[phenixbb] Failed to refine B factors of some residues and ligands
christianroth034 at gmail.com
Mon Oct 31 09:11:50 PDT 2016
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
> Best wishes,
> 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?
> 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.
>> 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,
>>> 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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