Starting phenix.real_space_refine on Fri Jul 19 09:48:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/07_2024/8b0l_15787.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/07_2024/8b0l_15787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/07_2024/8b0l_15787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/07_2024/8b0l_15787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/07_2024/8b0l_15787.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/07_2024/8b0l_15787.cif" } resolution = 3.13 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= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3861 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 14 5.16 5 C 2658 2.51 5 N 662 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4033 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3983 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 36, 'TRANS': 473} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.05, per 1000 atoms: 0.76 Number of scatterers: 4033 At special positions: 0 Unit cell: (60.298, 80.948, 85.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 1 15.00 O 698 8.00 N 662 7.00 C 2658 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: 1.75 Conformation dependent library (CDL) restraints added in 697.9 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 59.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.536A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 removed outlier: 3.609A pdb=" N PHE A 28 " --> pdb=" O THR A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 33 through 48 removed outlier: 4.018A pdb=" N ALA A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 70 Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.837A pdb=" N VAL A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 116 removed outlier: 4.195A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 126 through 142 removed outlier: 3.534A pdb=" N ALA A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 150 through 164 removed outlier: 4.329A pdb=" N ASP A 157 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 158 " --> pdb=" O GLN A 155 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 4.488A pdb=" N GLY A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 190 Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 204 through 209 removed outlier: 4.162A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.268A pdb=" N TRP A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 257 removed outlier: 4.198A pdb=" N LEU A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.922A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 412 through 416 removed outlier: 4.201A pdb=" N TRP A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 437 Processing helix chain 'A' and resid 481 through 487 Processing helix chain 'A' and resid 488 through 510 removed outlier: 3.704A pdb=" N ARG A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 227 Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 264 removed outlier: 6.935A pdb=" N ILE A 263 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 304 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 377 removed outlier: 6.690A pdb=" N GLU A 381 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 408 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR A 383 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE A 410 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 385 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 407 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER A 443 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 409 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 451 " --> pdb=" O GLN A 459 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 579 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: 1.20 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 616 1.31 - 1.43: 1146 1.43 - 1.56: 2355 1.56 - 1.68: 3 1.68 - 1.81: 26 Bond restraints: 4146 Sorted by residual: bond pdb=" C8 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C30 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 1.331 1.397 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CA PHE A 344 " pdb=" CB PHE A 344 " ideal model delta sigma weight residual 1.529 1.570 -0.041 1.54e-02 4.22e+03 7.15e+00 bond pdb=" C6 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 1.432 1.396 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 1.427 1.397 0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 4141 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.24: 191 107.24 - 113.93: 2326 113.93 - 120.61: 1668 120.61 - 127.30: 1400 127.30 - 133.98: 69 Bond angle restraints: 5654 Sorted by residual: angle pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O14 PTY A 601 " ideal model delta sigma weight residual 92.90 109.53 -16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O12 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O13 PTY A 601 " ideal model delta sigma weight residual 119.61 109.32 10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C11 PTY A 601 " pdb=" C8 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 111.29 120.05 -8.76 3.00e+00 1.11e-01 8.52e+00 angle pdb=" C31 PTY A 601 " pdb=" C30 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 111.62 120.14 -8.52 3.00e+00 1.11e-01 8.07e+00 angle pdb=" N THR A 315 " pdb=" CA THR A 315 " pdb=" C THR A 315 " ideal model delta sigma weight residual 109.85 112.97 -3.12 1.58e+00 4.01e-01 3.89e+00 ... (remaining 5649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.06: 2341 20.06 - 40.13: 83 40.13 - 60.19: 12 60.19 - 80.25: 0 80.25 - 100.31: 4 Dihedral angle restraints: 2440 sinusoidal: 974 harmonic: 1466 Sorted by residual: dihedral pdb=" CA GLY A 71 " pdb=" C GLY A 71 " pdb=" N ILE A 72 " pdb=" CA ILE A 72 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual -59.77 40.54 -100.31 1 3.00e+01 1.11e-03 1.26e+01 dihedral pdb=" CA ASN A 314 " pdb=" C ASN A 314 " pdb=" N THR A 315 " pdb=" CA THR A 315 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 334 0.024 - 0.048: 168 0.048 - 0.072: 64 0.072 - 0.095: 44 0.095 - 0.119: 25 Chirality restraints: 635 Sorted by residual: chirality pdb=" CA ILE A 270 " pdb=" N ILE A 270 " pdb=" C ILE A 270 " pdb=" CB ILE A 270 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ILE A 231 " pdb=" N ILE A 231 " pdb=" C ILE A 231 " pdb=" CB ILE A 231 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 632 not shown) Planarity restraints: 708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 421 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 422 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 34 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 35 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 205 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.017 5.00e-02 4.00e+02 ... (remaining 705 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1000 2.80 - 3.32: 4009 3.32 - 3.85: 6877 3.85 - 4.37: 8068 4.37 - 4.90: 14214 Nonbonded interactions: 34168 Sorted by model distance: nonbonded pdb=" O ALA A 98 " pdb=" OG SER A 102 " model vdw 2.270 2.440 nonbonded pdb=" O PHE A 151 " pdb=" OG SER A 154 " model vdw 2.278 2.440 nonbonded pdb=" O SER A 261 " pdb=" OG SER A 294 " model vdw 2.283 2.440 nonbonded pdb=" OD2 ASP A 331 " pdb=" OG SER A 376 " model vdw 2.297 2.440 nonbonded pdb=" ND2 ASN A 336 " pdb=" O GLY A 368 " model vdw 2.317 2.520 ... (remaining 34163 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.410 Find NCS groups from input model: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.003 0.067 4146 Z= 0.207 Angle : 0.665 16.632 5654 Z= 0.290 Chirality : 0.041 0.119 635 Planarity : 0.004 0.034 708 Dihedral : 10.816 100.314 1500 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.48 % Allowed : 3.12 % Favored : 96.39 % 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: 1.39 (0.41), residues: 508 helix: 2.21 (0.34), residues: 253 sheet: -0.26 (0.69), residues: 69 loop : -0.37 (0.51), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 492 HIS 0.001 0.001 HIS A 425 PHE 0.008 0.001 PHE A 174 TYR 0.008 0.001 TYR A 104 ARG 0.003 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.463 Fit side-chains REVERT: A 33 VAL cc_start: 0.8740 (t) cc_final: 0.8329 (p) REVERT: A 230 ASP cc_start: 0.8294 (t0) cc_final: 0.7954 (t0) REVERT: A 468 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7045 (tm-30) REVERT: A 488 ASN cc_start: 0.8490 (m-40) cc_final: 0.8288 (m110) outliers start: 2 outliers final: 0 residues processed: 91 average time/residue: 0.1631 time to fit residues: 18.5065 Evaluate side-chains 54 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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-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: 71.5599 > 50: distance: 79 - 83: 35.275 distance: 83 - 84: 27.687 distance: 84 - 85: 31.689 distance: 84 - 87: 12.244 distance: 85 - 86: 17.061 distance: 85 - 89: 15.474 distance: 87 - 88: 34.427 distance: 89 - 90: 22.398 distance: 90 - 91: 4.278 distance: 90 - 93: 26.052 distance: 91 - 92: 40.873 distance: 91 - 95: 59.433 distance: 93 - 94: 60.165 distance: 95 - 96: 19.763 distance: 96 - 97: 19.656 distance: 96 - 99: 32.504 distance: 97 - 98: 26.335 distance: 97 - 103: 26.917 distance: 99 - 100: 45.039 distance: 100 - 101: 45.690 distance: 100 - 102: 41.230 distance: 103 - 104: 26.886 distance: 104 - 105: 42.760 distance: 104 - 107: 18.733 distance: 105 - 106: 41.583 distance: 105 - 111: 30.449 distance: 107 - 108: 37.174 distance: 107 - 109: 48.047 distance: 108 - 110: 17.121 distance: 111 - 112: 30.587 distance: 112 - 113: 36.272 distance: 112 - 115: 41.033 distance: 113 - 114: 39.319 distance: 113 - 119: 31.692 distance: 115 - 116: 36.573 distance: 115 - 117: 53.496 distance: 116 - 118: 31.516 distance: 119 - 120: 8.158 distance: 120 - 121: 34.433 distance: 120 - 123: 56.074 distance: 121 - 122: 35.302 distance: 121 - 133: 42.264 distance: 123 - 124: 20.623 distance: 124 - 125: 10.248 distance: 124 - 126: 24.462 distance: 125 - 127: 48.794 distance: 126 - 128: 31.545 distance: 126 - 129: 24.174 distance: 127 - 128: 12.008 distance: 128 - 130: 13.832 distance: 129 - 131: 37.998 distance: 130 - 132: 26.482 distance: 131 - 132: 42.708 distance: 133 - 134: 26.153 distance: 133 - 139: 27.670 distance: 134 - 135: 10.506 distance: 134 - 137: 33.973 distance: 135 - 136: 13.593 distance: 135 - 140: 34.777 distance: 137 - 138: 50.119 distance: 138 - 139: 36.637 distance: 140 - 141: 23.095 distance: 141 - 142: 26.699 distance: 141 - 144: 39.504 distance: 142 - 143: 41.690 distance: 142 - 149: 42.390 distance: 144 - 145: 39.454 distance: 145 - 146: 33.447 distance: 146 - 147: 13.385 distance: 146 - 148: 34.287 distance: 149 - 150: 33.180 distance: 150 - 151: 34.644 distance: 150 - 153: 12.438 distance: 151 - 152: 32.313 distance: 151 - 155: 34.056 distance: 153 - 154: 12.265 distance: 155 - 156: 14.829 distance: 156 - 157: 38.619 distance: 156 - 159: 5.623 distance: 157 - 158: 44.246 distance: 157 - 160: 29.246