The reason was very slow insert queries in InnoDB tables.
In order to save you some distress, for a possible solution, add following line to my.cnf and restart the mysql:
innodb_flush_log_at_trx_commit=0
innodb_flush_log_at_trx_commit=0
Example:
SSLEngine On
SSLProtocol TLSv1
SSLCertificateFile domain.crt
SSLCertificateKeyFile domain.key