How to shrink oversized InnoDB ibdata1 file?
Connect to the server via SSH
Create backup of all databases:
# plesk db dump --all-databases >> all_databases_back.sql
Remove the ibdata1 file:
# rm -f /var/lib/mysql/ibdata1
# service mysqld restart
This is the only way as InnoDB ibdata1 never shrinks after data is removed.
For detailed instruction please refer the article: https://dev.mysql.com/doc/refman/5.7/en/innodb-resize-system-tablespace.html