[phenixbb] Different stats with different number of macrocycles

Mark A. White mawhite at utmb.edu
Thu May 4 11:54:26 PDT 2017


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

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 

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 <pat.loll at drexel.edu>
To: Pavel Afonine <PAfonine at LBL.GOV>, phenixbb at phenix-online.org
Subject: Re: [phenixbb] Different stats with different number of
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.



> On 4 May 2017, at 12:20 PM, Pavel Afonine <PAfonine at LBL.GOV> 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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