Hi Yarrow, this seems to be a problem on our end then, which I will fix if you send me inputs necessary to reproduce it. This may take some time. The crash happens because in your PDB file you have atom(s) on special positions and that particular step in refinement moves them away from special position more than a predefined threshold. Unfortunately you can't overwrite that threshold and this is something that I need to fix. Practically I see two ways forward: 1) if these atoms are on special position *not* by accident (say because the model is too poor) but their location is supported by the data then I afraid you need to wait for the fix. Meanwhile you can try running refinement using different random seed (main.random_seed parameter), which may help. 2) If these atoms are there by accident then simply move them away from special position (in Coot, for example) and that will solve the problem. Pavel On 10/10/13 8:55 AM, Yarrow Madrona wrote:

Thank you Pavel,

Even setting this value up to 10 didn't seem to fix the issue. It seems to crash. log report is below.

=========================== Add C-beta restraints ============================

Adding C-beta torsion restraints... num c-beta restraints: 732

==================== 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: (0.5155158345734757, 0.37698455671246006, 0.504900074345152) site_special_frac: (0.5, 0.37698455671246006, 0.5) distance_moved: 1.01666 udp021848uds:Refine_P2122 yarrowmadrona$

...

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

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The error occurs because you're the actual flags used in refinement have changed due to the resolution being extended. As the error message notes, this is nothing to be worried about, so you can simply delete that REMARK line and continue with refinement. (Note that even if the flags already went to 3.0Å with the old data, you only used a subset of them to 3.5Å, and I assume that's what is used to calculate the checksum.) On Fri, Oct 11, 2013 at 6:32 AM, S. Saif Hasan wrote:

Hello,

I am refining a 3.0 A data set. Initially, I calculated the map at 3.5 A. I have now extended the resolution to 3.0 A, and I imported the FreeR-flags into the 3.0 A .sca file from the 3.5 A file. When I use the 3.0 A .mtz file, phenix.refine gives me this error- --------------------------------------------- The MD5 checksum for the R-free flags array summarized above is: 2ee90dd0a36800bb94370f83daf01698

The corresponding MD5 checksum in the PDB file summarized above is: 2e1cdfda59def2c4fb80ea6f1e452566

These checksums should be identical but are in fact different. This is because the R-free flags used at previous stages of refinement are different from the R-free flags summarized above. As a consequence, the values for R-free could be biased and misleading.

However, there is no problem if the R-free flags were just extended to a higher resolution, or if some reflections with no data or that are not part of the R-free set have been added or removed. In this case, simply remove the

REMARK r_free_flags.md5.hexdigest 2e1cdfda59def2c4fb80ea6f1e452566

record from the input PDB file to proceed with the refinement.

Otherwise it is best to recover the previously used R-free flags and use them consistently throughout the refinement of the model. Run this command again with the name of the file containing the original flags as an additional input. ---------------------------------------- Why does phenix.refine give me this message when I have imported the FreeR-flags from the low resolution file? And what should I do about fixing it?

Thank you for all suggestions.

Saif Purdue University

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