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.
saper@umich.edu phone (734) 764-3353 fax (734) 764-3323
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