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I'm worried when you say that you use the initial job's output MTZ. Refmac replaces F with a detwinned F in the output file so you wouldn't be refining against your measured data in the subsequent round. Best wishes Randy Read ---- Randy J. Read On 2 Mar 2012, at 02:00, wtempel <[log in to unmask]> 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 >