Hi Yarrow, please try increasing this parameter (default is 1.0) correct_special_position_tolerance and let me know if this does not help. Set to 2 or so. Pavel On 10/9/13 4:17 PM, Yarrow Madrona wrote:
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