You can use the npm module server-destroy. server-destroy keeps track of all connections and then closes them when destroy is called. Also, the destroy method takes a callback so you should pass your "done" function to your destroy method... Below is copied from the npm module description with the addition of a callback in the destroy call.
var enableDestroy = require('server-destroy');
var server = http.createServer(function(req, res) {
// do stuff, blah blah blah
});
server.listen(PORT);
// enhance with a 'destroy' function
enableDestroy(server);
// some time later...
server.destroy(done);
If open connections are not a problem you can simply pass the done function to the close function, server.close(done) as described in this post How to correctly unit test Express server