The objective function used by MODELLER is a sum over all of the restraints. See Section A.3 for equations defining the restraints and their derivatives with respect to atomic positions. See Section 6.6 for commands for calculating the objective function and Section A.2 for optimization methods. See the original papers for the most detailed definition and description of the restraints [Š ali & Blundell, 1993,Š ali & Overington, 1994].