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

Pavel Afonine pafonine at lbl.gov
Mon Sep 5 17:44:11 PDT 2016

Hi Tongqin,

I second Dorothee's point that we need more information to resolve this 
problem. If you still have this problem please send me inputs files 
(data, model, .eff from last refinement, as well as ligand .CIF files if 
any) and I will look into this once I have files.


On 8/31/16 09:29, Dorothee Liebschner wrote:
> 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 <mailto: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:

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