[phenixbb] question on bad geometry
fn1 at rice.edu
fn1 at rice.edu
Tue Aug 31 18:37:30 PDT 2010
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
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