[phenixbb] convergence in Phenix real space refinement

[Pavel Afonine]

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