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looks like your server's bottle-neck is mysql database: 292.3% CPU
to verify this, you can put a phpinfo.php page under a slow site's document root, when you feel the site slow, access phpinfo.php, see if it's fast. this is because phpinfo.php has no access to database; if phpinfo.php is fast then problem is not at web server, most likely mysql database slow down the whole site.
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