Hi Ashok, a usual suggestion here: first, try latest version of Phenix (1.20-4444) found here: https://phenix-online.org/download/nightly_builds.cgi to check if the problem still exists. Please get back to us if it does and we will investigate further. Pavel On 12/15/21 07:44, Ashok Nayak wrote:

Hi, Is there a way to say keep_origin=False in phenix real space refinement. I used it in the command line version of v3958. It didn't take that.

There is a model shift after the refinement which I think is because the program brings the map to the origin and hence the refined model as well.

Thanks, Ashok