Because today 2013-11-14Thu, it’s 2 years after your bug and no other people are complaining about the pycharm, now 3.0, problem, I believe it is actually probably a Mac OSX issue. Numerous programs on my brand new 10.8.5 machine run way way over 100%. Pycharm updating skeletons was just taking 330% and making my fan spin crazily.
From lots of previous googling I found a little script that can temporarily fix the problem;
http://www.willnolan.com/cputhrottle/cputhrottle.html
Run it as so;
sudo CpuThrottle xxx 25
where xxx = your process ID per Activity Monitor, and 25 = whatever %cpu you wish to limit it to. Upon clicking return, it will only last as long as one does not click ctrl-c. I read on the mac boards about a bug in the code where it would seek to use all available resources in looking for system updates, the same as this thing is doing. So I guess, alas we have to live with it. At least we have the little tool. Sigh.