Starting phenix.real_space_refine on Thu May 15 20:44:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tkt_25981/05_2025/7tkt_25981.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tkt_25981/05_2025/7tkt_25981.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/7tkt_25981/05_2025/7tkt_25981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tkt_25981/05_2025/7tkt_25981.map" model { file = "/net/cci-nas-00/data/ceres_data/7tkt_25981/05_2025/7tkt_25981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tkt_25981/05_2025/7tkt_25981.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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 28 5.16 5 C 8844 2.51 5 N 2080 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13252 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNA': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 104 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNA': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 104 Restraints were copied for chains: B, C Time building chain proxies: 8.90, per 1000 atoms: 0.67 Number of scatterers: 13252 At special positions: 0 Unit cell: (105.226, 105.226, 122.763, 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 28 16.00 P 12 15.00 O 2288 8.00 N 2080 7.00 C 8844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 153 " distance=0.00 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 387 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 63.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.108A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.109A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 416 " --> pdb=" O GLN B 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.010A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 Processing helix chain 'C' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 306 through 315 removed outlier: 4.107A pdb=" N ILE C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 416 " --> pdb=" O GLN C 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.776A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 306 through 315 removed outlier: 4.107A pdb=" N ILE D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 416 " --> pdb=" O GLN D 412 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2088 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: 3.97 Time building geometry restraints manager: 3.78 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: 3845 1.34 - 1.45: 1694 1.45 - 1.57: 7881 1.57 - 1.69: 16 1.69 - 1.81: 56 Bond restraints: 13492 Sorted by residual: bond pdb=" C10 PGW B 513 " pdb=" C9 PGW B 513 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C10 PGW D 502 " pdb=" C9 PGW D 502 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW B 510 " pdb=" C9 PGW B 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW A 510 " pdb=" C9 PGW A 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 ... (remaining 13487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 17753 4.21 - 8.43: 379 8.43 - 12.64: 8 12.64 - 16.86: 0 16.86 - 21.07: 16 Bond angle restraints: 18156 Sorted by residual: angle pdb=" C10 PGW B 513 " pdb=" C9 PGW B 513 " pdb=" C8 PGW B 513 " ideal model delta sigma weight residual 127.02 105.95 21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW D 505 " pdb=" C9 PGW D 505 " pdb=" C8 PGW D 505 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW C 513 " pdb=" C9 PGW C 513 " pdb=" C8 PGW C 513 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW A 513 " pdb=" C9 PGW A 513 " pdb=" C8 PGW A 513 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " pdb=" C8 PGW C 510 " ideal model delta sigma weight residual 127.02 106.26 20.76 3.00e+00 1.11e-01 4.79e+01 ... (remaining 18151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 7976 34.68 - 69.36: 208 69.36 - 104.04: 52 104.04 - 138.71: 12 138.71 - 173.39: 32 Dihedral angle restraints: 8280 sinusoidal: 3692 harmonic: 4588 Sorted by residual: dihedral pdb=" C3' CMP C 501 " pdb=" O3' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.95 -160.95 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C3' CMP D 507 " pdb=" O3' CMP D 507 " pdb=" P CMP D 507 " pdb=" O1P CMP D 507 " ideal model delta sinusoidal sigma weight residual -60.00 100.94 -160.94 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C3' CMP A 501 " pdb=" O3' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.94 -160.94 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 8277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1311 0.034 - 0.069: 547 0.069 - 0.103: 191 0.103 - 0.137: 39 0.137 - 0.171: 12 Chirality restraints: 2100 Sorted by residual: chirality pdb=" C02 PGW C 503 " pdb=" C01 PGW C 503 " pdb=" C03 PGW C 503 " pdb=" O01 PGW C 503 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" C02 PGW D 509 " pdb=" C01 PGW D 509 " pdb=" C03 PGW D 509 " pdb=" O01 PGW D 509 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA GLN D 412 " pdb=" N GLN D 412 " pdb=" C GLN D 412 " pdb=" CB GLN D 412 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 2097 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 513 " -0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW B 513 " 0.161 2.00e-02 2.50e+03 pdb=" C8 PGW B 513 " -0.158 2.00e-02 2.50e+03 pdb=" C9 PGW B 513 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 505 " 0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW D 505 " -0.161 2.00e-02 2.50e+03 pdb=" C8 PGW D 505 " 0.158 2.00e-02 2.50e+03 pdb=" C9 PGW D 505 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 513 " 0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW C 513 " -0.161 2.00e-02 2.50e+03 pdb=" C8 PGW C 513 " 0.158 2.00e-02 2.50e+03 pdb=" C9 PGW C 513 " -0.156 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1950 2.76 - 3.29: 12129 3.29 - 3.83: 21391 3.83 - 4.36: 22528 4.36 - 4.90: 40837 Nonbonded interactions: 98835 Sorted by model distance: nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 262 " pdb=" OD2 ASP B 388 " model vdw 2.264 3.040 ... (remaining 98830 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: 0.10 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'B' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'C' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'D' and (resid 10 through 416 or resid 502 or (resid 504 through 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 508 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resi \ d 509 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28)) or resid 510 through 511 or resid 513 through 514)) } 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: 0.940 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 31.910 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.040 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.007 0.171 13492 Z= 0.327 Angle : 1.264 21.069 18158 Z= 0.478 Chirality : 0.044 0.171 2100 Planarity : 0.008 0.159 2172 Dihedral : 21.053 173.393 5316 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1544 helix: 1.56 (0.18), residues: 936 sheet: 0.59 (0.57), residues: 84 loop : -1.78 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 264 HIS 0.002 0.001 HIS C 292 PHE 0.005 0.001 PHE D 386 TYR 0.009 0.001 TYR B 26 ARG 0.001 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.12057 ( 728) hydrogen bonds : angle 5.41712 ( 2088) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00659 (13492) covalent geometry : angle 1.26412 (18156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.374 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2453 time to fit residues: 54.6258 Evaluate side-chains 125 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.157068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123753 restraints weight = 21024.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123520 restraints weight = 15827.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123976 restraints weight = 13986.713| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13492 Z= 0.132 Angle : 0.620 9.100 18158 Z= 0.289 Chirality : 0.041 0.132 2100 Planarity : 0.004 0.042 2172 Dihedral : 21.069 163.069 2372 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.30 % Allowed : 7.61 % Favored : 92.09 % 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: 0.84 (0.23), residues: 1544 helix: 1.93 (0.18), residues: 928 sheet: -0.65 (0.41), residues: 156 loop : -1.94 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.003 0.001 HIS A 149 PHE 0.012 0.001 PHE D 40 TYR 0.013 0.001 TYR D 25 ARG 0.002 0.000 ARG C 382 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 728) hydrogen bonds : angle 4.13000 ( 2088) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00300 (13492) covalent geometry : angle 0.62040 (18156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 1.519 Fit side-chains REVERT: A 82 LEU cc_start: 0.7433 (tt) cc_final: 0.6702 (mp) REVERT: B 57 ASP cc_start: 0.5581 (t0) cc_final: 0.5180 (p0) REVERT: B 82 LEU cc_start: 0.7429 (tt) cc_final: 0.6693 (mp) REVERT: C 82 LEU cc_start: 0.7422 (tt) cc_final: 0.6706 (mp) REVERT: D 82 LEU cc_start: 0.7423 (tt) cc_final: 0.6708 (mp) REVERT: D 369 MET cc_start: 0.7664 (tpp) cc_final: 0.7453 (tpt) outliers start: 4 outliers final: 0 residues processed: 126 average time/residue: 0.2413 time to fit residues: 46.1271 Evaluate side-chains 115 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 142 optimal weight: 0.0980 chunk 136 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 0.0370 chunk 50 optimal weight: 3.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.159827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126476 restraints weight = 21306.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126438 restraints weight = 15634.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127040 restraints weight = 13846.225| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13492 Z= 0.107 Angle : 0.590 9.093 18158 Z= 0.271 Chirality : 0.040 0.135 2100 Planarity : 0.004 0.039 2172 Dihedral : 18.217 163.544 2372 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.60 % Allowed : 12.76 % Favored : 86.64 % 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: 1.11 (0.23), residues: 1544 helix: 2.05 (0.18), residues: 928 sheet: -0.95 (0.45), residues: 120 loop : -1.43 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 176 HIS 0.001 0.000 HIS B 149 PHE 0.040 0.001 PHE A 40 TYR 0.008 0.001 TYR D 170 ARG 0.001 0.000 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 728) hydrogen bonds : angle 3.76579 ( 2088) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00231 (13492) covalent geometry : angle 0.59027 (18156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.353 Fit side-chains REVERT: A 82 LEU cc_start: 0.7391 (tt) cc_final: 0.6707 (mp) REVERT: B 82 LEU cc_start: 0.7377 (tt) cc_final: 0.6706 (mp) REVERT: C 82 LEU cc_start: 0.7381 (tt) cc_final: 0.6710 (mp) REVERT: D 82 LEU cc_start: 0.7384 (tt) cc_final: 0.6711 (mp) outliers start: 8 outliers final: 0 residues processed: 148 average time/residue: 0.2222 time to fit residues: 50.2904 Evaluate side-chains 123 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 68.7831 > 50: distance: 88 - 92: 15.624 distance: 92 - 93: 14.436 distance: 93 - 94: 15.973 distance: 93 - 96: 29.389 distance: 94 - 95: 33.611 distance: 94 - 100: 22.826 distance: 95 - 114: 61.740 distance: 96 - 97: 25.686 distance: 97 - 98: 40.457 distance: 97 - 99: 35.391 distance: 100 - 101: 27.512 distance: 101 - 102: 29.040 distance: 101 - 104: 38.918 distance: 102 - 103: 51.126 distance: 102 - 108: 19.725 distance: 104 - 105: 11.886 distance: 105 - 106: 20.437 distance: 105 - 107: 18.314 distance: 108 - 109: 9.694 distance: 109 - 110: 19.368 distance: 109 - 112: 40.675 distance: 110 - 111: 34.404 distance: 110 - 114: 41.837 distance: 112 - 113: 48.359 distance: 114 - 115: 21.842 distance: 115 - 116: 15.626 distance: 115 - 118: 27.839 distance: 116 - 117: 27.503 distance: 116 - 122: 36.430 distance: 117 - 140: 43.058 distance: 118 - 119: 32.270 distance: 119 - 120: 17.334 distance: 119 - 121: 13.671 distance: 122 - 123: 14.202 distance: 123 - 124: 26.869 distance: 123 - 126: 43.853 distance: 124 - 125: 13.528 distance: 124 - 129: 27.086 distance: 126 - 127: 41.520 distance: 126 - 128: 33.544 distance: 129 - 130: 26.759 distance: 130 - 131: 34.786 distance: 130 - 133: 15.951 distance: 131 - 132: 25.999 distance: 131 - 140: 18.234 distance: 133 - 134: 17.326 distance: 134 - 135: 24.767 distance: 135 - 136: 9.182 distance: 136 - 137: 7.663 distance: 137 - 138: 4.794 distance: 137 - 139: 6.014 distance: 140 - 141: 13.663 distance: 141 - 142: 24.828 distance: 141 - 144: 40.376 distance: 142 - 143: 21.563 distance: 142 - 148: 4.383 distance: 144 - 145: 16.276 distance: 145 - 146: 9.933 distance: 145 - 147: 16.441 distance: 148 - 149: 12.525 distance: 149 - 150: 23.190 distance: 149 - 152: 19.376 distance: 150 - 151: 34.067 distance: 150 - 156: 23.092 distance: 152 - 153: 6.315 distance: 153 - 154: 11.262 distance: 153 - 155: 12.310 distance: 156 - 157: 10.703 distance: 157 - 158: 12.217 distance: 157 - 160: 19.546 distance: 158 - 159: 14.795 distance: 158 - 165: 8.137 distance: 159 - 187: 13.350 distance: 160 - 161: 11.046 distance: 161 - 162: 10.150 distance: 162 - 163: 7.345 distance: 163 - 164: 5.368 distance: 165 - 166: 19.457 distance: 166 - 167: 24.499 distance: 166 - 169: 31.264 distance: 167 - 168: 18.100 distance: 167 - 173: 9.897 distance: 168 - 194: 4.841 distance: 169 - 170: 18.962 distance: 170 - 171: 16.312 distance: 170 - 172: 10.161 distance: 176 - 198: 3.008