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Why is the used disk usage above the limit set for a User?

If you're wondering why a User might be using more space than is assigned to him in his disk usage limit, there are a few reasons:

1) There is a soft limit and a hard limit.  The hard limit will be 1.1x the value you set in DA. This is to allow some grace if files are too big:

you can lower it to 1.0 if you want, to not have any room for temporary over-usage.

2) Also, not all files counted by DA are governed under the system quotas, eg:
- MySQL databases
- Files owned by apache
- Data for mailing lists
- etc..

since they're not chowned to the User, they won't be under the system quotas, so are not enforced by the system quotas, even though DA does count them.

3) If you want to suspend for overusage (not recommended)

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