Re: [phenixbb] questions related to Phenix refinement

Dear Pavel, Am 18.01.15 um 07:23 schrieb [email protected]:

Date: Sat, 17 Jan 2015 20:36:30 -0800 From: Pavel Afonine To: Smith Lee , "[email protected]" Subject: Re: [phenixbb] questions related to Phenix refinement Message-ID: <[email protected]> Content-Type: text/plain; charset="windows-1252"; Format="flowed"

Hello Smith,

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In the X-ray statistics by resolution bin of the Phenix.refine result, there is a column "%complete". For my refinement data, I find the better the resolution (from lower resolution to the higher resolution), the lower the completeness (for example for 40-6 A, %complete is 98, for 3.1-3.0 A, %complete is 60%, for 2.2-2.1 A, %complete is 6%).

Will you please tell me what does this "%complete" mean? why it decreases in the better diffraction bin? Completeness is how many reflections you have compared to theoretically possible. So the higher completeness the better. Ideally (and it's not that uncommon these days) you should have 100% complete data set in d_min-inf resolution. Anything below say 80 in any resolution bin is bad, and numbers you quote 6-60% mean something is wrong withe the dataset.

Given your standing in the community, the last sentence will lead many unexperienced people to believe that they should cut their data at the resolution where the completeness falls below "say 80"%. But that would be wrong. There is no reason to consider a completeness as "too low in a high-resolution shell" as long as the data in that shell are good. Particularly in refinement any reflection helps to improve the model, and to reduce overfitting. Of course, more complete is better! Nowadays there should be no reason _not_ to get >95% (>99% in high-symmetry spacegroups) completeness in the low resolution shells, unless people stick to the "collect minimum rotation range" paradigm, and get the starting angle (or the point group!) wrong. best, Kay