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

Christian Roth christianroth034 at gmail.com
Sun Oct 30 11:06:32 PDT 2016

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 

Could you find a solution for the previous case and give us some tips?



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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