This puzzle starts out with a lot of clashes. Clashes tend to push the protein apart, breaking hydrogen bonds, opening up voids, and causing hydrophobic segments to become exposed. All these things are Bad.
In this puzzle, the "Clashing Importance" slider is now available on the Behavior menu. A lower clashing importance means clashes won't push the protein apart as much during wiggle and other operations. Clashing importance is often called CI.
Set the clashing importance slider to a low value. The puzzle suggests a very low value 0.01. The exact value is not important, anything at 0.1 or below is good enough. Start a wiggle. The protein still pulls apart, but it should start to come together again.
Once the score stabilizes (maybe fluctuating within a narrow range), start to raise the clashing importance by moving the slider or using the arrow to the right of the slider.
In addition to the score, keep an eye on the clock and the counter in the upper left. At some point, the counter may start to spin, counting up rapidly while the protein isn't changing much. That when it's time to raise the CI again. If you're at CI 1.0, it's time to stop the wiggle.
When the counter seems stuck, you'll probably see the protein moving around a little, and hopefully the score is trending upward. Leave the CI alone until the counter starts spinning.
If you don't finish the puzzle on one wiggle, make sure you had CI 1.0 at the end. Then try shaking. Wiggle again if needed.