[warn] Init: SSL server IP/port conflict: www.domain.com:443

If you get this warning in your apache logs, don't worry, it's perfectly normal.

[warn] RSA server certificate CommonName (CN) `localhost' does NOT match server name!?
[warn] Init: SSL server IP/port conflict: www.domain.com:443
[warn] Init: You should not use name-based virtual hosts in conjunction with SSL!!

The reason it's there is because DA uses name based hosting.  What that means is you'll have many domains on one IP.  The warning comes up because of the fact that only 1 ssl certificate is valid per IP address.  An explanation on that can be found from the link below.

Note that these are just warnings, not errors.

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Similar errors for nginx:

nginx: [warn] conflicting server name "www.domain1.com" on 1.2.3.4:80, ignored
nginx: [warn] conflicting server name "www.domain2.com" on 1.2.3.4:80, ignored