[phenixbb] ensemble refinement rfree values

Kendall Nettles knettles at scripps.edu
Thu Dec 19 15:14:46 PST 2013

Hi Arjun,
Our recent paper in Structure makes an estimate of the noise in refinement by asking what happens if you assign two different Rfree sets and then refine the same structure with 256 different refinement strategies.  Based on that, I would say 0.5% difference in Rfree is within the noise range, and you might need 1% change to be sure it is meaningful. However, some structures showed more noise than others with this procedure.  I would second the suggestion to consider other metrics of quality in addition to Rfree.
Kendall Nettles

On Dec 19, 2013, at 10:27 AM, "Arjun Raman" <Arjun.Raman at utsouthwestern.edu<mailto:Arjun.Raman at utsouthwestern.edu>> wrote:

Dear Phenix Guys,

I have recently been trying my hand at the ensemble refinement option in phenix.refine. I generally observe an increase in rfree after performing the ensemble refinement with a well refined (using anisotropic B) structure, but the r-free increases are fairly small. For instance, 18.53% to 18.9% (1.8 Angstrom structure) or 20.45% to 21.1% (1.9 A)...I understand what this technically means (the ensemble refined model isn't as good) but given the noise in the calculation due to the limited number of reflections for the test set (~1000), would someone consider these rfree increases significant? My apologies if this question is a well-answered one...I can't seem to find much discussion about the range of rfrees to be expected or whether a 0.3-0.5% increase is large enough to toss out the refinement.  Normally, I would take the lower rfree but because the ensemble refinement procedure gives potentially much more information, this seemed like a relevant question to ask.

Thanks so much for your time,

Arjun Raman
Ranganathan Lab
UT Southwestern


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