As others have mentioned, your geometry/x-ray weight may need to be adjusted.
However, at 3.2 Angstroms I'd recommend against using atomic B-factors - the "rule of thumb" for this is 2.8 Angstroms for atomic B-factors (or at least it was back in the day). It might help to use an overall B-factor combined with one (or a few) TLS groups. Regarding how far to trust the density from the refined model - that's what (composite) omit maps are for. Good luck, Pete 商元 wrote: > Dear All, > I have a set of 3.2A data containing only 3000 reflections. From the SAD > phasing and iterative modeling and density modification, I get a preliminary > structure with bad geometric conformations(~8/160 ramachandran outliers in > Coot). After Phenix MLHL refinement, the geometry is still bad with (10% > ramachandran outliers and 25% Rotamer outliers), and the B-factors are all > too high(all between 80 to 170, average ~120), and R-factor/R-free have a > value of 0.328/0.326. > The poor geometry of my model and the unusual B-factors indicates there are > still a lot improvement in my model. The question is, as I only have ~3000 > reflections, and the atoms in the sequence is around 1000, and each atom > there are 4 parameters to be refined(X,Y,Z,B-factor, assuming occupancy is > 1), so how to refine my model to avoid over-refinement? Should I trust the > electron-density map of the refined mtz data, or should I adjust the local > geometries using Coot rotamers tools? How to set a reasonable B-factor values > in the refinement? > > Best Regards, > Yuan >
