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Fluctuations of anisotropic flow in lead-lead collisions at LHC energies arising in HYDJET++model are studied. It is shown that intrinsic fluctuations of the flow which appear mainly because of the fluctuations of particle multiplicity, momenta and coordinates are insufficient to match the measured experimental data, provided the eccentricity of the freeze-out hypersurface is fixed at any given impact parameter b. However, when the variations of the eccentricity in HYDJET++ are taken into account, the agreement between the model results and the data is drastically improved. Both model calculations and the data are filtered through the unfolding procedure. This procedure eliminates the non-flow fluctuations to a higher degree, thus indicating a dynamical origin of the flow fluctuations in HYDJET++ event generator.