[phenixbb] Question abount B-factor refinement - B-factors = 0

[Pavel Afonine]

Hi Cartsen,

I agree that zero B-factors is a warning sign. I would try do the following:

1) Look at the maps to check how they look like for the problem fragments.

2) You can try to run "optimize_wxu" to get the "best" weight between 
Xray target and B-factor restraints. Note that in this case "best" means 
lowest Rfree which does not guarantee the distribution of B-factors that 
you will like.

3) Manually tighten B-factor restraints until you get the distribution 
of B-factors that you think is reasonable.You can do this by either 
decreasing the default value of "wxu_scale" or increasing the value of 
"wu". Just to remind that for B-factors refinement the overall target is 
defined as

Etotal = Exray * wxu * wxu_scale + Eadp * wu

where Exray is Xray target, wxu - automatically determined weight, 
wxu_scale - adjustment scale (that user can adjust), wu - same as 
wxu_scale applied to Edp (B-factor restraints).

Without playing with the refinement myself I can't say more. Once the 
structure is published, I would be very interested to play with it since 
it seems like a good case to use it for further improvement of 
phenix.refine.

Pavel.




> Initially, I noticed that the B-factors within a residue have quite a large spread, when one runs a temperature factor variance analysis as implemented in coot (Yes I read Pavel's response about this ...). This prompted me to actually look at the B-factors in the PDB file. I noticed that actually for quite a few residues one or more of the B-factors refines to 0.00 For instance one of the less extreme examples:
>
> ATOM    118  N   HIS A  21     -28.768  35.430   2.317  1.00  4.73           N
> ATOM    119  CA  HIS A  21     -27.357  35.565   2.625  1.00  0.00           C
> ATOM    120  C   HIS A  21     -27.124  35.408   4.116  1.00  2.25           C
> ATOM    121  O   HIS A  21     -28.072  35.360   4.902  1.00  7.73           O
> ATOM    122  CB  HIS A  21     -26.853  36.940   2.186  1.00  8.10           C
> ATOM    123  CG  HIS A  21     -27.610  38.078   2.799  1.00 11.18           C
> ATOM    124  ND1 HIS A  21     -28.733  38.624   2.216  1.00 17.18           N
> ATOM    125  CD2 HIS A  21     -27.418  38.759   3.955  1.00 13.28           C
> ATOM    126  CE1 HIS A  21     -29.194  39.600   2.979  1.00 25.70           C
> ATOM    127  NE2 HIS A  21     -28.414  39.701   4.041  1.00 12.79           N
>
>
> As background the data extends to 1.8A, with an I/I(s) of ~15 and ~2.5 in the highest shell, CHI^2 are all around 1+/ 0.1. The Wilson B is 11.3A^2 and R/Rfree 16.8/19.8%. This is homesource date, at the synchrotron I could probably push the resolution further out to better than 1.6A. No hydrogens were added, nor was TLS used.
>
> In order to get around the problem I initally reset all B-values to the Wilson-B, enabled wxc refinement (latest CCI-APPs) and refined ADPs only for 10 macrocycles. After a couple of cycles the B-factor distribution settled into the following, which looks fairly reasonable to me, except for the min values of 0.00:
>
> |-ADP statistics (Wilson B = 11.289)------------------------------------------|
> |    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
> |    type    |iso    aniso | min     max     mean   | min   max    mean       |
> |    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
> |    all     : 2659   0      0.00    129.99  13.58    None  None   None       |
> |    all(noH): 2659   0      0.00    129.99  13.58    None  None   None       |
> |    Sol.    : 390    0      0.35    56.99   27.75    None  None   None       |
> |    Mac.    : 2269   0      0.00    129.99  11.14    None  None   None       |
> |    Hyd.    : 0      0      None    None    None     None  None   None       |
> |    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
> |       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
> |    Bin#      value range     #atoms | Bin#      value range     #atoms      |
> |      0:     0.000 -  12.999: 1778   |   5:    64.993 -  77.991:   17        |
> |      1:    12.999 -  25.997:  492   |   6:    77.991 -  90.990:    9        |
> |      2:    25.997 -  38.996:  210   |   7:    90.990 - 103.988:    4        |
> |      3:    38.996 -  51.994:  124   |   8:   103.988 - 116.987:    2        |
> |      4:    51.994 -  64.993:   19   |   9:   116.987 - 129.985:    4        |
> |                               =>continue=>                                  |
> |-----------------------------------------------------------------------------|
>
>
> B-factors of 0 indicate to me that there is a problem, not sure how to tackle this in phenix at this point. Could there be a problem with the bulk-solvent scaling? Should I restrict the minimum B-factor to 1.0 (ugggh)? Or should I tighten the B-factor restraints?
>
> Cheers,
>
> 	Carsten
>
>
>
>
>
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