Clue: By which to take control, organising checks often to incarcerate 50% of ruffians (6,2,3,4)
Answer: SCRUFF OF THE NECK
Explanation: Definition: By which to take control
An envelope ('to incarcerate') of RUFF ('50% of **RUFF**ians') in SCOFTHENECK, an anagram ('organising') of 'checks often'.