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
052044071b36-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 RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
