The servers are run with screen sessions, so the stop cron entries just kill the screen session; I guess that may not be the nicest way to do it, but it's also not a common thing that people would be in the server at that time
The screen session is killed at 3:59, and the new one is started at 4. I should probably add a restart one that will shutdown and restart the server all in one go instead of having to wait the 60 seconds.