[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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