Hi Rob, rmsd between cycles is a global metric that isn't sensitive to local changes. One can also look at maximal shift but then you'll face problem of oscillations -- for example, a side chain may flip back and forth between rotameric conformations for whatever reason (poor map, or equally good density for a few alternative conformations,...): in this case global rmsd won't show anything but max shift will be always large. All in all, it is not easy to find a reliable solution that will always work. This is why choosing number of cycles is left on the user to decide on (with the default 5 being fine enough in most cases). Also, part of the reason why it is not easy is because phenix.real_space_refine combined gradient-based minimization with local grid searches (side chain rotamer fitting). Pavel On 10/20/23 00:29, Robert Oeffner wrote:

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:

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Hi Rob,

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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