Mac Pro (4,1; early 2009) won't shutdown

This issue is with a Mac Pro (4,1; early 2009) running OS X 10.9.4 Mavericks. I have a strange problem, when I try to shutdown my Mac Pro. I get the grey screen with the activity indicator, but it does not shutdown, the indicator keeps spinning and spinning. I figured out how to run the Mac in verbose mode in order to locate the problem. So I think this is the relevant part from Console.app: 02.09.14 21:01:34,654 com.apple.launchd.peruser.502: (com.apple.PackageKit.InstallStatus) Throttling respawn: Will start in 10 seconds 02.09.14 21:01:34,700 WindowServer: CGXGetConnectionProperty: Invalid connection 52227 02.09.14 21:01:34,703 WindowServer: CGXGetConnectionProperty: Invalid connection 52227 02.09.14 21:01:34,703 WindowServer: CGXGetConnectionProperty: Invalid connection 52227 02.09.14 21:01:34,704 WindowServer: CGXGetConnectionProperty: Invalid connection 52227 02.09.14 21:01:34,704 WindowServer: CGXGetConnectionProperty: Invalid connection 52227 02.09.14 21:01:34,733 LaCie Network Assistant: windowWillClose 02.09.14 21:01:34,734 LaCie Network Assistant: windowWillClose 02.09.14 21:01:34,733 com.apple.launchd.peruser.502: (com.apple.universalaccessAuthWarn) Exited: Killed: 9 02.09.14 21:01:34,734 LaCie Network Assistant: windowWillClose 02.09.14 21:01:34,735 LaCie Network Assistant: windowWillClose 02.09.14 21:01:34,735 LaCie Network Assistant: windowWillClose 02.09.14 21:01:34,735 LaCie Network Assistant: windowWillClose 02.09.14 21:01:34,738 com.apple.launchd.peruser.502: (com.intego.commonservices.integomenu) Exited: Killed: 9 02.09.14 21:01:34,739 com.apple.launchd: (com.apple.ShareKitHelper) Exited: Killed: 9 02.09.14 21:01:34,742 NotificationCenter: Connection interrupted. 02.09.14 21:01:34,745 UserEventAgent: Captive: [UserAgentDied:142] User Agent @port=35335 Died 02.09.14 21:01:34,746 com.apple.launchd.peruser.502: (com.apple.iTunesHelper.108800) Exited with code: 1 02.09.14 21:01:34,748 com.apple.launchd.peruser.502: ([0x0-0x3a03a].com.apple.AppleSpell) Exited: Killed: 9 02.09.14 21:01:34,749 com.apple.launchd.peruser.502: (com.apple.ImageCaptureExtension2.26432) Exited: Killed: 9 02.09.14 21:01:34,756 com.apple.launchd.peruser.502: (com.apple.UserEventAgent-Aqua) Exited: Killed: 9 02.09.14 21:01:34,855 com.apple.launchd.peruser.502: (com.apple.gamed) Exited: Killed: 9 02.09.14 21:01:34,856 com.apple.launchd.peruser.502: (2BUA8C4S2C.com.agilebits.onepassword-osx-helper) Exited: Killed: 9 02.09.14 21:01:40,873 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:40,873 com.apple.kextd: Rescanning kernel extensions. 02.09.14 21:01:40,873 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:41,263 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:41,263 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:41,303 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:41,305 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:42,000 kernel: Resetting IOCatalogue. 02.09.14 21:01:42,111 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:42,113 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:42,195 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:42,195 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:42,202 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:42,205 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:44,767 loginwindow: ERROR | -[ApplicationManager quitPrivateProcesses] | Private process did not quit 02.09.14 21:01:44,823 sessionlogoutd: sessionlogoutd Launched 02.09.14 21:01:44,835 sessionlogoutd: DEAD_PROCESS: 89 console 02.09.14 21:01:44,840 loginwindow: ERROR | -[Application hardKill:] | Application hardKill returned -600 02.09.14 21:01:44,901 airportd: _doAutoJoin: Already associated to “FlooNetwork2”. Bailing on auto-join. 02.09.14 21:01:45,763 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:45,767 com.apple.kextd: Rescanning kernel extensions. 02.09.14 21:01:45,767 shutdown: halt by _spotlight: 02.09.14 21:01:45,000 kernel: Kext loading now disabled. 02.09.14 21:01:45,000 kernel: Kext unloading now disabled. 02.09.14 21:01:45,000 kernel: Kext autounloading now disabled. 02.09.14 21:01:45,000 kernel: Kernel requests now disabled. 02.09.14 21:01:45,767 shutdown: SHUTDOWN_TIME: 1409684505 767090 02.09.14 21:01:45,793 com.apple.kextd: Can't create kext cache under / - owner not root. 02.09.14 21:01:45,797 virusbarrierb: Unloading real-time scanner...