Following this how-to https://wiki.samba.org/index.php/Samba4/HOWTO/Join_a_domain_as_a_DC while joinning samba 4.0.9 to an existing windows 2003 AD,
it says in the how-to to run :
# bin/samba-tool domain join samdom.example.com DC -Uadministrator --realm=samdom.example.com
but its not working run
Run this one instead :
# bin/samba-tool domain join samdom.example.com DC -Uadministrator
the wiki page seems to be updated accordingly already. Apart of that you should have in mind that joining a Windows AD with Samba as additional DC is officially not supported.