When ntpd is configured to have a stratum-0 refclock and ntpstats logging is
on, it will create clockstat files.  The apparmor profile does not allow this
to happen, which seems to lead to strange delays of approximately 1 minute when
shutting down ntpd.  Adding

 /var/log/ntpstats/clockstats* lrw,

in the appropriate place in the usr.sbin.ntpd apparmor profile fixed both
issues for me.  In addition, since the location and name of the log file and
statistics directory is in fact configurable from ntp.conf, it seems prudent to
add a hint there that any changes there need to be accompanied by edits to the
apparmor profile.