I would try suspending (standby) with this command:
dbus-send --system --print-reply \
--dest="org.freedesktop.UPower" \
/org/freedesktop/UPower \
org.freedesktop.UPower.Suspend
Change Suspend to Hibernate if you want to hibernate instead
I would probably create an alias in ~/.bashrc such as alias standby="dbus-send --system --print-reply \
--dest="org.freedesktop.UPower" \
/org/freedesktop/UPower \
org.freedesktop.UPower.Suspend"
Note that the mentioned commands don't require superuser privileges.
After reviewing all the information I can find, I've come to the conclusion that you are affected by this kernel bug. which has affected numerous systems including Asus, Dell, HP, Lenovo, etc. This bug which will be marked for expiration in 47 days if no further activity occurs, is extremely hot, scoring 412 on the bug heat score and is reported as affecting 86 people at this moment. I recommend that you subscribe to it and provide any kernel related info that you can to help clarify the issue so that it remains open and the devs can squash it.
A likely workaround is upgrading/reverting to kernel 4.4.8 as noted here and confirmed here and here.
Work has been requested to reverse bisect the kernel but the bug is currently expired so it looks like the devs didn't get all the help they needed in determining the root cause of this behavior. Near as I can tell from perusing the bug report this problem appeared in kernel 4.4.0, was resolved in 4.4.8 and then reappeared sometime around 4.5.2 but I won't claim to be certain.
Another possible kernel upgrade workaround was reported here although I haven't found confirmation on that one.
If your using a kernel from the repository, it could be helpful if you were to launch ubuntu-bug linux
from the terminal to create a new bug report providing specific information regarding your kernel/issue.
You might wish to rule out out-of-order-execution as a culprit as well. You should be able to accomplish this by disabling all but CPU0 like:
for x in /sys/devices/system/cpu/cpu*/online; do
echo 0 >"$x"
done
You might also find this information useful in tracking down the root cause of this issue.
Sources:
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1574125/
https://unix.stackexchange.com/questions/145645/disabling-cpu-cores-on-quad-core-processor-on-linux
Best Answer
This appears to be bug in the gnome-settings-daemon.
A workaround has been proposed by Kim Nguyễn in the form of a python script, custom_suspend.py. He/she says: