mongoose: Sub document refs undefined, when not populating in 4.0.2

I am having a strange issue

var UserSchema = new Schema({
    application: { type: Schema.Types.ObjectId, ref: 'Application', required: true, index: true },
    name: { type: String, required: true, index: true },
  });

var User = mongoose.model('user', UserSchema)

User.findOne{ {_id: <id> }).exec(function(err, user) {
    console.log(user);
   //  { _id: <id>, name: <name> }  <-- application is missing even when explicitly set in db console
});

Any properties that are refs never get added to the document, if I remove the ‘ref’ statement, the objects load just fine. I am NOT trying to populate the sub-document in this instance, I just want the sub-document id.