[phenixbb] Failed to refine B factors of some residues and ligands

Zhou, Tongqing (NIH/VRC) [E] tzhou at mail.nih.gov
Wed Aug 31 07:12:18 PDT 2016

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:
[cid:image003.jpg at 01D20370.26FD7150]

Best regards,


Tongqing Zhou, Ph.D.
Co-head and Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
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