Hi Oleg,
I have a question. What does trigger Global real-space refinement ? I never seen it before except one structure I am currently working on. Also I do not see any options that switch on/off "Global real-space refinement " Please advise
it is a bit in flux at the minute as I keep changing underlying code and decision making strategies; the snapshots of these changes get into nightly builds and so one may observe some incoherent behavior from version to version. As you observe it is enabled by default but it does not always run. It runs if certain conditions on current model and data quality are met; also, if a run deemed unsuccessful phenix.refine will revert the result. At present these conditions are hard-wired in the code and you cannot alter them. This is going to change in next days (realistically weeks). If you want to refine against the map you can use phenix.real_space_refine that offers a broad array of options that are specific to map-model fitting, as documented here: https://www.phenix-online.org/documentation/reference/real_space_refine.html https://www.phenix-online.org/presentations/real_space_refine.pdf Pavel