Why do you get zeros? For the mean, that is expected. If it happens for the standard deviations, there is something wrong/odd.
To compare model variables in percentage deviations to the data, you need to obtain empirical data in percentage deviations from a trend. The easiest way is using the theoretical HP filter on the loglinearized model variables and comparing them to HP-filtered logged empircal data (see Pfeifer(2013): “A Guide to Specifying Observation Equations for the Estimation of DSGE Models”) for more details.