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1. Do, whatever you do, well.

2. Do well whatever you do.

3. Do whatever you do well.

4. Whatever you do, do well.

5. Whatever you do, do it well.

Which is correct and natural?

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3, 4, and 5 are natural.

2 is not wrong, but it is not natural.

1 is a mispunctuated version of 3.

CJ