Do you mean that you login as USER? If yes,
by default, PHP settings are not shown on the User level. You need to log in to ISPmanager as root and allow the user to view and manage those settings (PHP--> select a PHP version --> click "Settings", and activate them
http://prntscr.com/euhrnv).
You can also drill down to the User level -->PHP --> Settings --> Filter --> Show hidden --> Yes (
http://prntscr.com/euhss9 and
http://prntscr.com/euhslr)