Had that exact same problem on Ubuntu 15.10.
The File /etc/apparmor.d/usr.sbin.ntpd contains the following line:
# samba4 ntp signing socket
/{,var/}run/samba/ntp_signd/socket rw,
But the line should be
/var/lib/samba/ntp_signd/socket rw,
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https://bugs.launchpad.net/bugs/930266
Title:
Add samba4 ntp signing socket to ntpd apparmor profile
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