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proper quantify the vibrations. So that you know when they are improving, or not improving
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tune the dynamic notch filter to further reduce vibrations. This can only be done after step 2.
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If the copter is flying in correctly proceed to do an autotune
If you have any issues, post a .bin file again.
PS: we should do a blog post or something with the point highlighted above. We keep having support questions with the exact same issue.