Hi Tongqin, It is a bit difficult to diagnose with the information you provided. Could you please answer the following questions? - Did you also try to reset the B-factors to similar values than neighboring atoms? F.ex. the average B-factor in the model could be 50 A**2, but in the ligand region, it could be lower, let's say 20 A**2. Then the starting value using average B is quite far from the likely B-factor of the ligand. - What refinement strategy do you apply? How many macro-cycles? Do you use any non-default parameters for B-factor refinement? - Which Phenix version are you using? Best wishes, Dorothee On Wed, Aug 31, 2016 at 7:12 AM, Zhou, Tongqing (NIH/VRC) [E] < [email protected]> wrote:
Dear All,
I am refining a structure with diffraction to 2.2A resolution and 95 % overall completeness. Now the Rs are at 18% and 23%, respectively. But the program failed to refine B factors for several ligands, atoms had high B factors while showing positive Fo-Fc map around them. Occupancy was set to 1 and I also tried to reset B to mean B of the whole PDB. Any of you seeing this phenomenon? Thanks!
Shown below is HEPES that has high B factor and positive density around it after refinement:
Best regards,
*Tongqing*
*Tongqing Zhou, Ph.D.*
Co-head and Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4609B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 761-7068 (Tel)
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