[phenixbb] Different stats with different number of macrocycles

Schnicker, Nicholas J nicholas-schnicker at uiowa.edu
Thu May 4 11:36:17 PDT 2017

Hi Pat,

I believe they suggest using target weight optimization in this case. It can be specified on the command line as below:

optimize_xyz_weight=true  optimize_adp_weight=true

I've found for a couple structures I had to use this or else the geometry was much worse. They also recommend to use this in the last round of refinement.



From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Patrick Loll <pat.loll at drexel.edu>
Sent: Thursday, May 4, 2017 1:25:21 PM
To: Pavel Afonine; phenixbb at phenix-online.org
Subject: Re: [phenixbb] Different stats with different number of macrocycles

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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