SEQRES: protein chain sequences, based on PDB SEQRES records
ATOM: protein chain sequences, based on PDB ATOM records
CHK: checkpoint file, the raw output generated at the end of each iteration of PSI-BLAST searches
FMTX: frequency matrix format, it describes the substitution rates of each residue in the query sequence for each of the 20 residue types
MTX: scoring matrix file, it contains the PSSM obtained by converting substitution rates into scoring matrices, by calculating log odds ratio and taking integer parts
