[phenixbb] high average b-factor vs. Wilson B

Pavel Afonine pafonine at lbl.gov
Wed Aug 4 08:28:31 PDT 2010

  Hi Gino,

just a few comments:

> I am aware of all approximation made in defining the Wilson B-factor and how one should not take the Wilson B-factor too literally (etc.. etc...). But, as a matter of fact, Phenix kept over-refining my B-factor to crazy values.

I would say refining and not over-refining, because nobody knows where 
"over" starts.

> 1. Was your diffraction anisotropic? If so, try the
> Diffraction Anisotropy Server. The server applies a negative isotropic B-factor correction to your data. In my case, corrected structure factor amplitudes resulted in a 2.5% drop in the Rfree

That server removes reflections by sigma value and in selected 
directions. In some cases it can easily be a few thousands of Fobs. So, 
it it not surprising that the R-factors dropped. You can't compare the 
R-factors for the datasets containing different amount of reflections.

> and the average B-factor of my structure

and it is not surprising that the B-factor dropped: instead of keeping 
it in ATOM records you gave it away to uncle Sam, by applying negative-B 
correction. Just a trade, matter of where you keep these extra B-factor 

> How many macrocycles of refinement are you using?
> In my case Phenix kept bumping up the average B-factor of my structure by ~10A2 macrocycle. A 10 macrocycles refinement would bring the averaged B-factor to ~200A2. So don't over-refine.
> Stick to 2-3 cycles (provided your geometry is good, of course).

Interesting. I've never seen it before. Did you try to change the target 
weights for ADP refinement: manually or automatically? If you did and 
none helped (although I'm still not sure if help is needed) I would be 
interested to see the data and model.

> Do you have NCS and are you using TLS?
> If so, try to first use NCS to refine atom positions,
> then do TLS refinement without imposing NCS.
> If you think about, it doesn't make too much sense to use ncs-restraints when splitting a structure in TLS groups.

Regarding NCS: in ADP refinement it is applied only to local ADPs, and 
not total ones. See recent publication regarding this in PHENIX newsletter:
see page 28.

So you can safely refine everything in one go (I guess).

All the best!

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