[phenixbb] Different stats with different number of macrocycles

Pavel Afonine pafonine at lbl.gov
Thu May 4 11:47:54 PDT 2017

Hi Patric,

I guess to make refinement consisting of one macro-cycle yield the same 
result as 1st macro-cycle of refinement consisting of N macro-cycles 
(N>1), you need to set these parameters



You can do it using GUI or command line.

Normally, you need to run refinement until convergence, which is almost 
always more than 3-5 macro-cycles.


On 5/4/17 11:25, Patrick Loll wrote:
> 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> 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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