[phenixbb] Phenix.refine suddenly stopped to refine B-factors

krimmer at staff.uni-marburg.de krimmer at staff.uni-marburg.de
Mon Aug 12 02:38:14 PDT 2013


Dear all,

Phenix.refine suddenly stopped to refine B-factors, even though  
according to the settings it should refine them (checked box  
“individual B-factors”). This problem only occurs for one job. The  
weird thing is that this was always working and I did not do anything  
different, at least as far as I know. Also, this just happened to a  
colleague, totally independent from me. We never had this problem  
before. Here is a part of my log file:

          |-----overall-----|---macromolecule----|------solvent-------|
   stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
    0    :  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    1_bss:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    1_ohs:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    1_xyz:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    1_adp:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    1_occ:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    2_bss:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    2_ohs:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    2_xyz:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    2_adp:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    2_occ:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    3_bss:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    3_ohs:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    3_xyz:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    3_adp:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    3_occ:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    4_bss:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    4_ohs:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    4_xyz:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    4_adp:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    4_occ:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    5_bss:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    5_ohs:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    5_xyz:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    5_adp:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    5_occ:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    5_bss:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33
    5_ohs:  46.46   5.37  12.45  29.68   5.37  10.14  46.46   5.58  25.33

The values are not changing at all. The structure is almost done, but  
it still should change a bit during the refinement cycles. I noticed  
the problem because I added another water molecule to the structure,  
and the B-factor stayed at 30.00 which resulted in a negative density  
blob after refinement.

Thank you for your help!
Stefan








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