Twin refinement cannot be compared directly to untwinned - the R factors are between different parameters - without twinning it is assumed you have an amplitude obtained more or less from sqrt(I But for a twinned data set that I is actually [ I1 + twin_factor I2 ] so the amplitude is not really correct and twinned refinement will give a much better estimate.
However you need to be careful that you have assigned the same FreeR flag to reflection pair related by the twin law. The modern program in the CCP4 data reduction pipeline looks after this pretty automatically - all possible symmetry equivalents are assigned the same FreeR but older software did not do this.. You can check it by looking at some twin equivalents - in SG P32 these could be h k l and -h, -k, l or h k l and k h -l or h k l and -k, -h, -l . Ideally they all should have the same Free R flag.. Eleanor PS - the acid test is: Do the maps look better? E On 13 April 2017 at 19:52, Robbie Joosten <r.joos...@nki.nl> wrote: > Hi Alex, > > > > You are not giving the number after refinement without the twin > refinement. Nevertheless, R-free drops like this are not unheard of. You > should check your Refmac log file, it would warn you of potential space > group errors. Refmac will also give you a refined estimate of the twin > fraction. > > > > Cheers, > > Robbie > > > > Sent from my Windows 10 phone > > > > *Van: *Alex Lee <alexlee198...@gmail.com> > *Verzonden: *donderdag 13 april 2017 19:19 > *Aan: *CCP4BB@JISCMAIL.AC.UK > *Onderwerp: *[ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly > down > > > Dear All, > > I have a protein/dna complex crystal and data collected at 3A and another > set at 2.8A, space group P32. L test shows twinning (fraction around 0.11). > The structure solved by MR and model building of the complex finish (no > solvent built yet, I do not think it's good to build solvent in such low > resolution data). > > I did Refmac5 to refine my structure (restraint refinement) with or > without twinning, to my surprise, the Rfree drops a lot after twin > refinement of two data sets. Summary below: > > 2.8A dataset: before twin refine 34%, 29%; after twin refine:24%, 19% > 3A dataset: before twin refine 30%;26%; after refine 25%, 18% > > I know that a lot of threads in CCP4bb talking about Rfree after twin > refine and Rfree without twin refine can not compare directly. By drop R > free this much by twin refine, it gives me a feeling of too good to be true > (at such low resolution with such good Rfree, maybe overrefined a lot?), > but from the density map after twin refine, it does seem better than no > twin refine map. > > I do not know if reviewers are going to challenge this part. > > Any input is appreciated. > > > >
