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My aperture could not read my D3200 and D600 RAW files before. I used the old Nikon Transfer software to download the RAW files from the camera. It turns out that the old Nikon Transfer software corrupted the files. After I installed the latest Nikon transfer software from Nikon, everything is fine.
However, D3 is pretty old camera. You should be able to open it. May be if you download the RAW files using Nikon Transfer software, it will work. It's free and downloadable from Nikon website.