1.) 3 stacks max. , 2 better

penalize if more than 3 stacks

2.) half of sequence in invariant when folding between states

penalize if entire sequence is folding

strong penalty if is 3 dimensional (it looks like twists and turns during folding)

3.) molecule is partially free in state 1.

minor penalty if molecule is completely bound in state 1

4.) few kinks in both states

penalize if stack not nicely straight (1-1 mismatches ok,1 or 2)

the more stacks are jagged, more the penalty

penalize if more than 3 stacks

2.) half of sequence in invariant when folding between states

penalize if entire sequence is folding

strong penalty if is 3 dimensional (it looks like twists and turns during folding)

3.) molecule is partially free in state 1.

minor penalty if molecule is completely bound in state 1

4.) few kinks in both states

penalize if stack not nicely straight (1-1 mismatches ok,1 or 2)

the more stacks are jagged, more the penalty