Yeah, that's the same update that is delivered through the appstore (about 386M) - I have the same problem with that one as well (unable to restart).
Looking at the boot log (below) the only messages appear to be from Cisco VPN software. I might try uninstalling that and then installing the patch.
9/2/16 7:29:50.000 PM kernel[0]: ignored is_io_service_close(0x100000441,IOHIDParamUserClient)
9/2/16 7:29:50.000 PM kernel[0]: ignored is_io_service_close(0x100000441,IOHIDParamUserClient)
9/2/16 7:29:50.000 PM kernel[0]: ignored is_io_service_close(0x100000441,IOHIDParamUserClient)
9/2/16 7:29:50.000 PM kernel[0]: ignored is_io_service_close(0x100000441,IOHIDParamUserClient)
9/2/16 7:29:50.000 PM kernel[0]: ignored is_io_service_close(0x100000441,IOHIDParamUserClient)
9/2/16 7:29:50.000 PM kernel[0]: ignored is_io_service_close(0x100000441,IOHIDParamUserClient)
9/2/16 7:29:50.000 PM kernel[0]: ignored is_io_service_close(0x100000441,IOHIDParamUserClient)
9/2/16 7:29:50.000 PM kernel[0]: ignored is_io_service_close(0x100000441,IOHIDParamUserClient)
9/2/16 7:29:50.679 PM loginwindow[110]: ERROR | -[SessionLogoutManager startLogout:logoutSubType:showConfirmationUI:countDownTime:useTALOption:logoutO ptions:] | Attempt to start a: Shutdown, AFTER a Restart was already past the point where logout can change types
9/2/16 7:29:50.000 PM kernel[0]: ignored is_io_service_close(0x100000441,IOHIDParamUserClient)
9/2/16 7:29:50.983 PM acwebsecagent[303]: Connection : Failed to connect to 128.138.82.230:80. Code : 60
9/2/16 7:29:50.983 PM acwebsecagent[303]: Connection : Caught exception. Code : 60
9/2/16 7:29:50.983 PM acwebsecagent[303]: Connection : Failed to connect externally. Code : 60
9/2/16 7:29:50.983 PM acvpnagent[58]: Function: internalReadSocket File: ../../vpn/Common/IPC/UdpTcpTransports_unix.cpp Line: 497 Invoked Function: ::read Return Code: -31588336 (0xFE1E0010) Description: SOCKETTRANSPORT_ERROR_TRANSPORT_SHUTDOWN:The socket was shutdown by the operating system or a remote peer.
9/2/16 7:29:50.983 PM acvpnagent[58]: Function: callbackHandler File: ../../vpn/Common/IPC/SocketTransport.cpp Line: 1721 Invoked Function: CSocketTransport::internalReadSocket Return Code: -31588336 (0xFE1E0010) Description: SOCKETTRANSPORT_ERROR_TRANSPORT_SHUTDOWN:The socket was shutdown by the operating system or a remote peer.
9/2/16 7:29:50.983 PM acvpnagent[58]: Function: OnSocketReadComplete File: ../../vpn/Common/IP/HttpSessionAsync.cpp Line: 1466 Invoked Function: CSocketTransport::readSocket Return Code: -31588336 (0xFE1E0010) Description: SOCKETTRANSPORT_ERROR_TRANSPORT_SHUTDOWN:The socket was shutdown by the operating system or a remote peer.
9/2/16 7:29:50.983 PM acvpnagent[58]: Function: OnSocketReadComplete File: ../../vpn/Common/IP/HttpSessionAsync.cpp Line: 1614 Error while reading header:
9/2/16 7:29:50.983 PM acvpnagent[58]: Function: OnSendRequestComplete File: ../../vpn/Common/IP/HttpProbeAsync.cpp Line: 374 Invoked Function: CHttpSessionAsync::OnSendRequestComplete Return Code: -31588336 (0xFE1E0010) Description: SOCKETTRANSPORT_ERROR_TRANSPORT_SHUTDOWN:The socket was shutdown by the operating system or a remote peer.
9/2/16 7:29:50.984 PM acvpnagent[58]: Function: logProbeFailure File: ../../vpn/Agent/NetEnvironment.cpp Line: 1431 Invoked Function: CHttpProbeAsync::SendProbe Return Code: -27066355 (0xFE63000D) Description: HTTP_PROBE_ASYNC_ERROR_TIMEOUT HTTP (host: 128.138.82.230)
9/2/16 7:29:50.984 PM acvpnagent[58]: Function: TestAccessToSG File: ../../vpn/Agent/NetEnvironment.cpp Line: 1384 Invoked Function: CNetEnvironment::analyzeHttpResponse Return Code: -28966899 (0xFE46000D) Description: NETENVIRONMENT_ERROR_PROBE_INCOMPLETE:Network Probe could not contact target
9/2/16 7:29:50.984 PM acvpnagent[58]: Function: testNetwork File: ../../vpn/Agent/NetEnvironment.cpp Line: 777 Invoked Function: CNetEnvironment::IsSGAccessible Return Code: -28966899 (0xFE46000D) Description: NETENVIRONMENT_ERROR_PROBE_INCOMPLETE:Network Probe could not contact target
9/2/16 7:29:50.985 PM acvpnagent[58]: Function: TestNetEnv File: ../../vpn/Agent/NetEnvironment.cpp Line: 273 Incomplete probe count has been reset
9/2/16 8:20:31.000 PM bootlog[0]: BOOT_TIME 1472869231 0
9/2/16 8:20:33.000 PM syslogd[53]: Configuration Notice:
ASL Module "com.apple.AccountPolicyHelper" claims selected messages.
Those messages may not appear in standard system log files or in the ASL database.
9/2/16 8:20:33.000 PM syslogd[53]: Configuration Notice:
ASL Module "com.apple.Accounts" claims selected messages.
Those messages may not appear in standard system log files or in the ASL database.