the problem is that you did not ask phenix.refine to refine the rest
of the atoms isotropically (with your command below you only refine
anisotropic ADPs of atoms in chain Q, and the B-factors of all the
other atoms are not refined):
adp {
individual {
anisotropic = "chain Q"
}
I would do it like this:
adp {
individual {
anisotropic = chain Q and element CL
isotropic = not (chain Q and element CL)
}
}