[phenixbb] R-factor difference between phenix and sftools

Ed Pozharski ccp4pozharski at gmail.com
Mon Oct 13 11:32:51 PDT 2014

To be fair, I made the same mistake initially, but the question is about calculating Rs with sftools using output mtz from phenix.refine, not sfcheck.  Thusly, bulk solvent explanation does not seem to apply. My other theory (impossible to check without actual data) was that phenix.refine outlier reflection rejection makes the difference here, although it's surprising if effect is so noticeable. 

Sent on a Sprint Samsung Galaxy S® III

<div>-------- Original message --------</div><div>From: Pavel Afonine <pafonine at lbl.gov> </div><div>Date:10/13/2014  2:21 PM  (GMT-05:00) </div><div>To: Tim Gruene <tg at shelx.uni-ac.gwdg.de>, phenixbb at phenix-online.org </div><div>Subject: Re: [phenixbb] R-factor difference between phenix and sftools </div><div>
</div>Thanks Tim, yes missed this one!

Hi Simon,

the differences in R-factors you observe are most likely because we use improved bulk-solvent modeling and overall scaling procedure. This is described here:

Bulk-solvent and overall scaling revisited: faster calculations, improved results. 
Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A. Acta Cryst. D69, 625-34 (2013).

Specifically, Figures 3-4 in this paper make your observations very expectable. 

Other contributions to differences are discussed here:

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. 
P.V. Afonine, R.W. Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson, D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams J. Appl. Cryst. 43, 677-685 (2010).


On 10/13/14 11:10 AM, Tim Gruene wrote:
Dear Simon,

I found this a very puzzling observation and given the high throughput
of this board, it is likewise puzzling you have not received a reply yet
- or have you?

Best regards,

On 10/12/2014 08:25 PM, Simon Jenni wrote:
Hi, we refined a structure in phenix.refine (dev-1810) and the R-factors

   Final R-work = 0.3221, R-free = 0.3638

phenix.cc_star agrees:

   phenix.cc_star com_001.pdb com_001.mtz \
   f_obs_labels="F-obs,SIGF-obs" \
   f_model_labels="F-model,PHIF-model" \

   r_work: 0.322
   r_free: 0.364

so does phenix.model_vs_data:

   phenix.model_vs_data com_001.pdb com_001.mtz

   r_work          : 0.3221
   r_free          : 0.3638
   sigma_cutoff    : None

However, when I calculate the R-factors with sftools, I get a discrepancy
between the phenix and sftools results:

   sftools << eof
   read com_001_f_model.mtz
   select col R_FREE_FLAGS > 0
   correl col FOBS FMODEL
   select invert
   correl col FOBS FMODEL

   R-work: 33.6
   R-free: 38.1

Does anyone perhaps know what causes this difference?

With best regards, Simon

PS: The structure is in spacegroup P212121 with strong pseudocentering tNCS
(dimer in the asymmetric unit, native Patterson peak at 0.500 0.500 0.497).
No indication for a P21 twin (L-test and refinement in P21 with twin law),
not higher symmetry spacegroup I222 (alternating strong and weak
reflections are visible in the diffraction patterns, resolved structural
differences in the two protomers of the dimer). Two datasets from different
beamlines. As might be expected, the R-factors after refinement are
unusually high (e.g. 28/35 [conventional resolution cutoff at 3.1 A], 32/36
with Kay's CC cufoff at 2.6 A). I wanted to compare refinements between
different programs to see how they cope with the unexpected bimodal
amplitude distribution.

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