The requirement sounds extremely suspect: every atom in the structure
contributes to every reflection, so refining "only some atoms" makes as
little mathematical sense as refining against "only a subset of
reflections".
I agree with you that the requirement sounds dubious.
But the specific argument you make is not quite right.
Two common counter-examples are real-space refinement and rigid-body
placement of a known fragment relative to an existing partial model.
Not so: they're tricks to get out of local minima and maybe improve
phases, but they're /not/ useful for generating the model that "best"
fits the data, and would be useful for interpretation. Or would one
deposit a model for which real-space refinement has been the final step?
phx
