OK, let's start with the basics. Are you enforcing MFA? Do you see a "regular" credentials prompt or the ADAL one (browser control)? Run the Autodiscover test from ExRCA (http://aka.ms/rca) and also locally on the machine (hold ctrl, right-click Outlook's icon in the tray, Test E-Mail Autoconfiguration, enter username, clear the two Guessmart checkboxes and run the test). Can you access other O365/Azure AD applications with the same account?
Also run "dsregcmd.exe /status" to cover potential issues with the PRT.