Clear cache and restore factory settings

After you've installed the root binary, choose "+++++Go Back++++++" until you're back at the main menu. At this point, it would be a good idea to wipe the phone's caches and any data, which may give you problems during bootup. In the main menu, you'll want to choose "wipe cache partition" and "advanced" then "wipe davlik cache". At the main menu, choose "wipe data/factory reset". This will completely virginzie the phone.

Finally, choose "reboot system now". This should bring you up to the initial greeting screen. You should see the Android loading screen, and the prompts to set up your phone for the first time.

Congratulations! You now have a rooted Nexus, as you should. Once your newly rooted phone has booted up, you may be interested in other things, such as installing AdFree, or enabling LTE.