[phenixbb] special positions Refinement crash

[Yarrow Madrona]

Hello,

I am trying to do a refinement and I get an error that I think means I
have atoms on special positions. The refinement stops and gives the
following output given below. Any help would be appreciated. I am not sure
how to exactly determine which atoms are at special positions.

Thank you.

-Yarrow


|-real space refinement
(target=simple)---------------------------------------|
| start: r_work=0.5500 r_free=0.5441 rmsd: bonds=0.019 angles= 1.68
weight= 50|
| final: r_work=0.5309 r_free=0.5358 rmsd: bonds=0.029 angles= 2.45
weight= 80|
|
---------------------------------------------------------------------------
|

==================== Compute data/restraints target weights
===================

Traceback (most recent call last):
  File
"/usr/bin/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py",
line 11, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py",
line 159, in run
    call_back_handler=call_back_handler)
  File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py",
line 1593, in run
    reference_model_manager = self.reference_model_manager).result
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/strategies.py",
line 171, in __init__
    ion_placement_manager = ion_placement_manager)
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
line 87, in __init__
    self.call(self.weight,   "Compute data/restraints target weights")
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
line 137, in call
    func(prefix = prefix)
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
line 302, in weight
    log         = self.log)
  File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weights.py",
line 20, in run
    log                           = log)
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
line 368, in __init__
    self.xyz_weights_result = self.xyz_weights()
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
line 411, in xyz_weights
    log=self.log)
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
line 294, in __init__
    verbose=0)
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/memory_eraser.py",
line 29, in shake_sites
    max_iterations = max_iterations))
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
line 43, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
line 259, in run
    log)
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
line 127, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
line 89, in compute_functional_and_gradients
    self.apply_shifts()
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
line 70, in apply_shifts
    site_cart=self.tmp.sites_shifted[i_seq])
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/__init__.py",
line 609, in correct_special_position
    raise AssertionError(error_message)
AssertionError: Excessive special position correction:
  unit_cell: (56.278, 67.256, 106.26, 90, 90, 90)
  space_group_info: P 21 2 2
  special_op: 1/2,y,1/2
  site_frac: (0.5090941495765681, 0.42722892547242985, 0.5083083194012079)
  site_special_frac: (0.5, 0.42722892547242985, 0.5)
  distance_moved: 1.02047

Phenix v. 1.8.4-1496
-- 
Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697