The message does not always indicate an error. Often it is generated because JES, regardless of JES2 or JES3, has not fully come up yet. Review the OPSLOG to ensure that there are no other error messages and that JES does come up within a few seconds. If either of those are not true, open a support case if you need assistance to troubleshoot, and provide the archived OPSLOG for review.
OPS0053E js initialization not complete-
The product checked the current status of the job entry subsystem during
product initialization. The job entry subsystem was either not found or
was still initializing.
This may or may not be an error message. Verify that the reported JES
status is in fact correct. If the actual JES status did not match the
JES status reported by the product, check for any other error messages.
If possible, fix the problem identified by the error messages and
restart the product. If the problem cannot be resolved, contact CA
Customer Support to obtain additional assistance.