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(a)chem.ucla.edu
