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 70 residue limit. Players may insert up to 25 extra residues.
Ideal Loops: Penalizes loops that do not conform to preferred ABEGO patterns. Use Auto Structures to see which residues count as "loops."
Experiencing periods of frequent crashes (a few minutes apart, in swarms)and then periods of calm, with no apparent cause or pattern. Was suggested that I post my log file, but don't know the norm for doing such here. Post the full text of such here, or is there a way of attaching the file that I haven't found yet? Also, periods where hand folding just drags to a near standstill. Not anything hardware related that I can see, FoldIt's the only thing running. Windows 7, 32GB memory at 9-18%, i7 4770 CPU running about 19%.