What does the cryptic crossword clue "Graduate makes a case, penning short excuse (9)" mean?

The definition is "Graduate". The wordplay uses a deletion. ALIB (synonym="ALIB") in CRATE (synonym="case") = CALIBRATE; definition: "Graduate" The answer is CALIBRATE.

Graduate makes a case, penning short excuse (9)

Guardian Cryptic #28972 | 6 Down | 2023-01-20 flower

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