In Exchange 2016, after you have done your installation and all says successful, you login to the Exchange Management Shell and are presented with the following error:

Rebooting the server does not help.

Checked the PowerShell virtual directory and Basic plus Windows Integrated Authentication was set to $True.

Lastly, you need to check your bindings in IIS, you can do so by expanding sites and clicking on your default web site and then bindings on the right hand side, if you have the wrong information here it will give you the error above:

Once you remove the information that is incorrect or correct it and reboot then all should be working again in the EMS.

Hope it helps.

By edward