Residue IE Score (max +500)
Monitors that all PHE, TYR, and TRP residues are scoring well.
SS Design (max +250)
Penalizes all CYS residues. Penalizes GLY, ALA, SER, THR in helices. Penalizes GLY, ALA in sheets.
Residue Count (max +275)
Penalizes extra residues inserted beyond 110, at a cost of 55 points per residue. Players may use up to 115 residues in total.
If you look at the objectives when you first start, you'll see that there are two extra segments over the limit of 110. This will deduct 110 points from your score from the beginning. You can delete these two should you desire to.
These are located on the target, and a frozen so you can't change them, but they do not detract from your score.