[phenixbb] Refinement differences?

Mark A Saper saper at umich.edu
Tue Feb 9 13:54:27 PST 2016


Hi, 
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?   

In 2037:
                   start         final
  ---------------------------------------
  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

2155

                   start         final
  ---------------------------------------
  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.
saper at umich.edu     phone (734) 764-3353     fax (734) 764-3323



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