Through our chat here, we found that you have a repository that is not compatible with Xenial 16.04 . The actual repository shows that it stopped distros after 14.04 .

W: Failed to fetch ppa.launchpad.net/kilian/f.lux/ubuntu/dists/wily/main/… 404 Not Found W: Failed to fetch ppa.launchpad.net/kilian/f.lux/ubuntu/dists/wily/main/… 404 Not Found E: Some index files failed to download. They have been ignored, or old ones used instead.

The repositories that are giving you errors need to be disabled or removed from your system. The kilian/f.lux repositories need to be disabled.

The following locations are where the repositories are stored and can be disabled or removed from.

Screenshot from my system that will probably not match yours

Software & Updates in the Other Sofware tab

Unselect the repository that is giving you errors.

After the repository is unselected, re-run the sudo apt-get update then sudo apt-get autoremove to see if your problem has been fixed.

Hope this helps!