The dictionary is used to identify the chiral atoms of each of the model's residues. A clickable list is created of atoms whose chiral volume in the model is of a different sign to that in the dictionary.
During refinement and regularization, Coot will pop-up dialogs warning about chiral volume errors - if you have them. This can be annoying 1. You can inhibit this dialog like this:
(set-show-chiral-volume-errors-dialog 0)
There are two obvious ways:
1) mutate and auto-fit rotamer (mutate it to the residue type that it is)
2) RS Refine the residue and invert the chiral centre by pulling an atom. Usually you can pull the CA to the other side of the plane made by the chiral neighbouring atoms (using ctrl left-click). Sometimes giving the CB a good old tweak is the easier way.
Inverting the CB of THR is easier, just move the OG so that the plane of the neighbours is on the other side of the CB (again with ctrl left-click).