[phenixbb] FreeR set reduced by half in twin crystal refinement?
lauren at gate.sinica.edu.tw
Wed Oct 7 06:13:39 PDT 2009
I have a P31 twin crystal, resolution 2.0, and with twin fraction 0.451. I
use phenix.refine to refine the structure and with freeR set to 8%.
% phenix.refine data.sca model.pdb twin_law="h,-h-k,-l"
Final: r_work = 0.1793 r_free = 0.2258 bonds = 0.011 angles = 1.557
REMARK 3 FREE R VALUE : 0.2258
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.67
REMARK 3 FREE R VALUE TEST SET COUNT : 2013
After the refinement, it seems like my freeR set size reduced by half
(3.67%). Is it due to the twin effect, or something is wrong with my
And if I use ccp4 program "scalpeak2mtz " to convert the .sca to .mtz and
with freeR fraction set to 8%. Then refine it with phenix.
% phenix.refine data.mtz model.pdb twin_law="h,-h-k,-l"
Final: r_work = 0.1669 r_free = 0.1970 bonds = 0.010 angles = 1.406
REMARK 3 FREE R VALUE : 0.2022
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.80
REMARK 3 FREE R VALUE TEST SET COUNT : 4326
It turns out, my test set is still 8%, and R/Rfree looks even better than
the first one. So I am wondering which one is the correct one and why?
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