Re: [phenixbb] Different stats with different number of macrocycles

Patrick, At this resolution the (RMS bonds/angles =0.005 Å/0.9 deg) are over-constrained (Bad). At high resolution we should expect values ~ 0.018 Å/3.0 deg. At your moderate resolution RMS bonds/angle values of 0.008 Å/1.4 deg are typical (Good). Getting a very low RMSD just indicates that the model was over-constrained, and is no different than having the same B-factors for every residue. It is just not physically reasonable. -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.658A University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Fax. (409) 747-1404 mailto://[email protected] http://xray.utmb.edu QQ: "What is earnest is not always true; on the contrary, error is often more earnest than truth." - Benjamin Disraeli -----Original Message----- From: Patrick Loll To: Pavel Afonine , [email protected] Subject: Re: [phenixbb] Different stats with different number of macrocycles Date: Thu, 4 May 2017 14:25:21 -0400 Hi Pavel, I agree that the differences in the R values are not large, but I found the geometry differences compelling (RMS bonds/angles can be either 0.005 Å/0.9 deg or 0.008 Å/1.4 deg). I’m glad to hear the strategies may change based on macrocycle number (otherwise I’d question my understanding of refinement). Is there any way a user can change influence this choice of strategy? Given two models with essentially equivalent R values, I’d prefer the one with nicer geometry. Thanks, Pat

On 4 May 2017, at 12:20 PM, Pavel Afonine wrote:

Hi Patrick,

...

I am finishing a refinement at 2.5 Å, using the Phenix GUI. I performed a three-macrocycle refinement, and saw that the geometry (RMS bonds/angles) and R/Rfree all got better in the first macrocycle, and then worsened in the subsequent two macrocycles.

it's hard to comment on this one because I don't know how you define "worse". For example, I'd call the same "R/Rfree = 0.208/0.236" and "R/Rfree = 0.209/0.240" but some may think they are different.

...

OK, fine. So I repeated the refinement, except I performed only a single macrocycle (starting from the exact same input coordinates). However, the statistics after this one-macrocycle job did not match the stats seen after 1 macrocycle in the 3-macrocycle job (?!). This doesn’t make sense to me; if you’re starting from the exact same coordinates, shouldn’t the first macrocycle always wind up at the same place, regardless of whether or not the program goes on to do additional macrocycles of refinement?

phenix.refine may change internal strategies based on specified number of macro-cycles. So your observation is not too unexpected to me.

Pavel

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