[phenixbb] convergence in Phenix real space refinement

[Robert Oeffner]

Thanks Pavel, In one test example I noted that "moved from start" didn't 
change much after about 12 macro cycles. This would then be a necessary 
but not sufficient condition for convergence If I understand you 
correctly. Would there be any other statistics indicating convergence? 
In my test example CCmask hardly changed at all.

Rob

On 20/10/2023 04:03, Pavel Afonine wrote:
> Hi Rob,
>
>> I'm curious to know when convergence has been obtained in 
>> phenix_real_space_refine. I see the number "moved from start" in the 
>> log file and assume that once it doesn't change much after several 
>> macro cycles then convergence has been obtained when refining a 
>> structure. True? What is that value based on, the RMSD between the 
>> initial structure and the final structure? I didn't find this 
>> documented in the 2018 publication of the program.
>
> phenix.real_space_refine runs a set number of cycles that you can 
> adjust. In the log file it reports the rmsd between the initial and 
> current model. While this number can give you some idea about the 
> amount of model movement between cycles, it also may hide some useful 
> information: for example, if you refine a large structure and only a 
> few residues flipped their side chain conformations during refinement, 
> then this overall number probably won't tell you this.
>
> Pavel
>
>