[phenixbb] Phenix.refine suddenly stopped to refine B-factors
Pavel Afonine
pafonine at lbl.gov
Mon Aug 12 08:50:09 PDT 2013
Hi Stefan,
could you please send me inputs necessary to reproduce this problem? I
need .eff file, and data and model files (and any cif files if there are
any ligands).
Thanks,
Pavel
On 8/12/13 2:38 AM, krimmer at staff.uni-marburg.de wrote:
> 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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