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It is not where the R/Rfree "end up" it is the trajectory through the refinement process. As you refine then adjust your model the two should drop. If R drops Rfree stays the same or rises you have over refined. I suggest giving the journal the results of each stage of your refinement. On Tuesday, April 26, 2016, Professor James Henderson Naismith < [log in to unmask]> wrote: > Dear Colleagues. > We are having difficulty persuading a reviewer that our structure is not > over refined. > > The structure is a molecular replacement of complex with a published > relatively non-isomorphous native structure from another lab. > > The same Rfree set was used as the published data. > > Our complex is at 2.6A and R/Rfree end up at 18/22 > > PDB redo gets the same result, so does phenix.refine (with a trivial %). > All B-factors were reset and TLS used. > > The data are 2.61A and average B is 80A, there are 4500 residues, 68 > waters. Unfortunately Mol probity gives us 100th centile and the Rama is > also good, bond rms is 0.012 and we used NCS local restraints. > > There is no rotational NCS but there is a weak translation symmetry (does > not show up in data but when refined the monomers have a bead on a curved > string appearance). > > The referee has refused accept the paper until we make the R and Rfree > higher by some undefined target, since it is 'over refined' > > Does anyone have a useful program to make structures worse to some > threshold that is considered normal at 2.6 A or does anyone know a good > paper that points out Rfree is not susceptible to over refinement since by > definition it is not refined. > > best > Jim > > > > > Jim Naismith > St Andrews > > The University of St Andrews is a charity registered in Scotland : No > SC013532 > >