Do you just want the ML target function value, i.e. what phenix.refine prints out at regular intervals?  In that case, you can use the script appended below (run with phenix.python score.py), which is derived from $PHENIX/cctbx_project/mmtbx/examples/simple_command_line_cc.py.

from __future__ import division

import mmtbx.command_line

import sys

def master_phil () :

  return mmtbx.command_line.generic_simple_input_phil()

def run (args, out=sys.stdout) :

  cmdline = mmtbx.command_line.load_model_and_data(

    update_f_part1_for="map",

    args=args,

    master_phil=master_phil(),

    out=out,

    process_pdb_file=False,

    create_fmodel=True)

  fmodel = cmdline.fmodel

  tf = fmodel.target_functor(compute_gradients=False)

  score = tf_r.target_work()

  print score

if (__name__ == "__main__") :

  run(sys.argv[1:])