"More than 2,000 of the 30,490 emails Clinton turned over to the State Department contained classified information, including 110 emails in 52 email chains that contained classified information at the time they were sent or received. (Most emails were retroactively deemed to contain classified information by the U.S. agencies from which the information originated."
Source: Paragraph 12 of this document.
Note also she decommissioned the server after it was allegedly hacked by the Romanian "Guccifer" (who among others, Putin ended up with them)
He basically argued that he couldn't prove intent (which is not required for gross negligence) while giving information that indicated intent.