Okay Jim, I’ll bite. Seems strange to demand higher R-factors. However, what degree of NCS do you have? The phrase "over refined" doesn’t make much sense to me. I could imagine that the structure overfits the data and you can’t detect that because of some systematic bias in the free-R set (i.e. correlations arising from NCS). However, with the statistics and refinement protocol described it seems like your model is defensible. Paired refinements, trying different test sets (followed by re-refinement), and/or shaking the model a bit prior to re-refinement are all things that might be used to argue your case (assuming that you arrive at good numbers).
> On Apr 26, 2016, at 1:32 PM, 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
>
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