Dear Eric, I've just clarified the section in our documentation on how to tell if Phaser has solved your structure: http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Has_Phaser_Solved_It.3F
Briefly, the RFZ score is not that diagnostic of success or failure, particularly for high-symmetry space groups. For your space group, P6(2)22, the rotation function is evaluating the agreement between the observed data and the structure factors that you might get by adding up the contributions of 12 symmetry-related molecules. Because, at the rotation function stage, the relative phase angles of the contributions from symmetry-related molecules is not known, there's a lot of uncertainty so the signal-to-noise is low. That's why we emphasise the TFZ as the thing to look at. In your case, a TFZ of 8.4 for the first molecule is already pretty convincing, but even if the first molecule had a poor signal on its own, the TFZ of 13.7 for the second copy would tell you that the first one must have been right. I would say that you can be confident that this is basically right. (With the normal provisos: that doesn't rule out possible complications like pseudosymmetry, but as Phil Evans says the space group is a hypothesis, and you always have to be prepared to reconsider the hypothesis later if, say, it turns out to be difficult to refine the structure.) Best wishes, Randy Read > On 19 May 2015, at 01:36, Eric Karg > <0000052044071b36-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi all, > > Running Phaser using the apo protein as search model on a ~2.5 A dataset of a > protein-DNA complex, I get a single solution but with low RFZ. The map looks > reasonable but I was wondering why the RFZ is so low. Would this solution be > acceptable? > > SOLU SET RFZ=3.2 TFZ=8.4 PAK=0 LLG=66 TFZ==10.6 RFZ=2.9 TFZ=13.7 PAK=0 > LLG=203 > TFZ==14.0 LLG=1440 TFZ==34.2 > SOLU SPAC P 62 2 2 > SOLU 6DIM ENSE ensemble1 EULER 181.8 55.7 74.8 FRAC 0.27 0.26 -0.40 BFAC > -7.38 > SOLU 6DIM ENSE ensemble1 EULER 4.5 120.2 7.9 FRAC -0.31 0.20 -0.09 BFAC > 12.61 > Ensemble ensemble1 RMS variance(s): 0.87 > > Thank you for your help! ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
