I loved her none the less; I thought of her as the same benignant, gentle angel in my life; I reproached myself, not her, with having done him an injury; and I would have made him any atonement if I had known what to make, and how to make it.
Now has he made atonement to you — with his life!
There are no more uses of "atone" in the book.
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To atone for sins is a common religious theme.
Approved forms of faith, practice, and conduct were laid down as consistent with orthodoxy, and deviation from these standards had to be confessed and atoned for by a prescribed form of penance.
Dictionary of the History of Ideas -- http://etext.lib.virginia.edu/cgi-local/DHI/dhi.cgi?id=dv1-50(retrieved 05/20/06)