On Wed, May 29, 2013 at 4:13 PM, Sam Stampfer
When I refined my model in phenix, I used the twin law h,-h-k,-l. I read in the documentation that twinning can account for some of this discrepancy, but that the program is supposed to take twinning into account if it will lower the calculated R-work by more than 2%, which it doesn't seem to have done (or there is some other problem with my data).
Okay, the problem is that your data don't actually appear to be twinned. The automatic method used by phenix.model_vs_data (which is used internally for Table 1 and the validation GUI) only tries possible twin laws if the results of the "L test" show a suspicious distribution of intensities. Your data look fine, so it doesn't bother trying the twin laws. That the R-factors are lower when you refine with a twin law isn't necessarily indicative of the data actually being twinned - Garib Murshudov has looked into this in detail but I confess to being ignorant of the math (but I can probably dig up his paper on the subject if anyone is interested). However, I'm pretty sure the data are actually in a higher-symmetry space group. Will send details and new files off-list (probably tomorrow at this rate). I should probably change some of the programs and/or documentation to make it more clear what is being done internally, since it took me a bit of digging to realize what was going on. In general, though, always be very careful before running twinned refinement! I have seen several users do this by mistake when they really had higher symmetry. The maps will also be more model-biased when using twinned refinement, so it's good to avoid doing this unless absolutely necessary. -Nat