Hi Luca, the differences you quote are very small and I'd say insignificant. This is likely due to limited precision of coordinates and B-factors in PDB file. 0.1720/0.2086 and 0.1715/0.2080 are really the same. I wonder what happens if you ask phenix.refine to output model in mmCIF file and then use it as input to phenix.model_vs_data (mmCIF has more digits for coordinates and B-factor records). Pavel On 1/2/17 10:09, Luca Pellegrini wrote:
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: [email protected] Phone: 0044-1223-760469
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