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A honeycomb array of submicrometer holes in a Nb superconducting thin film has been fabricated to investigate the flux pinning effect. It is found that the minima positions reveal two regimes characterized by the matching fields and the fractional ones. It is believed that the complex behavior may come from more than one vortex being captured per pinning site. Furthermore, the temperature dependence of the saturation number of vortices per pinning site together with vortex-vortex interaction gives the complex vortex configurations.