[phenixbb] R-factor difference between phenix and sftools

Simon Jenni jenni at crystal.harvard.edu
Sun Oct 12 11:25:56 PDT 2014

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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