Nat, What do "correct" B-factors look like? What refinement strategy did you > use for them? >
1) If I see strong positive density in the Fo-Fc map along the backbone of two turns of an correctly placed alpha helix, therefore the B-factors are too high in that region. The model after refinement suggest less scattering in that region than is observed which is most likely explained by incorrectly high B-factors. 2) xyz, TLS and individual B-factors (no grouping). SS and ramachandran restraints on coordinates and NCS restraints on coordinates and B-factors. > > >> Note that the R-free value in the 3.4A shell is lower than the R-work >> (and also the Rpim in that shell!) which clearly indicates this refinement >> was not stable. >> > > I don't think it indicates anything about the "stability" of refinement - > my guess would be that the NCS is biasing R-free. I suppose it could also > indicate that the data in the 3.6-3.4 range are basically noise, although > if the maps look better then that would suggest the opposite. > I think the refinement is not parametrized correctly. Thank you, S. >
