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On Tuesday 17 June 2008 09:08:24 am Sampath Natarajan wrote: > Dear All, > I am refining a structure with 2.5A resolution by refmac5. I > could find the solution by MR using molrep. After fitting the model, I > refined the structure again with 0.3 weighting term, but the output PDB file > shows many splits in the residues. So I used 'auto' as a weighting term, > then I didn't find any splits. At the same time I noticed that figure of > merits is not increasing after model fitting. But the correlation > coefficient is more than 80%. Also while refining with auto weighting term, > the figure of merit goes down about 25% than previous. > > Finally I find that some of the residues show high B factor. Could > anyone give suggestions to reduce the B-factor? It is worth remembering that B is a measure of the uncertainty in the atomic position. So one generic answer is that to reduce B you need to be more certain about where your atoms are :-) If/when your model correctly describes the mean position for each atom, then B can be interpreting as representing 'motion' or more properly speaking displacement about that mean position. But if your atoms are not in the right place, then their high B factors are simply telling you that the calculated X-ray density doesn't support your current model. So following automated MR, high B factors are best viewed as a hint as to where your model needs to be rebuilt.