[phenixbb] Gap between R and Rfree

Nathaniel Echols NEchols at lbl.gov
Thu Feb 25 12:05:08 PST 2010

On Feb 25, 2010, at 11:45 AM, Young-Jin Cho wrote:
> Thanks everyone.
> First, I checked my data and showed almost no anisotropy.
> Second, I tried both refmac and phenix, had the similar results.
> Third, ncs may be the key... I re-processed hkl and cut the resolution and did ncs=true. It first generated error message and suggested to put distance limit upto 3. Then now the gap between R and Rfree is reasonable (.2834 and .3361 without substrate and water). 
> However I tried my previous pdb that has everything with old mtz file, Final R-work = 0.2389, R-free = 0.3158. In this case, I had to expand my limit upto 6.  
> I still need to look more or do further refine from newly generated mtz file though, (sorry that's why I was late for responding.... I wanted to confirm it). Anyway, seemingly setting up 'ncs' as Pavel mentioned is most possible answer to my case.

Other less likely (but still possible) things to look for:

1. Twinning with a small twin fraction - this can be easy to miss if your maps look decent and the R-free isn't ridiculously high.

2. Undiagnosed translational pseudosymmetry.  I think I spent several months of grad school trying to refine a structure like this because I didn't realize what the extra spots in my images meant.  (In my defense, they were more smudges than "spots", but R-free dropped a few percent lower when I reprocessed and re-refined with the correct symmetry.)

General question: this topic comes up over and over again here and on ccp4bb.  Is there a general FAQ list anywhere that covers all of these issues?  (I will add this to the Phenix FAQ, along with the answer to "how do I tell if my R-free is good", but most of the same answers apply to any software, not just Phenix.)


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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