[phenixbb] Different stats with different number of macrocycles

Pavel Afonine pafonine at lbl.gov
Thu May 4 09:20:39 PDT 2017

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.


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