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, [email protected] 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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