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Hi Jim, Agree, I have seen quite frequently Rs in this range for medium resolution structure, and they did not feel overrefined, whatever the definition is. Here a very pragmatic approach: Share the pdb and mtz with the referee and editor and ask them for feedback to make the structure acceptable in their opinion. Maybe they agree that you simply have a very good fit to the data. Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com > On Apr 26, 2016, at 4:56 PM, Keller, Jacob <[log in to unmask]> wrote: > > To take a slightly different tack, you could crank up the geometry restraints, and that should make your fit somewhat poorer and give pleasingly-worse R values. But maybe that reviewer would insist on a certain poverty of geometry as well? Or what if both the geometry and R-values improved? Then you’d really be in trouble. > > Maybe just cite the various facts about what is normal in the pdb and so on, ask the editors for an independent crystallographic review to evaluate the “over-refinement” issue? > > JPK > > From: CCP4 bulletin board [mailto:[log in to unmask] <mailto:[log in to unmask]>] On Behalf Of James Phillips > Sent: Tuesday, April 26, 2016 7:33 PM > To: [log in to unmask] <mailto:[log in to unmask]> > Subject: Re: [ccp4bb] Over refinement > > 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] <mailto:[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