Phenix.real_space_refine keeps pushing a residue out of density so I'd like to restrain it to its current position. Can you please let me know how to implement in the GUI the first example at point 14 at https://phenix-online.org/documentation/reference/real_space_refine.html#usage-examples?

phenix.real_space_refine model.pdb map.mtz \
reference_coordinate_restraints.enabled=true \
reference_coordinate_restraints.selection="chain A and resseq 12:21" \
reference_coordinate_restraints.sigma=0.05

Luca

Luca Pellegrini, PhD