The Build Mutants protocol uses MODELER to mutate one or more residues in a protein structure to user-specified amino acid types, and it will optimize the conformation of both the mutated residues and any surrounding residues that are within a user-specified Cut Radius parameter in the protocol.

If a residue is mutated to another residue with similar size, set Cut Radius = 0 to optimize this residue only.
If the mutated residue is much smaller or larger than the starting residue, it's recommended to use a small Cut Radius (4.5 Å) to optimize the neighboring residues.