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