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This bug has been copied from bug #1493531 and has been proposed to be backported to 7.4 z-stream (EUS).

Fixed upstream
ipa-4-5:
https://pagure.io/freeipa/c/c79cdccfa2361f013fb51e8225b4630abab8b557
ipa-4-6:
https://pagure.io/freeipa/c/f8e6c997b54564533250e536fbe250f460035235
master:
https://pagure.io/freeipa/c/7a3da27816f62240cebbac72de5c98a96ace0794

verified on ipa-server-4.5.0-22.el7_4.x86_64

...
 [1/1]: installing X509 Certificate for PKINIT
Full PKINIT configuration did not succeed
The setup will only install bits essential to the server functionality
You can enable PKINIT after the setup completed using 'ipa-pkinit-manage'
Done configuring Kerberos KDC (krb5kdc).
Applying LDAP updates
Upgrading IPA:. Estimated time: 1 minute 30 seconds
  [1/9]: stopping directory server
...

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory, and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

https://access.redhat.com/errata/RHBA-2017:3319