Oplog size is large, and I can't shrink it to match oplogMinRetentionHours

I’m running a 3 node cluster with v5.0.8.
The parameter oplogMinRetentionHours on primary is set to 12 hours, but oplog length is over 20 hours. How can I ‘wake up’ Mongo to shrink it back to 12 hours?
There is no problem with majority commit. Write commit is set to 1.
The oplog is much larger than the main collection. 99% of the database is this main collection.