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

Pavel Afonine pafonine at lbl.gov
Fri Aug 6 09:15:03 PDT 2010

  Hi Geoffrey,

thanks for sending me the data and model - this helped me to find out 
what happens in your and other similar repeatedly reported cases.

Have a quick look at the total model structure factor formula that is 
used in all phenix.refine, phenix.model_vs_data, phenix.maps and many 
other similar tools:

see page 6 here:


and glance through the page 29, PHENIX Newsletter:


As you see there is  overall anisotropic scale matrix Ucryst (see /Acta 
Cryst./ (2005). D*61*, 850-855 and references therein for deeper level 
of details). In refinement, the trace of this matrix is subtracted from 
it and added to individual ADPs and Bsol, making Fmodel invariant under 
this manipulation. Most of the time, this is a small value, but 
sometimes it is relatively large.

Now, let's see what happens in your particular case.
The Wilson B-factor is 27.
If we reset all B-factors to 27 and repeat the refinement until 
convergence using two scenarios:

1) we add the trace of Ucryst to individual ADPs,
2) we do not add the trace of Ucryst to individual ADPs,

we will get the following:

1) R-work = 0.1728, R-free = 0.2177
Bcryst (Ucryst reported as B) = (-10.42,-11.48,21.90,-0.00,0.00,0.00); 
trace/3= 0.00
ksol= 0.33   Bsol= 54.75
Average ADP = 43.56

2) R-work = 0.1744, R-free = 0.2171
Bcryst (Ucryst reported as B) = (4.42,3.35,36.58,0.00,0.00,0.00); 
trace/3= 14.78
ksol= 0.32   Bsol= 40.00
Average ADP = 29.03

Clearly, in case "2)" you get almost exact match of Wilson B and Average 
ADP (27 and 29), while in case "1)" the B-factors are higher. Note, the 
R-factors in both cases are "identical" (negligibly different given the 
resolution and the R-factor value).

So I guess everything is more or less consistent and clear. It depends 
where and how you keep different contributions to the total ADP, and 
which values you use to compute mean ADP.

Answering your very original question "Should I be concerned about 
this?": the answer is no. But I had a quick look at your maps: and this 
is what I would spend some more time: you have a lot of positive and 
negative peaks, some of them are very strong: larger than 6sigma! I 
guess you are missing some ions, and alternative conformations may need 
some more attention. This is normal, it just needs some care and time to 
be spent before your structure is ready to go (to PDB).


PS> I'm sending you the results of these two runs off list.

On 8/3/10 10:20 PM, Geoffrey Feld wrote:
> Dear PhenixBBers,
> I'm working on a 1.45 A structure I solved using MR (phaser) and I'm 
> pretty close to finishing, just plopping in waters and fixing 
> rotamers. Rw = 19.8 Rfree= 22.8. I am a little concerned because my 
> Wilson B is 27.00 while my average B for macromolecule is more like 
> 43, and for solvent is 48. I have enough data to use anisotropic ADP 
> refinement, which was a big help in bringing down the Rfree, but the 
> average B hasn't really moved much. Should I be concerned about this? 
> Should I try adjusting the wxu, or some other parameter?
> Thanks!

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