Dear all,
I recently upgraded my MacOS to Sequoia 15.3.1 and found that
previous phenix jobs that ran without
problem suddenly crashed with the installation
(phenix-1-21.2-5419) I had since August 2024. So I
installed the latest on-built (phenix-2.0rc-5617) but it
nonetheless crashed with the message below.
Any help would be greatly appreciated.
Best,
Xavier
XGRMAC:cyc3 > Could not import the compiled Python-sander
interface.Traceback (most recent call last):
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py",
line 8, in <module>
run_program(real_space_refine.Program)
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/iotbx/cli_parser.py",
line 980, in run_program
task.run()
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/programs/real_space_refine.py",
line 206, in run
self.rsr_result = rsr_wrappers.run_real_space_refine(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py",
line 52, in __init__
self._refined = macro_cycle_real_space.run(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py",
line 306, in __init__
self.caller(self.refine_xyz)
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py",
line 321, in caller
func()
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py",
line 704, in refine_xyz
self.minimization_ncs()
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py",
line 794, in minimization_ncs
weight = real_space_weight.run(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py",
line 84, in __init__
ro.refine(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py",
line 394, in refine
real_space_result = refinery(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py",
line 233, in __init__
refiner.refine(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py",
line 126, in refine
minimized =
mmtbx.refinement.minimization_ncs_constraints.lbfgs(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py",
line 424, in __init__
minimizer = scitbx.lbfgs.run(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py",
line 270, in run
return run_c_plus_plus(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py",
line 131, in run_c_plus_plus
f, g = target_evaluator.compute_functional_and_gradients()
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py",
line 456, in compute_functional_and_gradients
t,g = self.target_and_grads_object.target_and_gradients(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py",
line 242, in target_and_gradients
t_restraints, g_restraints = restraints_target_and_grads(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py",
line 110, in restraints_target_and_grads
ef = restraints_manager.energies_sites(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py",
line 1524, in energies_sites
pair_proxies = self.pair_proxies(
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py",
line 1427, in pair_proxies
check_bonded_distance_cutoff(sites_frac=sites_frac)
File
"/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py",
line 1308, in check_bonded_distance_cutoff
raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance:
59.7151 > 50:
distance: 0 - 1: 15.382
distance: 1 - 2: 14.133
distance: 1 - 3: 15.077
distance: 4 - 5: 11.010
distance: 5 - 6: 5.064
distance: 5 - 8: 12.166
distance: 6 - 7: 9.252
distance: 6 - 15: 4.656
distance: 8 - 9: 6.568
distance: 9 - 10: 41.112
distance: 9 - 11: 19.959
distance: 10 - 12: 4.365
distance: 11 - 13: 12.611
distance: 12 - 14: 28.654
distance: 13 - 14: 25.314
distance: 15 - 16: 7.291
distance: 16 - 17: 12.341
distance: 16 - 19: 4.354
distance: 17 - 18: 11.820
distance: 17 - 26: 9.661
distance: 19 - 20: 7.438
distance: 20 - 21: 17.074
distance: 20 - 22: 19.126
distance: 21 - 23: 7.637
distance: 22 - 24: 3.434
distance: 23 - 25: 24.169
distance: 24 - 25: 8.875
distance: 26 - 27: 10.037
distance: 27 - 28: 9.377
distance: 27 - 30: 12.844
distance: 28 - 29: 12.437
distance: 28 - 34: 22.926
distance: 30 - 31: 46.409
distance: 31 - 32: 6.849
distance: 31 - 33: 21.459
distance: 34 - 35: 12.375
distance: 34 - 40: 15.635
distance: 35 - 36: 10.511
distance: 35 - 38: 12.461
distance: 36 - 37: 11.525
distance: 36 - 41: 15.668
distance: 38 - 39: 9.083
distance: 39 - 40: 10.922
distance: 41 - 42: 15.925
distance: 42 - 43: 26.537
distance: 42 - 45: 20.600
distance: 43 - 44: 14.038
distance: 43 - 48: 40.043
distance: 45 - 46: 18.721
distance: 45 - 47: 12.152
distance: 48 - 49: 19.936
distance: 49 - 50: 9.210
distance: 49 - 52: 4.170
distance: 50 - 51: 6.051
distance: 50 - 56: 10.707
distance: 52 - 53: 13.486
distance: 53 - 54: 25.122
distance: 53 - 55: 30.977
distance: 56 - 57: 24.676
distance: 57 - 58: 6.469
distance: 57 - 60: 24.810
distance: 58 - 59: 19.649
distance: 58 - 65: 16.713
distance: 60 - 61: 19.749
distance: 61 - 62: 27.563
distance: 62 - 63: 31.258
distance: 63 - 64: 39.081
distance: 65 - 66: 17.034
distance: 66 - 67: 13.877
distance: 66 - 69: 30.087
distance: 67 - 68: 30.739
distance: 67 - 70: 22.852
distance: 70 - 71: 17.537
distance: 71 - 72: 19.009
distance: 71 - 74: 23.249
distance: 72 - 73: 32.627
distance: 72 - 81: 23.614
distance: 74 - 75: 30.150
distance: 75 - 76: 11.440
distance: 75 - 77: 13.841
distance: 76 - 78: 23.906
distance: 77 - 79: 27.669
distance: 78 - 80: 29.196
distance: 79 - 80: 27.009
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