Hi Wolfram, a few points:
- R-factors in twin refinement vs non-twin refinement are not directly comparable: G.N. Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261 http://www.science.az/acm/V10,%20N2,%202011,%20pdf/250-261.pdf - did you make sure free-R flags assigned "having twinning in mind" (what phenix.refine always does)? Otherwise you have a risk of having this: see page 14 here: http://phenix-online.org/presentations/latest/pavel_validation.pdf Pavel On Thu, Mar 1, 2012 at 6:00 PM, wtempel <wtem...@gmail.com> wrote: > Dear CCp4ers, > A good morning to everyone. > Today, I have a structure that I initially refined in space group P6522, > 1mol/asu. > Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; <I>/<sigma> > 3 > 2.61-2.55A: Rsym=39.6%, <I>/<sigma> > 10 > 50.00-6.13: Rsym=6.4% > Some mild anisotropy in the resolution limits is apparent on the > diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in > the other. > Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like > 3.5A resolution, with some difference density for loops that cannot be > interpreted with reasonable geometry. > Rsym is very similar for data scaled in P3, in all resolution shells. > Xtriage does not suggest merohedral twinning. > Nevertheless, I extended my free flags in sftools from P6522 to P32 and > cad'd them to amplitudes merged in spacegroup P32. Correspondingly, I > expanded my model to a homotetramer and ran Refmac with amplitude based > twinning. (Would this be a reasonable input to twin refinement?) > From the output coordinates: > REMARK 3 TWIN DETAILS > REMARK 3 NUMBER OF TWIN DOMAINS : 4 > REMARK 3 TWIN DOMAIN : 1 > REMARK 3 TWIN OPERATOR : H, K, L > REMARK 3 TWIN FRACTION : 0.269 > REMARK 3 TWIN DOMAIN : 2 > REMARK 3 TWIN OPERATOR : -K, -H, -L > REMARK 3 TWIN FRACTION : 0.171 > REMARK 3 TWIN DOMAIN : 3 > REMARK 3 TWIN OPERATOR : K, H, -L > REMARK 3 TWIN FRACTION : 0.258 > REMARK 3 TWIN DOMAIN : 4 > REMARK 3 TWIN OPERATOR : -H, -K, L > REMARK 3 TWIN FRACTION : 0.302 > Does this establish twinning versus underestimated symmetry? And what do I > need to know about my free-R? Did refmac assign a new flag? Whereas the > output file's flags are all 1s and 0s, the input file had 0 ... 19. During > the first run, Rfree dropped to <28%. But on a subsequent run, Rfree was > stuck >30% when I used the initial job's output MTZ. > Many thanks in advance for your helpful comments. > Wolfram Tempel > >
