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 65 residue limit. Players may insert up to 10 extra residues.

The filter is intended to give players the flexibility to temporarily add residues to a design-in-progress.

How would temporarily adding residues be beneficial? Just curious.

make what was a sheet into a helix, switch another helix to sheet. can add to one, subtract from other without redoing whole fold. good for those of us with poor layout skills :D

Compared performance on several recipes.
The performance penalty varies between 10 and 20 percent.
I can not find real difference between the different tools wiggle, shake, mutate and rebuild, it looks like all tools are somehow effected.