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 - 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