woflux wrote:device properties shows 488 Gb are used
Let's take a step back; in which application exactly are you seeing this?
And the space set aside for administrative purposes is fixed; meaning it needs the same amount of space even with zero files or with a million files. That is how the ext4 filesystem works, upon creation a portion of the disk is set aside for administrative purposes. That said, 5% does sound a bit much perhaps--on my 240 GB hard disk it is closer to 2%.
Some applications say they display GB and TB, when in fact they are showing GiB or TiB, which is a different unit and would mean a different amount of bytes. http://en.wikipedia.org/wiki/Byte#Unit_symbol
1 GiB = 1.07 GB
1 TiB = 1.1 TB
So for example when a hard disk manufacturer states he has a 1 TB hard disk, most applications will show that as 0.91 TiB. That is the same amount of bytes, but with a different notation. It's quite a difference, and may also here be clouding the figures you are looking at.