The magnetoresistance (MR) $Delta rho/rho$ of cage-glass compound Ho$_x$Lu$_{1-x}$B$_{12}$ with various concentration of magnetic holmium ions ($x$$leq$0.5) has been studied in detail concurrently with magnetization M(T) and Hall effect investigations on high quality single crystals at temperatures 1.9-120 K and in magnetic field up to 80 kOe. The undertaken analysis of $Deltarho/rho$ allows us to conclude that the large negative magnetoresistance (nMR) observed in vicinity of Neel temperature is caused by scattering of charge carriers on magnetic clusters of Ho$^{3+}$ ions, and that these nanosize regions with AF exchange inside may be considered as short range order AF domains. It was shown that the Yosida relation $-Delta rho/rho$$sim$$M^2$ provides an adequate description of the nMR effect for the case of Langevin type behavior of magnetization. Moreover, a reduction of Ho-ion effective magnetic moments in the range 3-9$mu_B$ was found to develop both with temperature lowering and under the increase of holmium content. A phenomenological description of the large positive quadratic contribution $Delta rho/rho$$sim$$mu_D^2 H^2$ which dominates in Ho$_x$Lu$_{1-x}$B$_{12}$ in the intermediate temperature range 20-120 K allows to estimate the drift mobility exponential changes $mu_D$$sim$$T^{-a}$ with $a$=1.3-1.6 depending on Ho concentration. An even more comprehensive behavior of magnetoresistance has been found in the AF state of Ho$_x$Lu$_{1-x}$B$_{12}$ where an additional linear positive component was observed and attributed to charge carriers scattering on the spin density wave (SDW). High precision measurements of $Deltarho/rho=f(H,T)$ have allowed us also to reconstruct the magnetic H-T phase diagram of Ho$_{0.5}$Lu$_{0.5}$B$_{12}$ and to resolve its magnetic structure as a superposition of 4f (based on localized moments) and 5d (based on SDW) components.
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