Also, there is one more information I forgot to mention---I also have the NMR assignment(HNCACB spectrum) of the protein, is it possible to combine the NMR data in my refinement?
Regards, On Fri, Jan 6, 2012 at 4:14 PM, 商元 <shangyuan5...@gmail.com> 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 >
