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In the context of Calabi-Yau string models we explore the origin of characteristic pattern of quark-lepton masses and the CKM matrix. The discrete $R$-symmetry $Z_K \times Z_2$ is introduced and the $Z_2$ is assigned to the $R$-parity. The gauge symmetry at the string scale, $SU(6) \times SU(2)_R$, is broken into the standard model gauge group at a very large intermediate energy scale. At energies below the intermediate scale down-type quarks and also leptons are mixed with unobserved heavydoi:10.1143/ptp.96.1249 fatcat:7gvq4n2a2fbtzle6iuyrjqqerm