Hi Sarah, if you send me the model and data files (off-list) I will be happy to have a look and may be I come up with an idea of how to improve things. I've seen quite a few cases that fit your description and in most of them there was a clear reason for geometry being poor. Knowing it is a key. So hopefully your case is not an exception. Pavel On 6/19/12 1:17 AM, Qian Sarah wrote:
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. p.s. phenix version: phenix-1.7.3-dev-1046. Thank you very much! best, Sarah