Mysql server are very slow

Hi everybody. Please help me with issue.
My main problem is that mysql are very slow. When i try create products in my CMS, it take mutch time. Example - create product take 4 min, delete product - 12 min.

I use CMS Magento 2.2 CE (community edition). Also there is 145 000 of products. Before we add products all was fine. Create product take about 5 sec, delete product about 5-10 sec.

Here is my system

Ubuntu 14 x64, Linux kernel 3.13, 16 cpu, SSD, 48 GB RAM
Percona MySQL - 5.6 - here is config - https://pastebin.com/TVu1Ed7c
Varnish server 4.1
PHP 7.0.22
Nginx 1.12
Redis Server 4.0.2

I try run some profiling tests of magento and mysql
Here is slow log results - https://pastebin.com/kbFw0F28
Here is example of mysql request that are very slow - https://pastebin.com/mi656h2h

When i run mysqltuner.pl it show me that everything is OK.
Also if there is 60 real users on my site i see mysql process takes very highload cpu. As example i have site on same CMS with 100 products and lower server< and it take about 500 users and feels ok.

So help me please with this issue. Thank you.