Starting phenix.real_space_refine on Fri Aug 2 15:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/08_2024/7f62_31470.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/08_2024/7f62_31470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/08_2024/7f62_31470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/08_2024/7f62_31470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/08_2024/7f62_31470.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/08_2024/7f62_31470.cif" } resolution = 3.6 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= 0.034 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 18 5.16 5 C 2104 2.51 5 N 552 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1579 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 1 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 3.19, per 1000 atoms: 0.96 Number of scatterers: 3321 At special positions: 0 Unit cell: (77, 53.9, 102.3, 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 18 16.00 O 647 8.00 N 552 7.00 C 2104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 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: 1.25 Conformation dependent library (CDL) restraints added in 560.8 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 9.8% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.007A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.936A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.197A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.625A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.075A pdb=" N ALA H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.998A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.919A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.072A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 68 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.133A pdb=" N GLU L 106 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 35 through 36 removed outlier: 4.195A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.725A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 90 through 91 removed outlier: 3.741A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 68 hydrogen bonds defined for protein. 153 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: 0.78 Time building geometry restraints manager: 1.36 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: 1046 1.34 - 1.46: 748 1.46 - 1.58: 1588 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 3406 Sorted by residual: bond pdb=" N TYR A 449 " pdb=" CA TYR A 449 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.29e-02 6.01e+03 6.35e+00 bond pdb=" C ASN A 448 " pdb=" N TYR A 449 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 5.04e+00 bond pdb=" C TYR A 449 " pdb=" O TYR A 449 " ideal model delta sigma weight residual 1.235 1.218 0.018 1.26e-02 6.30e+03 1.99e+00 bond pdb=" CE2 TYR A 449 " pdb=" CZ TYR A 449 " ideal model delta sigma weight residual 1.378 1.345 0.033 2.40e-02 1.74e+03 1.92e+00 bond pdb=" C SER L 95 " pdb=" O SER L 95 " ideal model delta sigma weight residual 1.241 1.231 0.011 9.80e-03 1.04e+04 1.19e+00 ... (remaining 3401 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.40: 93 106.40 - 113.29: 1753 113.29 - 120.18: 1159 120.18 - 127.07: 1584 127.07 - 133.96: 35 Bond angle restraints: 4624 Sorted by residual: angle pdb=" CA SER L 95 " pdb=" C SER L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 120.79 116.56 4.23 9.70e-01 1.06e+00 1.91e+01 angle pdb=" C SER L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta sigma weight residual 119.99 124.05 -4.06 1.08e+00 8.57e-01 1.41e+01 angle pdb=" CA TYR A 449 " pdb=" CB TYR A 449 " pdb=" CG TYR A 449 " ideal model delta sigma weight residual 113.90 119.63 -5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" N LEU A 452 " pdb=" CA LEU A 452 " pdb=" C LEU A 452 " ideal model delta sigma weight residual 109.41 113.80 -4.39 1.52e+00 4.33e-01 8.32e+00 angle pdb=" C PRO A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 120.65 124.21 -3.56 1.32e+00 5.74e-01 7.27e+00 ... (remaining 4619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 1770 15.33 - 30.66: 174 30.66 - 45.99: 49 45.99 - 61.32: 12 61.32 - 76.65: 4 Dihedral angle restraints: 2009 sinusoidal: 771 harmonic: 1238 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 26.90 66.10 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CA GLN H 3 " pdb=" C GLN H 3 " pdb=" N LEU H 4 " pdb=" CA LEU H 4 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -132.09 46.09 1 1.00e+01 1.00e-02 2.94e+01 ... (remaining 2006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 308 0.032 - 0.063: 120 0.063 - 0.095: 41 0.095 - 0.127: 22 0.127 - 0.159: 4 Chirality restraints: 495 Sorted by residual: chirality pdb=" CB ILE L 49 " pdb=" CA ILE L 49 " pdb=" CG1 ILE L 49 " pdb=" CG2 ILE L 49 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA VAL A 401 " pdb=" N VAL A 401 " pdb=" C VAL A 401 " pdb=" CB VAL A 401 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 492 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 448 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.02e+00 pdb=" C ASN A 448 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 448 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR A 449 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 521 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO H 14 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.020 5.00e-02 4.00e+02 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 44 2.52 - 3.11: 2497 3.11 - 3.71: 5200 3.71 - 4.30: 7066 4.30 - 4.90: 11389 Nonbonded interactions: 26196 Sorted by model distance: nonbonded pdb=" O VAL L 29 " pdb=" ND1 HIS L 93 " model vdw 1.925 3.120 nonbonded pdb=" CE2 TYR L 33 " pdb=" CD2 HIS L 93 " model vdw 1.951 3.560 nonbonded pdb=" CD2 TYR L 33 " pdb=" CD2 HIS L 93 " model vdw 1.983 3.560 nonbonded pdb=" OH TYR H 60 " pdb=" O THR H 65 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR H 33 " pdb=" O PHE H 99 " model vdw 2.207 3.040 ... (remaining 26191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 2.540 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.220 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 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 0.033 3406 Z= 0.166 Angle : 0.649 6.271 4624 Z= 0.369 Chirality : 0.043 0.159 495 Planarity : 0.004 0.047 593 Dihedral : 13.209 76.650 1207 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.11 % Favored : 91.65 % Rotamer: Outliers : 1.38 % Allowed : 1.65 % Favored : 96.97 % 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: -2.76 (0.39), residues: 419 helix: -4.04 (0.68), residues: 30 sheet: -0.91 (0.48), residues: 123 loop : -2.11 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 48 HIS 0.002 0.001 HIS L 35 PHE 0.011 0.001 PHE H 27 TYR 0.013 0.001 TYR H 95 ARG 0.001 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.9212 (m-80) cc_final: 0.8985 (m-80) REVERT: A 451 TYR cc_start: 0.4870 (OUTLIER) cc_final: 0.4556 (m-10) REVERT: A 489 TYR cc_start: 0.7475 (m-80) cc_final: 0.7107 (m-10) REVERT: H 4 LEU cc_start: 0.6374 (mt) cc_final: 0.5859 (mp) REVERT: H 101 ASN cc_start: 0.7598 (p0) cc_final: 0.7169 (p0) REVERT: H 103 GLU cc_start: 0.7792 (tp30) cc_final: 0.7303 (tm-30) REVERT: L 75 THR cc_start: 0.7609 (t) cc_final: 0.7089 (m) outliers start: 5 outliers final: 2 residues processed: 98 average time/residue: 0.2426 time to fit residues: 26.9948 Evaluate side-chains 54 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain L residue 94 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2673 > 50: distance: 6 - 8: 25.126 distance: 8 - 9: 22.123 distance: 9 - 10: 8.282 distance: 10 - 11: 19.621 distance: 10 - 12: 31.465 distance: 12 - 13: 29.749 distance: 13 - 14: 16.820 distance: 13 - 16: 7.063 distance: 14 - 15: 38.050 distance: 14 - 20: 11.829 distance: 16 - 17: 11.099 distance: 17 - 18: 41.472 distance: 17 - 19: 27.917 distance: 20 - 21: 10.257 distance: 21 - 22: 44.163 distance: 21 - 24: 34.490 distance: 22 - 23: 17.828 distance: 22 - 27: 42.296 distance: 24 - 25: 48.776 distance: 24 - 26: 14.809 distance: 27 - 28: 14.434 distance: 28 - 29: 37.116 distance: 28 - 31: 33.944 distance: 29 - 30: 55.687 distance: 29 - 36: 32.484 distance: 31 - 32: 34.210 distance: 32 - 33: 34.704 distance: 33 - 34: 20.762 distance: 34 - 35: 26.726 distance: 36 - 37: 14.297 distance: 36 - 42: 17.286 distance: 37 - 38: 25.967 distance: 37 - 40: 9.204 distance: 38 - 39: 22.892 distance: 38 - 43: 26.838 distance: 40 - 41: 35.122 distance: 41 - 42: 42.502 distance: 43 - 44: 16.024 distance: 44 - 45: 32.297 distance: 45 - 46: 15.678 distance: 45 - 47: 17.199 distance: 47 - 48: 19.728 distance: 48 - 49: 39.838 distance: 49 - 50: 48.651 distance: 49 - 51: 33.808 distance: 51 - 52: 15.233 distance: 52 - 53: 33.239 distance: 52 - 55: 16.535 distance: 53 - 54: 21.292 distance: 53 - 57: 18.268 distance: 55 - 56: 19.169 distance: 57 - 58: 22.650 distance: 58 - 59: 36.796 distance: 58 - 61: 9.203 distance: 59 - 60: 22.248 distance: 59 - 65: 38.023 distance: 61 - 62: 25.886 distance: 62 - 63: 14.299 distance: 62 - 64: 19.458 distance: 65 - 66: 21.331 distance: 66 - 67: 15.876 distance: 66 - 69: 25.621 distance: 67 - 68: 3.492 distance: 67 - 74: 32.669 distance: 69 - 70: 41.469 distance: 70 - 71: 45.616 distance: 71 - 72: 28.487 distance: 72 - 73: 23.712