On 22 May 2021, at 00:28, Pavel Afonine wrote:

Hi Florian,

you can't exclude selected atoms from refinement in phenix.real_space_refine. I might be able to suggest a workaround if you explain why you want to not refined particular atoms.

Hi Pavel, The residue is on a symmetry axis and moves into the density of a residue from a symmetry mate during real space refinement. But that’s all right, at the last step of my refinement strategy, I switch off real space refinement and keep reciprocal space refinement and it works just fine. Florian