Hi Nikos, what you describe is not expected and should not happen. This must be a bug or undesired behavior. Can you please send me the map and model, along with .eff and .log files (off list). I will investigate once I have files. Thanks! Pavel On 2/23/24 01:27, Nikos Pinotsis wrote:

Hi,

I am using real space refine with the latest phenix 1.21-5207 for fitting a model into a cryoEM map. During refiment one Trp goes clearly out of density (vertical to the density) although the map is very well defined at this part of the protein. I tried local_grid_search either for every cycle or last, however it didn't fix the problem. I know that this is reported a couple of years ago as fixed (dev-4218), I am wondering if something changed during the last version.

Another solution I can think it to keep the side chain of this Trp fixed. How can I do that?

thanks Nikos