How to repair Homebrew permissions after installing as root? I run brew as root, now it's defunct. No updates anymore. How to fix?

$ brew update &amp;&amp; brew upgrade
error: Unable to append to .git/logs/HEAD: Permission denied
error: Unable to append to .git/logs/refs/remotes/origin/master: Permission denied
Error: Failed to update tap: caskroom/cask

$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: Your XQuartz (2.7.4) is outdated
Please install XQuartz 2.7.7:
  https://xquartz.macosforge.org
Reset the permissions of /usr/local and Homebrew's caches to the current user:

sudo chown -R $USER:admin /usr/local /Library/Caches/Homebrew