Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.
Core Existence: Ensures that at least 30% 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, and PRO residues in helices and sheets.
Residue Count: Penalizes extra residues inserted beyond the 75 residue limit. Players may insert up to 10 extra residues.
Without the ideal loop filter how are we supposed to know if a loop is ideal or not? Normally I'd use the "show" checkbox on the filter. Seems to me you should keep the filter without giving a penalty or bonus.
That or add something to remix that indicates whether or not the loop in question is ideal.
This is why remix is practically useless for non-design puzzles.
We don't expect you to make Ideal Loops! We want to see what players can come up with if they are not restricted by the Ideal Loops Filter.
The Ideal Loop Filter has resulted in some very promising designs with much better backbones, but we don't know if it is necessary. It could be that Foldit players can find high-scoring, stable designs without it—especially now that Rebuild is disabled.