Hi Mark,

to me statistics from both refinement runs look essentially the same in a sense that if you run say 100 refinement jobs each one starting with slightly perturbed structure (shake in coordinates with rmsd~0.3-0.5A, shake in B-factor) you will get ensemble of essentially the same but still slightly different refined models. Variation in R-factors my be ~0.5-2% between models in the ensemble. Geometry may vary slightly as well. With this in mind I would say different numbers you get are within the spread and I doubt the differences are really significant.

The strangest thing to me is that you still get ~9% or rotamer outliers: 2155 is supposed to be much better in eliminating rotamer outliers (although it is still limited to without H included).

I agree with Eckhard: we made a lot of changed recently, such as re-do NCS how NCS works, using CDL (conformation dependent library for restraints), etc..

Of course there may be other reasons for differences between these two runs but this is all I can tell given amount of information provided!

All the best,
Pavel


On 2/9/16 13:54, Mark A Saper wrote:
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.
[email protected]     phone (734) 764-3353     fax (734) 764-3323





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