As DobieLover said,
Your current set up provides some protection but can be breached by larger predators.
My run is not predator proof so I insist that the chickens sleep in the coop.
Nest boxes do NOT count as usable floor space when calculating how much room you have for chickens, as the birds should not be in there for anything other than laying. So your usable coop space is the coop minus the nest boxes, unless nest boxes are elevated high enough that the birds can use...