Starting phenix.real_space_refine on Sat Jan 18 07:42:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p5a_20254/01_2025/6p5a_20254.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p5a_20254/01_2025/6p5a_20254.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/cci-nas-00/data/ceres_data/6p5a_20254/01_2025/6p5a_20254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p5a_20254/01_2025/6p5a_20254.map" model { file = "/net/cci-nas-00/data/ceres_data/6p5a_20254/01_2025/6p5a_20254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p5a_20254/01_2025/6p5a_20254.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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 142 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7150 2.51 5 N 2076 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11948 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3568 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 428} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 980 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 896 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "G" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3568 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 428} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 980 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "J" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "K" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 896 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.96, per 1000 atoms: 0.58 Number of scatterers: 11948 At special positions: 0 Unit cell: (126.44, 110.2, 106.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 142 15.00 Mg 4 11.99 O 2540 8.00 N 2076 7.00 C 7150 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.2 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 58.7% alpha, 8.2% beta 54 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.673A pdb=" N GLU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 183 removed outlier: 3.790A pdb=" N HIS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.808A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.567A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.558A pdb=" N SER A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.949A pdb=" N ILE A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.820A pdb=" N ALA A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.376A pdb=" N ASP A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 515 Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.974A pdb=" N ASN A 526 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 548 through 563 removed outlier: 3.515A pdb=" N ARG A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 568 removed outlier: 3.792A pdb=" N MET A 567 " --> pdb=" O ASN A 564 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 568 " --> pdb=" O THR A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 564 through 568' Processing helix chain 'B' and resid 620 through 639 Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.711A pdb=" N SER B 657 " --> pdb=" O VAL B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 682 Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 708 through 734 removed outlier: 3.626A pdb=" N LYS B 712 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 140 removed outlier: 3.673A pdb=" N GLU G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 149 Processing helix chain 'G' and resid 158 through 170 Processing helix chain 'G' and resid 172 through 183 removed outlier: 3.791A pdb=" N HIS G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 197 Processing helix chain 'G' and resid 206 through 213 removed outlier: 3.807A pdb=" N ILE G 210 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET G 213 " --> pdb=" O VAL G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 294 Processing helix chain 'G' and resid 305 through 315 removed outlier: 3.568A pdb=" N LEU G 311 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 354 removed outlier: 3.557A pdb=" N SER G 354 " --> pdb=" O HIS G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 376 Processing helix chain 'G' and resid 387 through 392 removed outlier: 3.950A pdb=" N ILE G 391 " --> pdb=" O ASN G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 408 removed outlier: 3.820A pdb=" N ALA G 404 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 422 Processing helix chain 'G' and resid 428 through 446 Processing helix chain 'G' and resid 465 through 480 removed outlier: 4.377A pdb=" N ASP G 471 " --> pdb=" O ASP G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 491 through 515 Processing helix chain 'G' and resid 521 through 526 removed outlier: 3.974A pdb=" N ASN G 526 " --> pdb=" O SER G 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 540 Processing helix chain 'G' and resid 548 through 563 removed outlier: 3.514A pdb=" N ARG G 563 " --> pdb=" O TYR G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 564 through 568 removed outlier: 3.792A pdb=" N MET G 567 " --> pdb=" O ASN G 564 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU G 568 " --> pdb=" O THR G 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 564 through 568' Processing helix chain 'H' and resid 620 through 639 Processing helix chain 'H' and resid 652 through 657 removed outlier: 3.711A pdb=" N SER H 657 " --> pdb=" O VAL H 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 667 through 682 Processing helix chain 'H' and resid 693 through 702 Processing helix chain 'H' and resid 708 through 734 removed outlier: 3.626A pdb=" N LYS H 712 " --> pdb=" O ASP H 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 205 removed outlier: 6.491A pdb=" N ALA A 257 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 272 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN A 255 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE A 274 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR A 253 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS A 225 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 300 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 227 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER A 302 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 229 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N LEU A 296 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N PHE A 335 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 298 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE A 337 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 300 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.796A pdb=" N ILE A 246 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA4, first strand: chain 'G' and resid 204 through 205 removed outlier: 6.491A pdb=" N ALA G 257 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE G 272 " --> pdb=" O GLN G 255 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN G 255 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE G 274 " --> pdb=" O TYR G 253 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR G 253 " --> pdb=" O PHE G 274 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS G 225 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE G 300 " --> pdb=" O CYS G 225 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU G 227 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER G 302 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE G 229 " --> pdb=" O SER G 302 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N LEU G 296 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N PHE G 335 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL G 298 " --> pdb=" O PHE G 335 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE G 337 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE G 300 " --> pdb=" O PHE G 337 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 239 through 241 removed outlier: 3.795A pdb=" N ILE G 246 " --> pdb=" O ASP G 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 356 through 358 475 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 256 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 3.31 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: 2863 1.34 - 1.45: 3084 1.45 - 1.57: 6177 1.57 - 1.69: 274 1.69 - 1.81: 56 Bond restraints: 12454 Sorted by residual: bond pdb=" C THR A 548 " pdb=" N PRO A 549 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.90e+00 bond pdb=" C THR G 548 " pdb=" N PRO G 549 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.85e+00 bond pdb=" C3' DT E -2 " pdb=" C2' DT E -2 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.08e+00 bond pdb=" C3' DT K -2 " pdb=" C2' DT K -2 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.05e+00 bond pdb=" O5' DA E -3 " pdb=" C5' DA E -3 " ideal model delta sigma weight residual 1.423 1.394 0.029 3.00e-02 1.11e+03 9.50e-01 ... (remaining 12449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 16522 1.09 - 2.19: 692 2.19 - 3.28: 152 3.28 - 4.38: 20 4.38 - 5.47: 12 Bond angle restraints: 17398 Sorted by residual: angle pdb=" C4' DA K -3 " pdb=" C3' DA K -3 " pdb=" C2' DA K -3 " ideal model delta sigma weight residual 102.40 107.10 -4.70 1.50e+00 4.44e-01 9.83e+00 angle pdb=" C4' DA E -3 " pdb=" C3' DA E -3 " pdb=" C2' DA E -3 " ideal model delta sigma weight residual 102.40 107.10 -4.70 1.50e+00 4.44e-01 9.80e+00 angle pdb=" C3' DA K -3 " pdb=" O3' DA K -3 " pdb=" P DT K -2 " ideal model delta sigma weight residual 120.20 116.46 3.74 1.50e+00 4.44e-01 6.21e+00 angle pdb=" C3' DA E -3 " pdb=" O3' DA E -3 " pdb=" P DT E -2 " ideal model delta sigma weight residual 120.20 116.46 3.74 1.50e+00 4.44e-01 6.21e+00 angle pdb=" C4 DT E -13 " pdb=" C5 DT E -13 " pdb=" C7 DT E -13 " ideal model delta sigma weight residual 122.40 118.97 3.43 1.50e+00 4.44e-01 5.23e+00 ... (remaining 17393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.76: 6564 34.76 - 69.51: 518 69.51 - 104.27: 12 104.27 - 139.02: 4 139.02 - 173.78: 6 Dihedral angle restraints: 7104 sinusoidal: 3798 harmonic: 3306 Sorted by residual: dihedral pdb=" C8 GTP A 601 " pdb=" C1' GTP A 601 " pdb=" N9 GTP A 601 " pdb=" O4' GTP A 601 " ideal model delta sinusoidal sigma weight residual 104.59 -31.60 136.20 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C8 GTP G 602 " pdb=" C1' GTP G 602 " pdb=" N9 GTP G 602 " pdb=" O4' GTP G 602 " ideal model delta sinusoidal sigma weight residual 104.59 -31.56 136.16 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C4' DT E -13 " pdb=" C3' DT E -13 " pdb=" O3' DT E -13 " pdb=" P DT E -12 " ideal model delta sinusoidal sigma weight residual -140.00 33.78 -173.78 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1645 0.048 - 0.095: 241 0.095 - 0.143: 55 0.143 - 0.191: 3 0.191 - 0.239: 2 Chirality restraints: 1946 Sorted by residual: chirality pdb=" C3' DA K -3 " pdb=" C4' DA K -3 " pdb=" O3' DA K -3 " pdb=" C2' DA K -3 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' DA E -3 " pdb=" C4' DA E -3 " pdb=" O3' DA E -3 " pdb=" C2' DA E -3 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO G 549 " pdb=" N PRO G 549 " pdb=" C PRO G 549 " pdb=" CB PRO G 549 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1943 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN G 268 " -0.034 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO G 269 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 269 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 269 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 268 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 269 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 172 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO G 173 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " 0.023 5.00e-02 4.00e+02 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 30 2.49 - 3.09: 7784 3.09 - 3.70: 18319 3.70 - 4.30: 27816 4.30 - 4.90: 43456 Nonbonded interactions: 97405 Sorted by model distance: nonbonded pdb=" OD1 ASN A 440 " pdb="MG MG A 602 " model vdw 1.890 2.170 nonbonded pdb=" OD1 ASN G 440 " pdb="MG MG G 603 " model vdw 1.907 2.170 nonbonded pdb=" O3' DA I 9 " pdb="MG MG G 601 " model vdw 2.077 2.170 nonbonded pdb=" O3' DA C 9 " pdb="MG MG A 603 " model vdw 2.078 2.170 nonbonded pdb=" OD2 ASP A 303 " pdb="MG MG A 603 " model vdw 2.135 2.170 ... (remaining 97400 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 128 through 569 or resid 603)) selection = (chain 'G' and (resid 128 through 569 or resid 603)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } 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: 1.950 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.420 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 0.032 12454 Z= 0.148 Angle : 0.526 5.475 17398 Z= 0.316 Chirality : 0.037 0.239 1946 Planarity : 0.004 0.052 1730 Dihedral : 20.140 173.780 4960 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -1.69 (0.22), residues: 1112 helix: -0.46 (0.18), residues: 622 sheet: -2.11 (0.47), residues: 60 loop : -1.85 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 442 HIS 0.002 0.001 HIS G 546 PHE 0.014 0.001 PHE A 272 TYR 0.008 0.001 TYR H 629 ARG 0.002 0.000 ARG G 569 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.050 Fit side-chains REVERT: A 273 ASP cc_start: 0.7712 (t70) cc_final: 0.7429 (t0) REVERT: A 476 MET cc_start: 0.8352 (tpp) cc_final: 0.7614 (tpt) REVERT: A 563 ARG cc_start: 0.7328 (ptm-80) cc_final: 0.6931 (ptm160) REVERT: A 567 MET cc_start: 0.7410 (tpp) cc_final: 0.7168 (tpt) REVERT: B 700 LEU cc_start: 0.8528 (tt) cc_final: 0.7511 (mt) REVERT: G 239 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7741 (mm-30) REVERT: G 273 ASP cc_start: 0.7731 (t70) cc_final: 0.7445 (t0) REVERT: G 476 MET cc_start: 0.8359 (tpp) cc_final: 0.7617 (tpt) REVERT: G 563 ARG cc_start: 0.7332 (ptm-80) cc_final: 0.6935 (ptm160) REVERT: G 567 MET cc_start: 0.7427 (tpp) cc_final: 0.7150 (tpt) REVERT: H 700 LEU cc_start: 0.8525 (tt) cc_final: 0.7504 (mt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3080 time to fit residues: 95.4572 Evaluate side-chains 134 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 546 HIS B 669 GLN B 685 ASN B 686 ASN G 150 ASN G 546 HIS H 669 GLN H 685 ASN H 686 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.109577 restraints weight = 15171.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112878 restraints weight = 9615.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.115133 restraints weight = 7102.186| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12454 Z= 0.333 Angle : 0.598 7.471 17398 Z= 0.333 Chirality : 0.041 0.142 1946 Planarity : 0.004 0.053 1730 Dihedral : 25.190 173.289 2698 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.59 % Allowed : 9.92 % Favored : 88.49 % 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: -0.38 (0.24), residues: 1112 helix: 0.58 (0.19), residues: 616 sheet: -1.10 (0.52), residues: 72 loop : -1.26 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 312 HIS 0.004 0.001 HIS A 342 PHE 0.013 0.001 PHE A 324 TYR 0.017 0.001 TYR A 559 ARG 0.004 0.001 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.099 Fit side-chains REVERT: A 310 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8599 (ttpp) REVERT: A 370 GLU cc_start: 0.7640 (tt0) cc_final: 0.7403 (tt0) REVERT: A 476 MET cc_start: 0.8497 (tpp) cc_final: 0.7859 (tpt) REVERT: A 563 ARG cc_start: 0.7342 (ptm-80) cc_final: 0.6970 (ptp90) REVERT: A 567 MET cc_start: 0.7468 (tpp) cc_final: 0.7210 (tpt) REVERT: B 674 GLU cc_start: 0.7800 (tp30) cc_final: 0.7215 (tp30) REVERT: B 696 GLU cc_start: 0.8085 (tp30) cc_final: 0.7825 (tm-30) REVERT: G 310 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8612 (ttpp) REVERT: G 476 MET cc_start: 0.8499 (tpp) cc_final: 0.7888 (tpt) REVERT: G 563 ARG cc_start: 0.7335 (ptm-80) cc_final: 0.6937 (ptp90) REVERT: G 567 MET cc_start: 0.7468 (tpp) cc_final: 0.7217 (tpt) REVERT: H 674 GLU cc_start: 0.7800 (tp30) cc_final: 0.7214 (tp30) REVERT: H 696 GLU cc_start: 0.8078 (tp30) cc_final: 0.7834 (tm-30) outliers start: 16 outliers final: 8 residues processed: 148 average time/residue: 0.2767 time to fit residues: 60.2841 Evaluate side-chains 124 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 310 LYS Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 439 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 95 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 546 HIS G 546 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114774 restraints weight = 15012.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118492 restraints weight = 9095.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120979 restraints weight = 6496.929| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12454 Z= 0.177 Angle : 0.500 6.741 17398 Z= 0.281 Chirality : 0.036 0.122 1946 Planarity : 0.004 0.056 1730 Dihedral : 24.628 176.507 2698 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.19 % Allowed : 12.70 % Favored : 86.11 % 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: 0.51 (0.25), residues: 1112 helix: 1.38 (0.20), residues: 618 sheet: -0.45 (0.66), residues: 48 loop : -1.04 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 312 HIS 0.003 0.001 HIS A 342 PHE 0.009 0.001 PHE G 493 TYR 0.017 0.001 TYR G 559 ARG 0.003 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.143 Fit side-chains REVERT: A 476 MET cc_start: 0.8336 (tpp) cc_final: 0.7853 (tpt) REVERT: A 563 ARG cc_start: 0.7421 (ptm-80) cc_final: 0.7014 (ptp90) REVERT: A 567 MET cc_start: 0.7336 (tpp) cc_final: 0.7127 (tpt) REVERT: G 239 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7676 (mm-30) REVERT: G 370 GLU cc_start: 0.7578 (tt0) cc_final: 0.7342 (tt0) REVERT: G 476 MET cc_start: 0.8338 (tpp) cc_final: 0.7843 (tpt) REVERT: G 563 ARG cc_start: 0.7441 (ptm-80) cc_final: 0.7004 (ptp90) outliers start: 12 outliers final: 0 residues processed: 135 average time/residue: 0.2528 time to fit residues: 49.3665 Evaluate side-chains 113 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 70.9017 > 50: distance: 107 - 114: 33.634 distance: 114 - 120: 40.559 distance: 115 - 116: 14.011 distance: 116 - 117: 48.697 distance: 116 - 121: 48.742 distance: 119 - 120: 39.241 distance: 121 - 122: 6.868 distance: 122 - 123: 41.890 distance: 123 - 124: 49.173 distance: 123 - 128: 55.460 distance: 124 - 152: 41.619 distance: 125 - 126: 69.559 distance: 125 - 127: 69.077 distance: 128 - 129: 27.975 distance: 128 - 134: 11.349 distance: 129 - 130: 23.565 distance: 129 - 132: 29.940 distance: 130 - 131: 10.091 distance: 130 - 135: 17.929 distance: 131 - 163: 34.358 distance: 132 - 133: 29.622 distance: 133 - 134: 33.456 distance: 135 - 136: 25.150 distance: 136 - 137: 23.526 distance: 136 - 139: 23.246 distance: 137 - 138: 32.693 distance: 137 - 143: 19.037 distance: 138 - 172: 17.565 distance: 139 - 140: 10.362 distance: 140 - 141: 24.962 distance: 140 - 142: 19.748 distance: 143 - 144: 11.201 distance: 144 - 145: 35.194 distance: 144 - 147: 47.053 distance: 145 - 146: 34.879 distance: 145 - 152: 40.862 distance: 146 - 184: 38.136 distance: 147 - 148: 17.616 distance: 148 - 149: 22.382 distance: 149 - 150: 15.284 distance: 149 - 151: 11.977 distance: 152 - 153: 22.913 distance: 153 - 154: 40.979 distance: 153 - 156: 6.282 distance: 154 - 155: 3.362 distance: 154 - 163: 36.821 distance: 155 - 195: 48.654 distance: 156 - 157: 3.681 distance: 157 - 158: 23.110 distance: 157 - 159: 12.794 distance: 158 - 160: 20.355 distance: 159 - 161: 35.564 distance: 160 - 162: 31.918 distance: 161 - 162: 32.492 distance: 163 - 164: 26.186 distance: 164 - 165: 13.493 distance: 164 - 167: 35.046 distance: 165 - 166: 7.902 distance: 165 - 172: 37.557 distance: 166 - 203: 32.324 distance: 167 - 168: 27.533 distance: 168 - 169: 24.985 distance: 169 - 170: 21.481 distance: 170 - 171: 17.665 distance: 172 - 173: 3.666 distance: 173 - 174: 45.251 distance: 173 - 176: 9.832 distance: 174 - 175: 11.492 distance: 174 - 184: 11.391 distance: 175 - 213: 27.626 distance: 176 - 177: 34.461 distance: 177 - 178: 17.205 distance: 177 - 179: 25.625 distance: 178 - 180: 15.100 distance: 179 - 181: 23.395 distance: 180 - 182: 11.247 distance: 181 - 182: 12.447 distance: 182 - 183: 8.672 distance: 184 - 185: 32.147 distance: 185 - 186: 19.861 distance: 185 - 188: 27.008 distance: 186 - 187: 28.030 distance: 186 - 195: 20.920 distance: 187 - 220: 29.783 distance: 188 - 189: 39.531 distance: 189 - 190: 26.586 distance: 190 - 191: 34.756 distance: 191 - 192: 12.282 distance: 192 - 193: 5.369 distance: 192 - 194: 4.180 distance: 195 - 196: 3.822 distance: 196 - 197: 28.890 distance: 196 - 199: 24.824 distance: 197 - 198: 25.185 distance: 197 - 203: 11.100 distance: 198 - 227: 35.248 distance: 199 - 200: 3.925 distance: 200 - 201: 5.841 distance: 200 - 202: 38.934