Being unable to change permissions as root on a built-in application or system file on OS X is indicative of System Integrity Protection, a new security feature added in 10.11, which
restricts the root account and limits the actions that the root user can perform on protected parts of OS X.
Protected parts include
/System and pre-installed applications, along with the traditional Unix tree.
Any item under a path listed in
/System/Library/Sandbox/rootless.conf, or with the
com.apple.rootless extended attribute listed by
xattr -l, is unmodifiable except by the users listed in the first column of that file, unless SIP has been disabled in recovery mode (which I would advise against, generally).
By nature, this protection includes the root user, and anyone with admin or
sudo rights. Only Apple-signed binaries can modify these files.
You can also see this popular reporting article on Ars Technica from when the feature was introduced for more details, including some more about how it works and what the purpose is.