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I caught him on my second dusk ball after one Thunder Bolt from my Xerneas (which put him at about 2/3 HP.) Tried a timer ball on first turn since that worked on Xerneas, but he got out after three shakes. (#`д´)ノ
I tried a quick ball, then a good amount of ultra balls (I went from 40 to 20), then I tried a lot of timer balls, and finally caught it with a dusk ball.
hmm I have 3 mewtwo's, so I don't remember the poke balls, but one of them definitely was with Timer ball :). it gave me a hard time to catch it, but Zygarde was much harder to catch.