[phenixbb] Different stats with different number of macrocycles

Pavel Afonine pafonine at lbl.gov
Thu May 4 12:02:54 PDT 2017

At resolution 2.5A I doubt you can distinguish difference of 0.005 or 
0.018A in bond length. Therefore, any bond/angle rmsd is good that:

a) does not exceed upper limit (which is, for example, 0.02/2.0; numbers 
vary based on personal opinions); AND
b) corresponds to lowest Rfree and acceptable Rfree-Rwork gap.

BTW, phenix.refine uses restraints for stereochemistry, not constraints.


On 5/4/17 11:54, Mark A. White wrote:
> 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://mawhite@utmb.edu
> 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 <pat.loll at drexel.edu 
> <mailto:Patrick%20Loll%20%3cpat.loll at drexel.edu%3e>>
> *To*: Pavel Afonine <PAfonine at LBL.GOV 
> <mailto:Pavel%20Afonine%20%3cPAfonine at LBL.GOV%3e>>, 
> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> *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 <PAfonine at LBL.GOV <mailto: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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