Residue IE Score (max +500)
Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence (max +1000)
Ensures that at least 25% of residues are buried in the core of the protein.

SS Design (max +500)
Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA, SER, THR in helices.

Residue Count (max +550)
Penalizes extra residues inserted beyond the starting 66, at a cost of 55 points per residue. Players may use up to 76 residues in total.

The fixed 4Fe-4S loop CISCGAC matches PDB 1FDN, 1FCA, and 2FDN (RCSB PDB motif search). All of these structures show the protein uniprot:P00198. This protein binds two clusters, one with the CISCGAC loop and the other with a CIDCGAC loop. A fourth cystine residue comes from outside the loops to stablize the complex, but this is not scored for in this puzzle.