On Tue, Jun 19, 2012 at 1:17 AM, Qian Sarah
Hi, this may not be a new problem, but I tried every stretagy that I know from bb, but the geometry is still very bad. So I wish I can get some help from here. Crystal information: SAD data. Resolution 3.0. There is no anisotropy in the data. R/Rfree : 22.7/26.8 (Rfree-flag is always from the Refine_data.mtz file generated after the first refinement.) RMS(bonds):0.02 RMS(angles): 1.453 Ramachandran outliers: 3.0% Ramachandran favored: 91.2% Rotamer outliers: 18.7% !! Clashscore: 31.84 overall score: 3.47 I tried different strategies, like autobuild and then refine; set wxu/wxc=0.3/0.3; turn on "Ramachandran restrains", "fix bad sidechain romaters"etc, however the paramters are still very bad, especially the rotamer outliers. Then I rebuild them manually in coot,after refinement the parameters are even worse.
A few suggestions: 1. Don't use Ramachandran restraints in Phenix - please! 2. Do use Ramachandran restraints when rebuilding in Coot - fix the problems manually, perform local real-space refinement, and check that the result makes sense. Ensuring that the geometry is as good as possible before you run another round of refinement will make Phenix work better. 3. Don't adjust the weights manually; use the automatic weight optimization. It takes a long time to run (unless you have lots of CPU cores), but it's going to save you time in the end. My guess is this is going to help with some of the 4. At this resolution the rotamer fitting in phenix.refine is unlikely to work very well. You need to fix these problems manually too, I'm afraid. If you're willing to send us the model and data (off-list), we may have additional suggestions.
p.s. phenix version: phenix-1.7.3-dev-1046.
You should update to the latest official release. -Nat