[phenixbb] question on bad geometry

[fn1 at rice.edu]

Hi everyone,

I have a structure at 2.3 A refined in phenix to R/Rfree=0.23/0.28.  
However, the geometry is not that good, the followings are the output  
from phenix.model_vs_data,

     Stereochemistry statistics (mean, max, count):
       bonds            :   0.0080   0.0547 3244
       angles           :   1.1669  12.1085 4374
       dihedrals        :  15.7241  85.6280 1202
       chirality        :   0.0706   0.2831 536
       planarity        :   0.0036   0.0246 573
       non-bonded (min) :   2.1217
       Ramachandran plot, number of:
         outliers : 17    (4.02  %)
         allowed  : 37    (8.75  %)
         favored  : 369   (87.23 %)
       Rotamer outliers        : 30 (8.62 %) goal: < 1%
       Cbeta deviations >0.25A : 0
       All-atom clashscore     : 40.51 (steric overlaps >0.4A per 1000 atoms)

I tried to use fix_rotamer=True, but it doesn't help at all. As to the  
rotamer outliers, the value is far higher than the ideal one. Does  
that mean I need to manually adjust the model? Or will autobuild help  
improve the geometry?

Thanks!
Fengyun