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Your best bet is to break down the source into broad mythical elements and rebuild your story from that. Harry's tale is both a coming-of-age and a Hero's Journey, and you don't get much more arc...
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#4: Attribution notice removed
Source: https://writers.stackexchange.com/a/14581 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#3: Attribution notice added
Source: https://writers.stackexchange.com/a/14581 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
Your best bet is to break down the source into broad mythical elements and rebuild your story from that. Harry's tale is both a coming-of-age and a Hero's Journey, and you don't get much more archetypal than those. JKRowling admits she modeled Harry-Ron-Ginny after Luke-Han-Leia, and Lucas was working with Joseph Campbell's _Hero With a Thousand Faces._ (An excellent book; I suggest you read that or the easier digest, _The Power of Myth._) So you start with the absolute basic building blocks (hero/ine, helpers, lack of family, villain, hero/ine must learn tools to defeat villain, guides) and create your unique story from those blocks. Your #3 is a good stepping stone on the way, but I think you should keep pushing it. Why a school? Why not an individual master? What if it's not friends she gathers but rivals assigned to assist her by an overlord, and they have to _learn_ to work together? What if the villain turns out to be a long-lost family member? You get the idea. As an additional step, when you finish it and hand it off to a beta or editor, make it clear that your story was originally inspired by this other work, and ask that the reader keep watch to make sure no elements are too directly lifted from it. And do not use "Hogwarts in Japan" as your elevator pitch if you're worried about copying your source material.