this tutorial works perfectly well for me only by changing all exposed hydrophobic in hydrophilic (even the one hidden, you have to rotate te view) and using mutate all. Warning : you have to wait that lutate all have finished its job.
Win 7.
Can you precise your OS ?

Windows 7 x64. My hardware is superior and is not the issue. software clash, maybe. I understand the need to rotate the view and whatnot. This sort of thing isn't new to me, I have been doing 3D modeling digitally for thirteen years as a hobby. I have done plenty of mutating, and let it finish. It persistently stuck at 3 points shy. I have a history finding hard-to-diagnose, hard-to-fix glitches, including in programs that many people claimed didn't have these bugs (Borderlands 2, most recently). This one may be a little hard to track down. Sorry if that's the case, but I'm positive it's a bug, if pulling isn't intended.

It has been pointed out to me that my reply appears far more caustic than intended. I do not often think in terms of the tone conveyed or how it would be perceived. I apologize for any offense I may have caused. That was very much not my intention.

Tested this puzzle 5 times with different AAs before using Mass Mutate. The first time I got exactly the required score of 8745 and then four times in a row 8747.
Latest DevPrev on Win7-64

Sounds like something wrong on my end, then. That's a little unusual, with the regular maintenance I do on my system, but I'm willing to accept it as an artifact of my system, I suppose.

What were the amino acids it mutated to when you were 3 points shy?

AEKLLKEFANKH

It looks like it does get into a local maximum there with mass mutate. Thanks for catching that!

Thank you for checking into it! :-) I was starting to think I was crazy or doing something wrong.