if you are referring to the out of bounds set up. you must do the eagle shadow puzzle and the clock puzzle BEFORE you insert any of the two key cards into the door. 
or else the game will soft lock.

It can be any time before you insert the keys, but the optimal time is doing the eagle puzzle while you are in the process of getting jack into the main room for the OoB set up.

as for the clock puzzle you will see runners do that when they are on the way to grab the blue keycard.

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