[phenixbb] Atoms with iso. B <=0

[Stephen Weeks]

Dear phenixBBers

     I have a curious case of refinement of a 2.6 Angs structure, where
some of the atoms have a calculated b-factor of 0.00.  It seems to be
somewhat random where this occurs and includes atoms within the backbone
e.g. the nitrogen in the following residue:

ATOM   2014  N   THR A 264      -2.685  42.357 -35.833  1.00  0.00
  N
ATOM   2015  CA  THR A 264      -3.952  41.776 -35.425  1.00  1.50
  C
ATOM   2016  CB  THR A 264      -4.684  41.052 -36.593  1.00  1.70
  C
ATOM   2017  OG1 THR A 264      -4.077  39.772 -36.846  1.00  2.24
  O
ATOM   2018  CG2 THR A 264      -4.669  41.867 -37.855  1.00  1.72
  C
ATOM   2019  C   THR A 264      -3.687  40.729 -34.368  1.00  2.42
  C
ATOM   2020  O   THR A 264      -2.571  40.210 -34.263  1.00  2.63
  O

The structure contains 4 NCS related monomers but with a quick glance I
don't see any obvious correlation between each one as to which atoms are
 0.00. I did use phenix.pdbtools to randomise the B-factors (no atoms had a
value 0.00 afterwards) but  upon repeating  the refinement the same problem
occurs.

Does anyone have a suggestion how to fix this ?

Cheers

Stephen
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