Congratulations! Your certificate and chain have been saved at
/etc/letsencrypt/live/www.antilopagold.su/fullchain.pem. Your cert
will expire on 2016-11-01. To obtain a new or tweaked version of
this certificate in the future, simply run certbot-auto again. To
non-interactively renew all of your certificates, run
"certbot-auto renew"
The certonly command only gives you a certificate. Installing that certificate in your web server is up to you.
Mozilla’s SSL Configuration Generator is usually a good starting point. You mentioned that you’re using both nginx and apache - I assume nginx is acting as a reverse proxy, in which case you’ll need to install the certificate on nginx (apache can remain as is).
You may need to reload or cycle nginx. First try running:
sudo ./nginx -s reload
in my nginx.conf I have:
server {
…
ssl_certificate /etc/letsencrypt/live/site.com/fullchain.pem;
ssl_certificate_key /etc/letsencrypt/live/site.com/privkey.pem;
Check that you have the new certs in nginx.conf and then of course reload.
so I need to change pathes to
ssl_certificate /etc/letsencrypt/live/www.antilopagold.su/cert.pem
ssl_certificate_key /etc/letsencrypt/live/www.antilopagold.su/privkey.pem
Almost - ssl_certificate should point to the fullchain.pem file (in the same directory as cert.pem). It’s a combination of cert.pem and chain.pem (the intermediate/issuer certificate, without this you might get warnings with some clients).
The path for ssl_certificate_key is correct. You might want to look into some of the other config directives suggested by Mozilla’s SSL Configuration Generator, but what you have there should give you a basic working configuration.