I had to shut it down and restart. Couldn't get it to wake up.
It could be that the system started it's automatic maintenance routines around 3:00-5:00 AM.
If the maintenance routines haven't been run in a while, the process could have cause the freeze (really a system crash), by adding extra CPU demand during an already demanding process.
I would check your hard drive with Disk Utility (Verify/Repair disk). This is simply because a crash can leave directory files in a mess. You will need to boot to the OS X install disk to use the "Repair Disk" function.
Using Disk Warrior, if you have it, is better.
You should be able to run a process overnight, but just to be sure maintenance tasks don't interfere, use Terminal to run your maintenance scripts manually.
Open Terminal.
At the command line prompt type
sudo periodic daily weekly monthly and press Return.
Enter your admin password, and press Return.
The processes will be running, and will be done when the command line prompt reappears.
You can then load your project, and let it go.
It should all run without a problem.
FYI- more explanation on the maintenance scripts:
http://www.thexlab.com/faqs/maintscripts.html