As Tony wrote, it's important to have in both lines those settings.
Since my (and obviously your) project was created yet before arm64 was added to standard, it is not reflected in "Valid Architectures" even if it is shown as Standard.
What I did:
I went to Project (vs. Target) configuration
Typed "arm64" in the Valid Architectures (it's automatically reflected in targets and schemas
After clean/build I even get some warnings about improper conversion of float to CGFloat, etc., so the settings obviously applied.
After confirming the correct architectures, make sure your device is NOT connected to your computer when ARCHIVING the final build to submit to the App Store.
The reason this warning appears is because the DEVICE you have connected is probably not arm64 compatible.
Change your iOS development target to at least 5.1.1 or alternatively delete the standard architectures setting and re-apply it. You might have seen a warning that arm64 is not compatible with your build target. On the overview page, check both the build and target "deployment target" settings. In my case, the target was 6.0, but the project was 5.0.
Also, check "Valid Architectures" in both your target and your project. I had the right settings on the project but not on the target. After this, it worked for me.
Switch between project/target on the overview page in the top left corner of the box.
Just Create a New Project using latest xCode version and find the Build settings. The new project created using latest version have 64 support by default.