I can not explain my disk usage
First of all, empty your trash, reboot &amp; try out disk utility again if you haven't already. If that doesn't do it though you'll have to dig a bit more.

Here's the terminal command for finding hidden files &amp; folders: defaults write com.apple.finder AppleShowAllFiles YES. Put sudo in front of that if it doesn't work - you'll have to enter your user password in this case. Once you've done this restart finder by clicking the apple icon in the menu bar and heading into 'Force Quit...'.

Now if you open Finder, select 'Go' &amp; 'Computer' from the menu bar, go into the drive in question. I would put this into 'list' view and make sure that the size option is on. For any folders that aren't showing their size, highlight them (hold command + click to select multiple) and then hit command + i to pull up the Get Info menu for them. You'll see that under the size field they're 'Calculating Size'. Just keep those windows up &amp; wait for them to finish - for the sizes you're dealing with this could take potentially hours. Add them up again &amp; see if the size is accounted for.

If there's still 500gb or so missing I would recommend to backup &amp; reinstall OS X. You can select only exactly what you want to using Time Machine, see the size before you even finish backing up, and then restore.