Hi Yuan, Bad geometry is a general issue for most low resolution structure refinement. There are quite a lot papers discussing it. I think you can try to set a reference structure or set high restrain in refinement, which should be easily achieved in Phenix. How did you know the B-factors are too high? There is no standard for a single case. B-factors varies from crystal to crystal even them have the same molecular content. Wilson-B factor may be a good indicator. I am a little bit worried about your R and R-free. Them are too close (Rfree is even lower than R!). What is your space group? If you want to reduce refining parameters to increase data/para ratio, you can try group B-factor refinement in Phenix. For combining NMR data, you should have NOE assignment.
Best, Zhiyi On 1/6/12, 商元 <[email protected]> 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 >
