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I am refining several structures (all the same except point mutations, 2.0-2.8 A resolution) with Refmac5 (TLS+ISOT). One data set goes to 2.0 A and the refinement seems fine with REMARK 3 R VALUE (WORKING SET) : 0.20075 REMARK 3 FREE R VALUE : 0.23986 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.944 First, I also noticed there were "problems making U positive....,' during the refinement, actually, some of them were really big, say, -6. The low B also worries me, so I ran TLSANL, the total B of some residues went negative. I then submitted the output pdb to PARVATI server, it came back horrible, essentially listing all atom with "Non positive definite ellipsoid" ..., the mean anisotropy is 0.15, all my other structures have mean anisotropy of ~0.45 and normal average B about 40-50. I am not sure what I did wrong. Can anybody advise how to generally deal with this? Thanks, Tongqing
