Pscore represents minus logarithm of the Pvalue. Pvalue 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 N_{algn}, number of gaps N_{gaps}, number of matched Secondary Structure Elements and the SSE match score. The higher Pscore (the lower Pvalue), the more surprising, or statistically significant, is the match. Pscore has been calibrated on the nonredundant database containing all SCOP folds (about 700 structures). This means that Pscores lower than 3 indicate statistically insignificant matches. Keep in mind, though, the approximate nature of the estimate.
