P-score represents minus logarithm of the P-value. P-value measures the probability of achieving the same or better quality of match at a chance, i.e. at random picking the structures from the database. "Quality of match" is a complex characteristics, which accounts for RMSD, number of aligned residues Nalgn, number of gaps Ngaps, number of matched Secondary Structure Elements and the SSE match score. The higher P-score (the lower P-value), the more surprising, or statistically significant, is the match.

P-score has been calibrated on the non-redundant database containing all SCOP folds (about 700 structures). This means that P-scores lower than 3 indicate statistically insignificant matches. Keep in mind, though, the approximate nature of the estimate.