[phenixbb] Phenix.model_vs_data - Rfree difference

[Luca Pellegrini]

Hello,

I am trying to find out the reason for a large R-free difference that I am getting between phenix.refine and phenix.model_vs_data:

phenix.refine
R-work/R-free 0.1702/0.1974

phenix.model_vs_data
R-work/R-free 0.1728/0.1795

Initial refinement was using the intensities in an XDS_ASCII.HKL dataset, followed by a few refinement cycles against the same dataset, but using amplitudes calculated in Aimless, with the ‘skip scaling just merge’ option and keeping the FreeR reflections. When I checked R-free values for the last refinement run before the conversion, there was no large discrepancy:

phenix.refine
R-work/R-free 0.1720/0.2086

phenix.model_vs_data
R-work/R-free 0.1715/0.2080

Can anyone please advise? Apart from this, refinement went well - both the 1.9A map and the model look fine. 

Thanks for the help & happy New Year,

Luca

Luca Pellegrini, PhD
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
Cambridge CB2 1GA
UK

Email: lp212 at cam.ac.uk
Phone: 0044-1223-760469