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 [email protected]