Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.
SS Design: Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA, SER, THR in helices.
Residue Count: Penalizes extra residues inserted beyond the starting 75, at a cost of 32 points per residue. Players may use up to 90 residues in total.