Note that in your dayfile you got the message:
Mar 11 18:53:39 gate ntpd[28986]: refclock_atom: time_pps_kcbind failed:
Operation not supported
you want to remove whatever it is in your configuration deck that tries to
do the kcbind,- this is a kernel option not supported by linux-PPS
--
Reg.Clemens
reg at dwf.com