Starting phenix.real_space_refine on Thu Jul 24 01:51:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zu1_60478/07_2025/8zu1_60478.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zu1_60478/07_2025/8zu1_60478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zu1_60478/07_2025/8zu1_60478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zu1_60478/07_2025/8zu1_60478.map" model { file = "/net/cci-nas-00/data/ceres_data/8zu1_60478/07_2025/8zu1_60478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zu1_60478/07_2025/8zu1_60478.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3217 2.51 5 N 818 2.21 5 O 952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5009 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5009 Classifications: {'peptide': 618} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 583} Time building chain proxies: 4.14, per 1000 atoms: 0.83 Number of scatterers: 5009 At special positions: 0 Unit cell: (68.1472, 76.032, 83.9168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 952 8.00 N 818 7.00 C 3217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 545.7 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 46.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 Processing helix chain 'A' and resid 15 through 19 removed outlier: 3.592A pdb=" N GLY A 19 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 65 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 195 through 199 removed outlier: 4.366A pdb=" N PHE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 199' Processing helix chain 'A' and resid 214 through 236 Processing helix chain 'A' and resid 239 through 253 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 312 through 321 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.702A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 351 " --> pdb=" O TYR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.816A pdb=" N GLY A 367 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 416 removed outlier: 3.774A pdb=" N ALA A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 408 " --> pdb=" O TRP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 479 through 501 Processing helix chain 'A' and resid 505 through 523 removed outlier: 3.727A pdb=" N ARG A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 removed outlier: 3.528A pdb=" N TYR A 538 " --> pdb=" O ARG A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 569 through 578 removed outlier: 3.912A pdb=" N SER A 573 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS A 574 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 591 Processing helix chain 'A' and resid 600 through 616 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 removed outlier: 4.573A pdb=" N LEU A 146 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 removed outlier: 6.502A pdb=" N SER A 114 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 185 removed outlier: 3.665A pdb=" N GLN A 208 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 287 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438 removed outlier: 6.566A pdb=" N SER A 475 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 450 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 473 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TRP A 452 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 471 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.522A pdb=" N GLY A 528 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 532 through 533 Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 218 hydrogen bonds defined for protein. 594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1586 1.34 - 1.46: 1182 1.46 - 1.57: 2374 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 5184 Sorted by residual: bond pdb=" CG GLU A 57 " pdb=" CD GLU A 57 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.14e+00 bond pdb=" CG LEU A 424 " pdb=" CD1 LEU A 424 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" CB ILE A 425 " pdb=" CG2 ILE A 425 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.00e+00 bond pdb=" CB PRO A 113 " pdb=" CG PRO A 113 " ideal model delta sigma weight residual 1.506 1.471 0.035 3.90e-02 6.57e+02 7.90e-01 bond pdb=" C ALA A 38 " pdb=" N PRO A 39 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 5.92e-01 ... (remaining 5179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 6694 1.13 - 2.26: 286 2.26 - 3.39: 63 3.39 - 4.52: 17 4.52 - 5.65: 5 Bond angle restraints: 7065 Sorted by residual: angle pdb=" CA TYR A 53 " pdb=" CB TYR A 53 " pdb=" CG TYR A 53 " ideal model delta sigma weight residual 113.90 119.12 -5.22 1.80e+00 3.09e-01 8.40e+00 angle pdb=" C LEU A 56 " pdb=" N GLU A 57 " pdb=" CA GLU A 57 " ideal model delta sigma weight residual 121.58 115.93 5.65 1.95e+00 2.63e-01 8.39e+00 angle pdb=" CA TYR A 547 " pdb=" CB TYR A 547 " pdb=" CG TYR A 547 " ideal model delta sigma weight residual 113.90 109.85 4.05 1.80e+00 3.09e-01 5.06e+00 angle pdb=" C VAL A 36 " pdb=" N GLU A 37 " pdb=" CA GLU A 37 " ideal model delta sigma weight residual 123.09 127.14 -4.05 1.94e+00 2.66e-01 4.35e+00 angle pdb=" CA TYR A 242 " pdb=" CB TYR A 242 " pdb=" CG TYR A 242 " ideal model delta sigma weight residual 113.90 110.15 3.75 1.80e+00 3.09e-01 4.33e+00 ... (remaining 7060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2647 16.35 - 32.70: 254 32.70 - 49.05: 37 49.05 - 65.40: 11 65.40 - 81.74: 5 Dihedral angle restraints: 2954 sinusoidal: 1158 harmonic: 1796 Sorted by residual: dihedral pdb=" CA TYR A 286 " pdb=" C TYR A 286 " pdb=" N THR A 287 " pdb=" CA THR A 287 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA TYR A 547 " pdb=" C TYR A 547 " pdb=" N VAL A 548 " pdb=" CA VAL A 548 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ALA A 38 " pdb=" C ALA A 38 " pdb=" N PRO A 39 " pdb=" CA PRO A 39 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 2951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 482 0.042 - 0.083: 159 0.083 - 0.124: 43 0.124 - 0.166: 2 0.166 - 0.207: 1 Chirality restraints: 687 Sorted by residual: chirality pdb=" CA GLU A 57 " pdb=" N GLU A 57 " pdb=" C GLU A 57 " pdb=" CB GLU A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL A 546 " pdb=" CA VAL A 546 " pdb=" CG1 VAL A 546 " pdb=" CG2 VAL A 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE A 179 " pdb=" N ILE A 179 " pdb=" C ILE A 179 " pdb=" CB ILE A 179 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 684 not shown) Planarity restraints: 918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 556 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 557 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 271 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 272 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 242 " -0.014 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR A 242 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 242 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 242 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 242 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 242 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 242 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 242 " -0.000 2.00e-02 2.50e+03 ... (remaining 915 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 71 2.67 - 3.23: 4696 3.23 - 3.79: 8208 3.79 - 4.34: 11548 4.34 - 4.90: 18743 Nonbonded interactions: 43266 Sorted by model distance: nonbonded pdb=" O TYR A 2 " pdb=" ND2 ASN A 611 " model vdw 2.118 3.120 nonbonded pdb=" OH TYR A 28 " pdb=" OD2 ASP A 150 " model vdw 2.179 3.040 nonbonded pdb=" O ARG A 600 " pdb=" NE2 GLN A 604 " model vdw 2.232 3.120 nonbonded pdb=" OE2 GLU A 75 " pdb=" OH TYR A 242 " model vdw 2.249 3.040 nonbonded pdb=" OG SER A 377 " pdb=" O PRO A 456 " model vdw 2.252 3.040 ... (remaining 43261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 16.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5184 Z= 0.155 Angle : 0.572 5.647 7065 Z= 0.305 Chirality : 0.044 0.207 687 Planarity : 0.005 0.045 918 Dihedral : 13.123 81.745 1822 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.33), residues: 616 helix: 1.65 (0.35), residues: 230 sheet: 1.21 (0.96), residues: 27 loop : -0.53 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 602 HIS 0.004 0.001 HIS A 280 PHE 0.010 0.002 PHE A 346 TYR 0.027 0.002 TYR A 242 ARG 0.003 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.16620 ( 218) hydrogen bonds : angle 6.08188 ( 594) covalent geometry : bond 0.00352 ( 5184) covalent geometry : angle 0.57230 ( 7065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.509 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 1.3441 time to fit residues: 89.4835 Evaluate side-chains 48 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.9653 > 50: distance: 89 - 119: 6.149 distance: 93 - 94: 4.888 distance: 93 - 96: 4.606 distance: 94 - 95: 4.208 distance: 95 - 126: 8.877 distance: 99 - 100: 3.434 distance: 99 - 102: 4.834 distance: 101 - 135: 10.308 distance: 103 - 104: 5.740 distance: 104 - 105: 7.496 distance: 104 - 106: 8.980 distance: 107 - 108: 3.067 distance: 108 - 109: 5.495 distance: 110 - 144: 9.044 distance: 112 - 113: 3.396 distance: 112 - 114: 4.007 distance: 113 - 115: 4.180 distance: 115 - 117: 3.929 distance: 116 - 117: 4.789 distance: 119 - 120: 5.587 distance: 120 - 121: 4.278 distance: 120 - 123: 6.502 distance: 121 - 122: 4.310 distance: 121 - 126: 6.069 distance: 122 - 149: 11.201 distance: 123 - 124: 8.244 distance: 123 - 125: 4.290 distance: 129 - 155: 9.770 distance: 130 - 131: 6.224 distance: 131 - 132: 3.703 distance: 133 - 134: 5.314 distance: 135 - 136: 4.121 distance: 136 - 137: 4.634 distance: 137 - 138: 5.831 distance: 137 - 144: 4.212 distance: 138 - 166: 13.432 distance: 139 - 140: 5.354 distance: 140 - 141: 7.241 distance: 141 - 142: 7.942 distance: 142 - 143: 9.756 distance: 144 - 145: 6.175 distance: 145 - 146: 5.281 distance: 145 - 148: 7.660 distance: 146 - 147: 4.735 distance: 146 - 149: 3.902 distance: 147 - 174: 7.791 distance: 149 - 150: 3.284 distance: 150 - 151: 9.020 distance: 150 - 153: 11.597 distance: 151 - 152: 4.543 distance: 152 - 178: 16.395 distance: 153 - 154: 14.081 distance: 155 - 156: 9.768 distance: 156 - 157: 5.813 distance: 156 - 159: 7.694 distance: 157 - 158: 5.709 distance: 157 - 166: 30.858 distance: 158 - 182: 8.681 distance: 159 - 160: 13.678 distance: 160 - 161: 8.313 distance: 161 - 162: 8.765 distance: 162 - 163: 4.312 distance: 163 - 164: 4.604 distance: 163 - 165: 6.101 distance: 166 - 167: 32.718 distance: 167 - 168: 6.718 distance: 167 - 170: 22.462 distance: 168 - 169: 7.386 distance: 168 - 174: 6.756 distance: 169 - 191: 12.672 distance: 170 - 171: 8.886 distance: 171 - 172: 13.286 distance: 172 - 173: 11.874