Does penance (6)
I believe the answer is:
'does penance' is the definition.
(I've seen this in another clue)
This is all the clue.
(Other definitions for atones that I've seen before include "Makes up for wrong done with a stone" , "Makes up for injury inflicted" , "Makes redress" , "Makes up for injury or offence" , "Makes reparation" .)