I had this same problem, the solution was that I had not symlinked my siteconf file correctly. Try running vim /etc/nginx/sites-enabled/mysite.com—can you get to it? I was getting “Permission Denied.”
If not run:
rm /etc/nginx/sites-enabled/mysite.com
ln -s /etc/nginx/sites-available/mysite.com /etc/nginx/sites-enabled/mysite.com