Checks the organ controls (5)

I believe the answer is:

stops

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'checks' is the definition.
('stop' can be a synonym of 'check')

I cannot understand how the remainder of the clue works.

(Other definitions for stops that I've seen before include "Halts" , "Checks" , "Ends" , "Prevents" , "Ceases" .)

I've seen this clue in The Globe and Mail.

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