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

[Zhou, Tongqing (NIH/VRC) [E]]

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

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)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
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