)/Rfree ~ 1/sqrt(Ntest) lifted from Kleywegt and Brunger, Structure, 15 August 1996, 4:897–904 (but the original analysis from an earlier paper) So for 1000 free reflections and an R-free of 24% the sigma is about 0.75% and exceeds the range of variation that you're seeing, i.e. not a significant fluctuation in R-free. Phil Jeffrey Princeton Pavel Afonine wrote: [snip]
Also, the values 0.2377, 0.2388, 0.2399 ... look all the same to me. If you run 100 identical refinement runs where in each refinement the only difference is the random seed, you will get an ensemble of refined structures and the Rfree/Rwork spread can be as large as 1-2% or so (it depends on the resolution). This is because the random seed is involved in target weights calculation and therefore a small change in the random seed may slightly change the weights and this may be enough for the refinement to take another route to another "local minimum".