Well - R / Rfree gaps are not really the thing to worry about after a MR solution. Both seem to have decreased sensibly, so now you need to worry about the map quality - can you see things to rebuild? water structure ? etc.
It is possible the NC translation will affect the R factors. NC translation can make whole classes of reflections very weak, and of course weak reflections will have high R factors.. But I dont understand how an NC translation can make P31 SG be pseudo P62? ? Eleanor On 26 September 2014 21:56, Nat Echols <[email protected]> wrote: > On Fri, Sep 26, 2014 at 8:17 PM, Kimberly Stanek <[email protected]> > wrote: > >> Before refinement in phenix the R/Rfree gap is rather small, however >> even after one round of refinement I am finding that this gap increases to >> almost 0.06. I have a feeling that the high symmetry present has something >> to with this R/Rfree gap but was hoping some of you may have some helpful >> suggestions for how to deal with it. >> > > It's normal for the R/R-free gap to increase during the first round of > refinement in molecular replacement - in fact, unless you are solving a > near-identical crystal form and keeping the original R-free flags, this is > almost guaranteed to happen. MR will use all reflections and the limited > refinement Phaser does uses very coarse parameterization (rigid-body and > group B-factor), so the R-free will usually be quite low and sometimes even > lower than R-work. Restrained refinement will immediately start to open > the gap, but if it's working properly, it won't keep expanding throughout > refinement. At this resolution a gap in the range of 0.02-0.04 would be > normal - less than this is unusual. > > My guess is you just need to change the relative weights of the X-ray > target and geometry restraints so that the latter are stronger. Also, use > NCS restraints if you aren't already. > > -Nat >
