Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.
Core Existence: Ensures that at least 10% of the residues are buried in the core of your design.
Fragment Score: Scans for parts of your design that are unlikely to fold up naturally. Use Rebuild and Remix tools to fix these regions of your design!
Disulfide Filter: Yields a bonus of up to 1000 points for 2 or 3 disulfide bonds. More than 3 disulfides will incur penalties.