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

Christian Roth christianroth034 at gmail.com
Mon Oct 31 09:11:50 PDT 2016

Hi Dorothee

to answer your questions

The resolution is about 2.0 Ang and the average B around 55. The Bfactor 
from the ligand was set to the default of 20 by Coot when placing the 

It seems that setting the B-value to the average B of the structure 
nearly solves the problem (most of the ligand fine, just parts with 
unusuallly high values). Setting it to a bit higher values 70 for a 
start and the ligand refines fine.

I noticed that in the first macrocycle with and initial factor of 20, 
the B's are nearly unchanged (20 +- 2) Red diff density appears as 
expected. In the second cycle The minimizer let the B-factors "explode" 
to about 200 and that basically is the overkill and it never recovers.




Am 31.10.2016 um 15:59 schrieb 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 <mailto: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 <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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