Hi Ina,
I am refining a structure of 2.3A resolution. The R values with and without bulk solvent and anisotropic scale are quite different as you can see here:
Start R-work = 0.3751, R-free = 0.5562 (no bulk solvent and anisotropic scale) Final R-work = 0.3741, R-free = 0.5557 (no bulk solvent and anisotropic scale)
Start R-work = 0.2298, R-free = 0.2974 Final R-work = 0.2261, R-free = 0.2970
the values reported with "(no bulk solvent and anisotropic scale)" correspond to the R-factor values calculated using Fmodel = scale * exp(AnisoScale) * (Fcalc + k_sol * exp(-b_sol*s2/4) * Fmask) where AnisoScale = k_sol = b_sol = 0, which means "no bulk solvent and anisotropic scale". given a typical solvent content of macromolecular crystals ~50% and always some anisotropy, the values do not look too surprising to me. Actually, the R-factors before bulk-solvent correction and scaling are rather confusing (although may be useful in some cases) so phenix.refine does not output them anymore at the very bottom of .log file (you can still find them somewhere in the log file). Pavel.