I used Phenix, build 2037 to refine a a new structure. I reran the refinement (with the identical parameters) in build 2155 (v1.10.1) and obtained different statistics and slightly worse geometry. Any idea why?

start final
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R-work: 0.2488 0.2244
R-free: 0.3003 0.2851
RMS(angles): 1.67 0.80
RMS(bonds): 0.020 0.004

Ramachandran outliers: 1.2% (Goal: < 0.2%)
Ramachandran favored: 94.5% (Goal: > 98%)
Rotamer outliers: 8.7% (Goal: 1%)
C-beta outliers: 0 (Goal: 0)
Clashscore: 3.14
Overall score: 2.19

start final

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R-work: 0.2488 0.2331

R-free: 0.3003 0.2856

RMS(angles): 1.77 0.72

RMS(bonds): 0.020 0.004

Ramachandran outliers: 1.4% (Goal: < 0.2%)

Ramachandran favored: 93.4% (Goal: > 98%)

Rotamer outliers: 9.4% (Goal: 1%)

C-beta outliers: 0 (Goal: 0)

Clashscore: 4.10

Overall score: 2.36

_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of Michigan
Ann Arbor MI 48109-1055 U.S.A.
[email protected] phone (734) 764-3353 fax (734) 764-3323