[phenixbb] R/Rfree discrepancy Phenix vs Refmac

Sabine Schneider sabine.schneider at mytum.de
Fri Aug 12 04:49:40 PDT 2011


I am refining a structure at 2.1A solved by MR. For curiosity I'm 
testing things like 'shaking' coordinates, simulated annealing, 
refinement Refmac vs Phenix and so on, to see what influence that has on 
stats, maps etc.

For instance after MR I did a bit of shaking the coordinates with pdbset 
(noise 0.1), followed by simulated annealing in Phenix.
Phenix states after SA:

Start R-work = 0.2671, R-free = 0.2992
Final R-work = 0.2312, R-free = 0.2666

When I use the output pdb of phenix directly in Refmac (with same mtz as 
input for Phenix)
Refmac tells me:
Initial R factor    0.2392   R free    0.2887

So I am quite puzzled about the discrepancy. Or can someone tell me if I 
made an error in reasoning somewhere?

Thanks a lot for the help!

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