Table 4.

The undertaker conformation-change operators that had the highest expected value for the change to the cost function (counting the change as 0 when the operator made the cost worse) for the last 300 generations of the optimization by undertaker for the SAM-T08 server on the server-only models. InsertAligment and InsertSpecificFragment are most useful earlier in the optimization, as they make very large changes to the conformation. They rarely improved the best model - most often they were successful when repairing a damaged model that was in the pool for the genetic optimization. CloseGap does a short fragment insertion immediately adjacent to a chain break. FixOmega adjusts the peptide bond to be 180 degrees and does a compensating adjustment to the adjacent phi or psi angle. OneRotamer replaces one side-chain with a side-chain from a PDB file, and TweakHbondSubtree changes the distance and direction of a hydrogen bond by a small amount.

Operator	avg improvement
InsertAlignment	0.0071242
InsertSpecificFragment	0.00385188
CloseGap	0.0033171
FixOmega	0.00286841
OneRotamer	0.00276826
TweakPeptide	0.00268681
BigBackrub	0.00261841
Backrub	0.00258232
HealPeptide	0.00199681
TweakHbondSubtree	0.00183261