On Wed, Apr 20, 2011 at 12:21 PM, Alexandra Deaconescu
I would like to optimize my weights during Phenix refinement. I am running Phenix 1.6.4-486 using the gui, and I have checked the "optimize weights", but I cannot see the results of the optimization in the output, so I do not know the relationship between Rfree/geometry and wc and wxc_scale (I might not want to pick the automatically selected wxc_scale for the lowest Rfree, but would like to find a reasonable values to give me good geometry). Some earlier posts indicated that this is not output in the log file, but I am running a more recent version...
It definitely should be in the log file, although it probably doesn't explicitly state "optimizing weights" anywhere. (The GUI doesn't display any information about weight optimization other than the log output - but I could be convinced to add something.) It won't run every macro-cycle by default (this is a separate option); if you run 3 macrocycles, I think the weights get optimized in the 2nd.
Same question for the ADP refinement.... I am working at 2.8A and my B factors are high (higher I think than what one would expect at this resolution).
How much higher? What does Xtriage say the overall isotropic and anisotropic B-factors for the data are? (These aren't perfectly correlated with the atomic B-factors, but they should track them to some degree.) The POLYGON graph in the validation output is helpful here - there is a very wide distribution of B-factors in the PDB. The attached image shows the mean backbone B-factor at 2.7-2.9A - I'm not sure I believe some of the extreme values, but it's clear that a mean B above 100 is still possible. PS. You should upgrade to version 1.7. -Nat
