Hi Justin,
According to your description, it seems like the smart card is not being recognized by Mac.
Could you please help to clarify the below:
1. When you insert your card into your reader - do any indicator lights flash?
There should be at least one LED on the reader to show card activity.
2. Did you see the smart card being detected into Keychain?
Once the driver and the card reader worked properly, the Mac should recognize the card.
If the above failed, you may need to contact the card vendor for a driver and card reader that are working on 10.11.4.
Once the card can be recognized by the OS and Keychains is able to get certificates, that's when the software side (the Centrify side) comes in. Then you will need to follow the below guide to finish the setup:
Please feel free to contact us if you need any assistance.
Kind Regards,
Albert