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

[Dorothee Liebschner]

Hi Christian,

Could you answer the following questions:

- what is the resolution of the data set?
- what is average B of the protein?
- what are the starting B values for the ligand?
- did you try lowering starting B for the ligand and repeat the refinement?
Is this behavior reproducible with different refinement options?

Best wishes,

Dorothee

On Sun, Oct 30, 2016 at 11:06 AM, Christian Roth <christianroth034 at gmail.com
> wrote:

> Hi Phenix Team,
>
> regarding that ligand issue in this thread, we observed the same with a
> ligand in one of our structures now. After refinement the ligand is
> surrounded by pos diff density and the B-Factors are around 200 (way above
> any useful range in that case).
>
> The cif was generated using elbow and phenix runs with options Real space
> refinement, TLS on, individual B, and optimizing weights. Nothing crazy.
>
> Could you find a solution for the previous case and give us some tips?
>
>
> Cheers
>
>
> Christian
>
>
>
>
> Am 06.09.2016 um 01:44 schrieb Pavel Afonine:
>
> 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.
>
> Pavel
>
> 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> 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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