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In /etc/my.cnf under [mysqld]
180827 21:43:14 InnoDB: 5.5.59 started; log sequence number 1589339
180827 21:43:14 [ERROR] /usr/libexec/mysqld: unknown variable 'db_file_format=Ba........
ERROR 1146 (42S02): Table ‘mysql.servers’ doesn’t exist
This happened to me on a system running Centos with the REMI repo and a new version of Mysql 5 (which the official Centos/RHEL does not support on version 5).
The solution is just to run this program "mysql_upgrade", after that flush privileges will work.