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By default, Coot uses a 5 atom (CA-1, C-1, O-1, N-2, CA-2) planar peptide restraints. These restraints should help in low resolution fitting (the main-chains becomes less distorted), reduce accidental cis-peptides and may help “clean up” Ramachandran plots.
(add-planar-peptide-restraints)
And similarly they can be removed:
(remove-planar-peptide-restraints)
There is also a GUI to add and remove these restraints in
Extensions -> Refine... -> Peptide Restraints...