Slow UPDATE queries after migrate to new server - php

Question

I have moved my website to new faster dedicated server (64GB RAM, CPU 4c/8t 3.7GHz in OVH). The problem is that now my site works even slower, not faster.
I figured out that this is because of slow UPDATE queries to my mysql. I have read many topics, tried many configurations without any luck. Mysql config is almost default so I don't understand why it is not working. This is not overload because I turned off website and make test from phpmyadmin - same results.
So I have this query in phpmyadmin and execute this few times on both server. Tables (InnoDB) and data are exactly the same.
UPDATE `user` SET `last_date` = "2017-02-05 03:40:50" WHERE `id`=3;
Times on new server:
0.0553 s
0.0265 s
0.0229 s
0.0369 s
0.1579 s <---
0.0191 s
Times on old server:
0.0024 s
0.0042 s
0.0015 s
0.0015 s
0.0015 s
0.0012 s
New server software: Debian 8, Mysql 5.5.31, Apache 2.2.16, PHP 7.1
Old server software: Debian 6, Mysql 5.5.31, Apache 2.2.16, PHP 5.3
I've tried copy entire my.cnf from old to new but results are the same. So why the same config works great on old system, but not on new fresh one?
New server my.cnf
port = 3306
socket = /var/run/mysqld/mysqld.sock
socket = /var/run/mysqld/mysqld.sock
nice = 0
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
skip-external-locking
bind-address = 127.0.0.1
key_buffer = 16M
max_allowed_packet = 16M
thread_stack = 192K
thread_cache_size = 8
myisam-recover = BACKUP
query_cache_limit = 1M
query_cache_size = 0
general_log_file = /var/log/mysql/mysql.log
general_log = 0
slow_query_log_file = /var/log/mysql/mysql-slow.log
slow_query_log = 1
long_query_time = 2
expire_logs_days = 10
max_binlog_size = 100M
innodb_buffer_pool_size = 16G
max_connections = 2048
skip_name_resolve = 1
quick
quote-names
max_allowed_packet = 16M
key_buffer = 16M
Old server my.cnf
port = 3306
socket = /var/run/mysqld/mysqld.sock
socket = /var/run/mysqld/mysqld.sock
nice = 0
user = mysql
pid-file = /var/run/mysqld/mysqld.pid
socket = /var/run/mysqld/mysqld.sock
port = 3306
basedir = /usr
datadir = /var/lib/mysql
tmpdir = /dev/shm
bind-address = 0.0.0.0
key_buffer = 128M
max_allowed_packet = 40M
thread_stack = 192K
thread_cache_size = 8
myisam-recover = BACKUP
max_connections = 1000
table_cache = 4096
thread_concurrency = 10
max_heap_table_size = 48M
tmp_table_size = 48M
general_log_file = /var/log/mysql/mysql.log
general_log = 1
slow_query_log = 1
slow_query_log_file = /var/log/mysql/mysql-slow.log
long_query_time = 2
expire_logs_days = 10
max_binlog_size = 100M
innodb_buffer_pool_size = 4500M
quick
quote-names
max_allowed_packet = 16M
key_buffer = 16M
Why is this happening?
Edit:
I have tried also:
Make query directly from mysql terminal.
Restart apache after my.cnf change.
PHP 5.