Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Ensures that at least 40% 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 don't know about other people, but the 40% core filter makes the puzzles much less fun for me. I spend most of the week failing to meet it, and then maybe get lucky in one of my end game scripts - or not.

That's good to know!

We wanted to try out the more stringent threshold to see how it would affect player designs. However I think 40% is probably more stringent than necessary for good designs, so we can relax it in the future.