[phenixbb] automatic weight optimization

Michael Thompson miket at chem.ucla.edu
Sun Jun 30 23:06:04 PDT 2013


Hello Phenix Folks,

I have a few questions about the automatic weight optimization in phenix.refine. I have read the manual, but I feel like maybe I'm missing something. I apologize in advance if these are naive questions, but here goes. I ran phenix.refine with a .def file, in which I set the following parameters:

 target_weights {
    optimize_xyz_weight = True
    optimize_adp_weight = True
    wxu_scale = 2.72
 }


My goal was to optimize both xyz and adp weights. In the log file, I see something like this:


===================== xyz refinement (lbfgs minimization) =====================

    R-FACTORS           RMSD     CLASH  RAMA  ROTA CBET WEIGHT    TARGETS
 work  free  delta  bonds  angl                                  data   restr
21.06 20.38  -0.67  0.033   2.0    6.1   0.0   6.6    0   none  0.154  0.1685
19.79 21.26   1.47  0.012   1.3    7.6   0.0   5.8    0  2.494  0.131  0.0499

Legend:
  - first line corresponds to starting state (before refinement)
  - R-factors reported in percent
  - delta is Rfree-Rwork in percent
  - CLASH is all-atom Molprobity clashscore
  - ROTA is percent of side-chain rotamer outliers
  - RAMA is percent of Ramachandran plot outliers
  - CBET is number of Cbeta deviations
  - WEIGHT is relative weight between X-ray (or neutron) target and restraints
  - TARGETS: the values of X-ray (or neutron) and restraints target functions

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
19.79 21.26   1.47  1.909  20.062  0.661    0.131
19.80 21.28   1.49  1.761  20.011  0.007    0.130
19.77 21.41   1.64  1.838  19.884  0.030    0.125
20.30 22.63   2.34  2.369  19.168  0.122    0.111
20.17 22.82   2.64  2.886  18.929  0.243    0.107
20.07 23.04   2.97  3.771  18.737  0.365    0.104
20.04 23.14   3.10  4.106  18.751  0.486    0.103
20.00 23.19   3.19  4.496  18.794  0.608    0.103
19.98 23.23   3.25  4.846  18.851  0.729    0.102
19.97 23.27   3.29  5.115  18.940  0.851    0.102
19.95 23.30   3.36  5.420  18.988  0.972    0.101
19.94 23.33   3.39  5.579  19.008  1.094    0.101
19.93 23.29   3.36  5.598  18.917  1.215    0.101
  max suggested <Bi-Bj> for this run:   10.00
  max allowed Rfree-Rwork gap:   5.0
  range of equivalent Rfree:   0.0
Best ADP weight:    0.007
Accepted refinement result:
19.80 21.28   1.49  1.761  20.011  0.007    0.130


The output kind of makes me feel like the adp weight is being optimized, but the xyz weight might not be. There is a list of statistics for varying values of the adp weight, but there is no similar list in the output from the xyz refinement stages.

So my questions are:

Is the xyz weight being optimized? Did I miss something in the input that is required to turn on xyz weight optimization? If the weight is indeed being optimized, then I must be misinterpreting the log file. How can I check to make sure the xyz weight optimization is running?

Thanks for the help!!

Mike Thompson










-- 
Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

miket at chem.ucla.edu


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