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

[Dorothee Liebschner]

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] <
tzhou at mail.nih.gov> 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)
>
> (301) 793-0794 (Cell)
>
> (301) 480-2658 (Fax)
>
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