Do the running after each round. Meaning after you complete the first round of 21 reps of each exercise, run 400m. Do the 400m run after the 15 reps and after the 9 reps.
If you are a beginner scale:
15-12-9
thrusters
swings
box jumps
200m run
Advanced:
15-12-9
thrusters
swings
box jumps
400m run