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 Design: Penalizes all CYS residues. Penalizes GLY, ALA, and PRO residues in helices and sheets.
Residue Count: Penalizes extra residues inserted beyond the 85 residue limit. Players may insert up to 10 extra residues.
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 get it. If we're given the freedom to insert residues, why are we being penalized? Wouldn't it make more sense to take away the ability to insert residues?
This is just something that I've been wondering for a long time. If this is the wrong place to say this, my deepest apologies.
Drum -- I might use this to tweak the length of helices, sheets or loops easily and adjust without redoing whole fold. Since I'm slow at hand folding, I might add somewhere and subtract elsewhere. Can leave an ideal loop in place if I manage to find one :)