Aug 21 01:46:01 Omega ntpd[348]: frequency error -508 PPM exceeds tolerance 500 PPM

The real question is whether the clock is consistently that slow
(actually fast - I think that's the correction rate), or badly behaved.


I would suggest upping the limit and letting it stabilize.  Then do
'ntpdc -c loopinfo' once a minute and graph the frequency results.
Also, what do the jitter and offset columns say?