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.
Ideal Loops: Penalizes loops that do not conform to preferred ABEGO patterns. Use Auto Structures to see which residues count as "loops."
I got a really strange thing.
After creating a nice fold with blueprint , wiggling and mutating residues I wiggled the whole structure in the very end, but instead of increasing the score it goes from 9822 points (including 810 bonus points) down into the 7000s and the beta-strands disassemble again.
I tried almost everything, but it always ends in this strange behavior. Also the Rama map looks perfect before wiggling...
Before you wiggle that last time, try removing the constraints that are left behind by the blueprint tool. Open blueprint, and drag the rectangles off the sequence of letters. Then try the wiggle.
You were right, there were still some squares left over the sequence.
Removing them helped a lot ;)