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

[Schubert, Carsten [PRDUS]]

Hi,

I have a question about B-factor refinement in phenix. This is a reiteration of one or two of threads with the same subject dating back to September last year:

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