[phenixbb] leave residue inside its electron density when neighbor is too close

[Murpholino Peligro]

What is the recommended approach to tell phenix.refine to leave the residue
inside its electron density? (crystal neighbors)
The green model is the input to phenix.refine, the maps and the yellow
model are the output of phenix.refine. As you can see, phenix.refine will
move the residue outside the density (to avoid clashes I guess?) I have
tried setting the occupancy of OXT to 0.5, but it is not good. (you can see
there is a water in a special position, just above the bad residue) Any
more ideas?
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