[phenixbb] ensemble refinement rfree values

Tom Burnley tom.burnley at stfc.ac.uk
Thu Dec 19 08:18:52 PST 2013

Hi Arjun,

To assess the quality of different models it's important to look at a
range of metrics including but not restricted to Rfree.  These include
Rfree:Rwork ratio, geometric indicators etc.  I'm sure others can
advise you further here.

For the ensemble refinement specifically, just to check, did you try
arraying the pTLS and bath offset? This can have a big effect, for
more info see here:


All the best,


On 19 December 2013 15:25, Arjun Raman <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
> ________________________________
> UT Southwestern Medical Center
> The future of medicine, today.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

Dr Tom Burnley, PhD
Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

More information about the phenixbb mailing list