It might be possible that there's a problem in the low resolution portion of your data. You could check the wilson plot to make sure it looks normal at that range, and possibly change the low-resolution cutoff refmac is using.
Pete Jan Abendroth wrote: > Hi all, > I have a number of low-ish resolution data sets that show a strange B-factor > behaviour: > All are just better than 3AA resolution, collected on a strong synchrotron > beamline. Some, yet not tremendous radiation decay. > Wilson scaling, obviously not very reliable at this resolution, gives me a > Wilson B of about 40, already a low number. Refinement in refmac5 (5.5.0053) > with individual B-factors refinement leads to an average B factor of around > 16 with several individual B factors hitting the B=2 limit... > When I convert Is to Fs in truncate simply using the square root, things get > even a bit worse, the average B now is 14. > When I try to do an overall B-factor refinement, still individual B-factors > appear in the output file. > > refinement details: 2.8AA resolution,medium ncs for two ncs related chains, > no riding hydrogens, simple scaling, MKLF target, isotropic B factors > Rwork: 0.206, Rfree=0.286, bonds=0.018, angles=1.89 ... obviously I could > retrain a bit more... > > Any ideas how to handle this? Basically, my question is: how do I get the > overall B factor to realistic numbers? > Thanks a lot for any hints > > Jan > -- > Jan Abendroth > deCODE biostructures > Seattle / Bainbridge Island, WA, USA > work: JAbendroth_at_decode.com > home: Jan.Abendroth_at_gmail.com >
