Object returned from findOne is not a plain object but Mongoose document. You should use {lean:true}
option or .toObject()
method to convert it into plain JavaScript object.
mongoose.model('calculations').findOne({calcId:req.params.calcId}, function(err,calculation){
if(err) handleErr(err, res, 'Something went wrong when trying to find calculation by id');
var plainCalculation = calculation.toObject();
delete plainCalculation._id;
console.log(plainCalculation); //no _id here
});