Core Existence: Monomer (max +2500)
Ensures that at least 25 residues are buried in the core of the monomer unit. The threshold of "buriedness" between core and surface residues is more stringent than usual, so residues may have to be "extra buried" to be counted toward the core.
Core Existence: Complex (max +3000)
Ensures that at least 60 residues are buried in the core of the entire complex (including the interface between monomer units).
Rewards networks that comprise at least three hydrogen bonds involving core residues. Networks must be at least 70% satisfied (i.e. 70% of all oxygens and polar hydrogens in a network must make a hydrogen bond).
SS Design (max +500)
Prohibits all CYS residues. Prohibits GLY, ALA residues in sheets and helices.
Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.
Scoring engine is treating my entire symmetric chain as a non-ideal loop! That does not seem right!?
You're right, that definitely shouldn't happen. Can you share this solution with scientists, and I'll take a closer look?