[phenixbb] refinement (was: Shake)

Nathaniel Echols NEchols at lbl.gov
Thu Jan 14 09:49:44 PST 2010

On Jan 14, 2010, at 3:51 AM, v_kukshal at cdri.res.in wrote:
> i am solving one of my structure  with resolution 3.0 .
> i used phenix auto build for building . R factor and Rfree is now 20.4   24.9 but 69 residue out of 800 residue are outlier in ramchandran plot . further refinment increses the r factor how should i can step further 

In addition to what Pavel said: 20.4/24.9 is excellent for 3.0A resolution (try phenix.polygon to see for yourself) - and perhaps unrealistic, since you have so many Ramachandran outliers.  If you fix the outliers (and any other geometry problems) and R-free increases again after refinement, you may still want to accept those results, if the final values of R/R-free are otherwise reasonable.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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