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] mailto:[email protected] phone (734) 764-3353 fax (734) 764-3323
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]