Interaction Energy: Monitors that all PHE, TYR, and TRP residues are scoring well.
SS Design: Prohibits all CYS residues. Prohibits GLY, ALA residues in sheets. Prohibits GLY, ALA, SER, THR in helices.
Residue Count: Normalizes for extra residues inserted beyond the starting 95, at a cost of 32 points per residue. Players may use up to 120 residues in total.
The Residue Count filter doesn't seem to be making a deduction, even with the maximum of 25 additional residues.
Sorry if this wasn't clear in the puzzle description!
The Residue Count objective should not give any penalties in this puzzle. With the starting count of 95 residues, the objective should give a bonus of +800 points. With the maximum addition of 25 residues, the objective should give no bonus (zero points).