After entering
shutdown now
in terminal I get everything running normally and then:
All processes ended withing 2 seconds...done
INIT: Going single user
INIT: Sending processes the TERM signal
INIT: Sending processes the KILL signal
Give root password for maintenance(or....
I press Ctrl + D, and it shows me login screen Debian. Shutdown through GUI works properly.
UPDATE 1
It seems some process hangs.
Moreover, I've managed to power off the server through several retries. Recently I've installed only ntp and ntpdate, nothing more.
I suppose it might be it conflicting with iptables.