The primary optimization tool is gradient descent minimization within the Rosetta energy function ('wiggle'). To help correct for unfavorable geometries, which can occur from large chemical identity shifts, small molecule design puzzles use a 'dual space' minimization which alternates between both Cartesian and internal coordinate degrees of freedom . Ideal geometries for ligands are enforced by the 'cart_bonded' geometric deviation penalty , with ideal geometries derived from the Merck Molecular Force Field (MMFF) values .