[phenixbb] bad geometry problem

Qian Sarah oceanlineqwm at gmail.com
Tue Jun 19 01:17:25 PDT 2012

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(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!

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