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Radiation hardness is one of the most important characteristics in a space-borne instrument, particularly imaging devices. The charge-coupled device (CCD) is now used in the X-ray region. A "notch" structure inside the CCD is widely employed to make it radiation hard. Using a proton beam, we confirmed that the notch structure improved the charge transfer inefficiency (CTI) by a factor of three. We applied a mesh technique in the proton beam experiment of a CCD. The proton beam energy is 600 keV, which induces greater damage than do the beam of high energy widely reported. The CCD employed has 1024 × 1024 pixels with a notch structure. The mesh technique enables us to confine the proton beam to a circular region of 2 μm diameter within a 24×24 μm2 pixel. The CCD was kept at -100°C during the irradiation. Some pixels are damaged in the notch region while others in the out-of-notch region. After the proton irradiation, we measured the CTI using 2×107 X-ray photons from 55Fe, and found that the CTI of pixels damaged in the notch region is larger by a factor of 2.5 than that of pixels damaged in the out-of-notch region. It is still in open question as to whether pixels damaged in the out-of-notch region show a substantial radiation damage effect.