[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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