Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.
Core Existence: Ensures that at least 25% of the residues are buried in the core of your design.
Secondary Structure: Checks that no more than 50% of residues are in helices; penalties are incurred if more than 50% of residues form helices.
Secondary Structure 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 95. Players may use up to 120 residues in total.
Ideal Loops: Penalizes loops that do not conform to preferred ABEGO patterns. Use Auto Structures to see which residues count as "loops."
I had hoped this larger protein would allow a Rossmann 2 by 2 fold. It did not ever get to ideal loops with either 6 segment sheets, as in the Koga & Koga paper or 8 segment sheets. I have submitted both to scientists. I think it proves our "ideal loop" library is too small