When exclamation mark (!) is used for comment, it cannot be separated by white spaces from a commented definition. It fails with RuntimeError: Syntax error: improper definition name ""
The problem is, that it can be well hidden and diffictult for user to track the error down.

Example:
Functional:

!input {
something = True
}

Not Functional:

! input {
something = True
}

https://github.com/cctbx/cctbx_project/blob/master/libtbx/phil/init.py