_my_ip_ - - [03/Jul/2016:21:49:38 +0300] "GET /.well-known/acme-challenge/letsencrypt_1467571776 HTTP/1.1" 200 0 "-" "curl/7.49.1"
66.133.109.36 - - [03/Jul/2016:21:49:40 +0300] "GET /.well-known/acme-challenge/MWZg0FbUF5hWltZluIIBaRL8fmjmkzVRCOtjy2kx3VY HTTP/1.1" 200 108 "-" "Mozilla/5.0 (compatible; Let's Encrypt validation server; +https://www.letsencrypt.org)"{
  "type": "http-01",
  "status": "invalid",
  "error": {
    "type": "urn:acme:error:connection",
    "detail": "Could not connect to http://_my_domain_/.well-known/acme-challenge/4wH8ExUFaU6WSvCV9HsTvAfk-qP5JlTDQKlCj_A-JYk",
    "status": 400
  },
  "uri": "https://acme-v01.api.letsencrypt.org/acme/challenge/nRVGtmUnZ7CZLVR77kKJ6GpX9cpb_S2nGvIwbP7G-lA/156923365",
  "token": "4wH8ExUFaU6WSvCV9HsTvAfk-qP5JlTDQKlCj_A-JYk",
  "keyAuthorization": "4wH8ExUFaU6WSvCV9HsTvAfk-qP5JlTDQKlCj_A-JYk.Mmh2-LDwRdCnyW40RPuE3Be8JnxdX2ruzpShBFjyNxA",
  "validationRecord": [
    {
      "url": "http://_my_domain_/.well-known/acme-challenge/4wH8ExUFaU6WSvCV9HsTvAfk-qP5JlTDQKlCj_A-JYk",
      "hostname": "_my_domain_",
      "port": "80",
      "addressesResolved": [
        "_ip_server_"
      ],
      "addressUsed": "_ip_server_"
    }
  ]
}# include /etc/nginx/nginx-modsecurity-enable.conf
What error do you have? Just renewed existing certs on a server with nginx+apache without an issue.
Setting up certificate for a hostname: server1.example.com
Getting challenge for server1.example.com from acme-server...
Waiting for domain verification...
Challenge is invalid. Details: Could not connect to server1.example.com. Exiting..