Долгий отклик сервера (Ubuntu+Apache+Nginx+Mysql+PHP)

Столкнулся с проблемой - сервер выдачу делает 4,5 секунды... в логах всё чисто. Не могу понять, где копаться. На фронте выключили все примочки по вордпрессу. Мэмкэш включен и настроен с запасом. Конфиг мускула

[client]
port=3306
socket=/var/run/mysqld/mysqld.sock
[mysqld_safe]
socket=/var/run/mysqld/mysqld.sock
[mysqld]
user=mysql
pid-file=/var/run/mysqld/mysqld.pid
socket=/var/run/mysqld/mysqld.sock
port=3306
basedir=/usr
datadir=/var/lib/mysql
tmpdir=/tmp
lc-messages-dir=/usr/share/mysql
log_error=/var/log/mysql/error.log
# MyISAM #
myisam-recover-options         = FORCE,BACKUP
default-storage-engine         = InnoDB
skip-name-resolve
sql-mode                       =         STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_AUTO_VALUE_ON_ZERO,NO_ENGINE_SUBSTITUTION,NO_ZERO_DATE,NO_ZERO_IN_DATE,ONLY_FULL_GROUP_BY
sysdate-is-now                 = 1
innodb                         = FORCE
innodb-flush-method            = O_DIRECT
innodb-log-files-in-group      = 2
log-queries-not-using-indexes  = 1
slow-query-log                 = 5
slow-query-log-file            = /var/lib/mysql/mysql-slow.log
symbolic-links = 0
skip-external-locking
key_buffer_size = 256M
tmp_table_size         = 128M
max_heap_table_size    = 128M
sort_buffer_size = 1M
read_buffer_size = 1M
read_rnd_buffer_size = 4M
myisam_sort_buffer_size = 64M
thread_cache_size = 16M
query_cache_limit   = 32M
query_cache_type = 0
innodb_flush_log_at_trx_commit = 1
max_allowed_packet = 64M
innodb_buffer_pool_instances = 1
table_open_cache = 400M
query_cache_size  = 64M
open-files-limit               = 65535
table-definition-cache         = 4096
table-open-cache               = 4096
net_read_timeout = 200
net_write_timeout = 200
innodb_file_per_table =1
innodb_buffer_pool_size = 1G
innodb_log_file_size = 512M
innodb_buffer_pool_instances   = 2
max_connections = 10000
max_user_connections = 200
wait_timeout = 28800
interactive_timeout = 28800
!includedir /etc/mysql/conf.d/