Z-score measures the statistical significance of a match in terms of Gaussian statistics. If quality of match may be considered a random value at random picking the structures from sufficiently large database, it should obey the Gaussian distribution, with probability that same-or-better quality match may be found expressed as P = erfc(Z/2). If two structures may be matched uniquely to each other, then P equals to P-value.

The higher Z-score, the higher is statistical significance of the match.