Starting phenix.real_space_refine on Thu Jul 18 22:39:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/07_2024/8do2_27588_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/07_2024/8do2_27588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/07_2024/8do2_27588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/07_2024/8do2_27588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/07_2024/8do2_27588_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/07_2024/8do2_27588_trim.cif" } resolution = 2.95 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= 0.003 sd= 0.049 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 28 5.16 5 C 2803 2.51 5 N 674 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4226 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "A" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3462 Classifications: {'peptide': 449} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'SXU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.10, per 1000 atoms: 0.73 Number of scatterers: 4226 At special positions: 0 Unit cell: (85.05, 76.65, 79.8, 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 28 16.00 O 721 8.00 N 674 7.00 C 2803 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 - 3.50 Amino acid : False - 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: 1.67 Conformation dependent library (CDL) restraints added in 674.7 milliseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 4 sheets defined 74.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 66 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 69 through 95 Processing helix chain 'A' and resid 9 through 14 Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 108 through 134 Processing helix chain 'A' and resid 139 through 171 removed outlier: 5.903A pdb=" N ALA A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 197 Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 241 through 260 removed outlier: 3.752A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 340 through 345 removed outlier: 3.547A pdb=" N TYR A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.617A pdb=" N ALA A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 408 through 438 Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 442 through 468 Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 265 Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324 removed outlier: 6.470A pdb=" N THR A 323 " --> pdb=" O VAL A 338 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 939 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: 1.21 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 943 1.33 - 1.46: 1358 1.46 - 1.59: 1970 1.59 - 1.72: 0 1.72 - 1.85: 47 Bond restraints: 4318 Sorted by residual: bond pdb=" C22 SXU A 501 " pdb=" S20 SXU A 501 " ideal model delta sigma weight residual 1.759 1.852 -0.093 2.00e-02 2.50e+03 2.19e+01 bond pdb=" N03 SXU A 501 " pdb=" S02 SXU A 501 " ideal model delta sigma weight residual 1.648 1.737 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C33 SXU A 501 " pdb=" S02 SXU A 501 " ideal model delta sigma weight residual 1.768 1.852 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" N19 SXU A 501 " pdb=" S20 SXU A 501 " ideal model delta sigma weight residual 1.661 1.740 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C09 SXU A 501 " pdb=" C10 SXU A 501 " ideal model delta sigma weight residual 1.509 1.568 -0.059 2.00e-02 2.50e+03 8.72e+00 ... (remaining 4313 not shown) Histogram of bond angle deviations from ideal: 93.66 - 101.73: 17 101.73 - 109.80: 359 109.80 - 117.87: 2906 117.87 - 125.93: 2516 125.93 - 134.00: 52 Bond angle restraints: 5850 Sorted by residual: angle pdb=" O21 SXU A 501 " pdb=" S20 SXU A 501 " pdb=" O29 SXU A 501 " ideal model delta sigma weight residual 117.02 93.66 23.36 3.00e+00 1.11e-01 6.06e+01 angle pdb=" O01 SXU A 501 " pdb=" S02 SXU A 501 " pdb=" O40 SXU A 501 " ideal model delta sigma weight residual 119.05 101.62 17.43 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C04 SXU A 501 " pdb=" N03 SXU A 501 " pdb=" C05 SXU A 501 " ideal model delta sigma weight residual 115.30 125.30 -10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N GLY A 176 " pdb=" CA GLY A 176 " pdb=" C GLY A 176 " ideal model delta sigma weight residual 110.20 114.45 -4.25 1.32e+00 5.74e-01 1.04e+01 angle pdb=" N ARG A 223 " pdb=" CA ARG A 223 " pdb=" C ARG A 223 " ideal model delta sigma weight residual 110.23 114.84 -4.61 1.45e+00 4.76e-01 1.01e+01 ... (remaining 5845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 2361 17.18 - 34.35: 185 34.35 - 51.53: 22 51.53 - 68.71: 4 68.71 - 85.88: 4 Dihedral angle restraints: 2576 sinusoidal: 1030 harmonic: 1546 Sorted by residual: dihedral pdb=" CA ASN A 241 " pdb=" C ASN A 241 " pdb=" N LEU A 242 " pdb=" CA LEU A 242 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" N ARG B 20 " pdb=" CA ARG B 20 " pdb=" CB ARG B 20 " pdb=" CG ARG B 20 " ideal model delta sinusoidal sigma weight residual 60.00 113.15 -53.15 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" CB MET B 47 " pdb=" CG MET B 47 " pdb=" SD MET B 47 " pdb=" CE MET B 47 " ideal model delta sinusoidal sigma weight residual -60.00 -108.15 48.15 3 1.50e+01 4.44e-03 8.60e+00 ... (remaining 2573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 402 0.029 - 0.057: 174 0.057 - 0.085: 80 0.085 - 0.114: 22 0.114 - 0.142: 10 Chirality restraints: 688 Sorted by residual: chirality pdb=" CB VAL A 14 " pdb=" CA VAL A 14 " pdb=" CG1 VAL A 14 " pdb=" CG2 VAL A 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CB ILE A 123 " pdb=" CA ILE A 123 " pdb=" CG1 ILE A 123 " pdb=" CG2 ILE A 123 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ASN A 288 " pdb=" N ASN A 288 " pdb=" C ASN A 288 " pdb=" CB ASN A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 685 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 239 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 240 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 82 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 83 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C22 SXU A 501 " 0.010 2.00e-02 2.50e+03 9.64e-03 1.86e+00 pdb=" C23 SXU A 501 " 0.000 2.00e-02 2.50e+03 pdb=" C24 SXU A 501 " 0.012 2.00e-02 2.50e+03 pdb=" C25 SXU A 501 " -0.006 2.00e-02 2.50e+03 pdb=" C26 SXU A 501 " -0.010 2.00e-02 2.50e+03 pdb=" C27 SXU A 501 " -0.000 2.00e-02 2.50e+03 pdb=" C28 SXU A 501 " 0.011 2.00e-02 2.50e+03 pdb=" S20 SXU A 501 " -0.016 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 950 2.78 - 3.31: 4236 3.31 - 3.84: 7269 3.84 - 4.37: 8081 4.37 - 4.90: 14578 Nonbonded interactions: 35114 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OG SER A 346 " model vdw 2.254 2.440 nonbonded pdb=" O ARG A 236 " pdb=" ND2 ASN A 241 " model vdw 2.261 2.520 nonbonded pdb=" O TYR A 131 " pdb=" OG1 THR A 134 " model vdw 2.362 2.440 nonbonded pdb=" O LEU A 181 " pdb=" OG1 THR A 185 " model vdw 2.372 2.440 nonbonded pdb=" OH TYR A 364 " pdb=" OD2 ASP A 436 " model vdw 2.394 2.440 ... (remaining 35109 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: 0.760 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.005 0.093 4318 Z= 0.320 Angle : 0.735 23.356 5850 Z= 0.348 Chirality : 0.040 0.142 688 Planarity : 0.004 0.049 711 Dihedral : 12.560 85.884 1584 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.22 % Allowed : 0.00 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.37), residues: 531 helix: 2.26 (0.26), residues: 398 sheet: -3.75 (0.84), residues: 20 loop : -0.55 (0.63), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.010 0.001 PHE B 52 TYR 0.008 0.001 TYR A 457 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.471 Fit side-chains REVERT: B 30 ARG cc_start: 0.7222 (ttt90) cc_final: 0.6850 (mmt180) REVERT: A 294 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 368 MET cc_start: 0.7431 (tpp) cc_final: 0.7038 (tpp) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 1.5480 time to fit residues: 94.1230 Evaluate side-chains 43 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.3888 > 50: distance: 38 - 50: 3.399 distance: 52 - 57: 27.710 distance: 57 - 58: 56.669 distance: 58 - 59: 26.746 distance: 59 - 60: 40.909 distance: 59 - 61: 42.073 distance: 61 - 62: 48.743 distance: 62 - 63: 45.267 distance: 63 - 64: 27.366 distance: 63 - 65: 25.662 distance: 65 - 66: 39.903 distance: 66 - 69: 39.925 distance: 68 - 103: 39.570 distance: 69 - 70: 23.360 distance: 70 - 71: 17.571 distance: 73 - 74: 12.428 distance: 74 - 75: 41.293 distance: 74 - 77: 60.347 distance: 75 - 76: 37.472 distance: 75 - 79: 36.643 distance: 77 - 78: 51.351 distance: 79 - 80: 22.173 distance: 80 - 81: 32.413 distance: 80 - 83: 29.147 distance: 81 - 91: 4.903 distance: 83 - 84: 21.093 distance: 84 - 85: 17.054 distance: 84 - 86: 8.961 distance: 85 - 87: 16.194 distance: 86 - 88: 15.861 distance: 87 - 89: 11.332 distance: 88 - 89: 11.131 distance: 89 - 90: 9.264 distance: 91 - 92: 12.322 distance: 92 - 93: 21.301 distance: 92 - 95: 26.130 distance: 93 - 94: 23.439 distance: 93 - 103: 43.999 distance: 95 - 96: 29.406 distance: 96 - 97: 21.724 distance: 96 - 98: 14.716 distance: 97 - 99: 38.364 distance: 98 - 100: 19.395 distance: 99 - 101: 30.406 distance: 100 - 101: 25.430 distance: 101 - 102: 21.792 distance: 103 - 104: 18.846 distance: 104 - 105: 23.280 distance: 104 - 107: 13.068 distance: 105 - 106: 38.620 distance: 105 - 111: 34.607 distance: 107 - 108: 7.417 distance: 108 - 109: 41.120 distance: 108 - 110: 52.500 distance: 112 - 113: 40.067 distance: 112 - 115: 37.633 distance: 113 - 117: 29.008 distance: 115 - 116: 44.969 distance: 117 - 118: 20.336 distance: 117 - 123: 64.214 distance: 118 - 119: 12.404 distance: 118 - 121: 25.372 distance: 119 - 120: 43.279 distance: 119 - 124: 39.122 distance: 121 - 122: 17.952 distance: 122 - 123: 55.842 distance: 124 - 125: 39.314 distance: 124 - 130: 36.417 distance: 125 - 126: 59.588 distance: 125 - 128: 24.359 distance: 126 - 127: 14.461 distance: 126 - 131: 28.850 distance: 128 - 129: 18.406 distance: 129 - 130: 52.988 distance: 141 - 145: 3.167