Starting phenix.real_space_refine on Thu Jan 18 20:05:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw3_27750/01_2024/8dw3_27750.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw3_27750/01_2024/8dw3_27750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw3_27750/01_2024/8dw3_27750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw3_27750/01_2024/8dw3_27750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw3_27750/01_2024/8dw3_27750.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw3_27750/01_2024/8dw3_27750.pdb" } resolution = 4.26 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= 0.002 sd= 0.019 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 33 5.16 5 C 5897 2.51 5 N 1564 2.21 5 O 1857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9351 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1140 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1521 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1624 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "H" Number of atoms: 1609 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 bond proxies already assigned to first conformer: 1646 Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1703 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.84, per 1000 atoms: 0.62 Number of scatterers: 9351 At special positions: 0 Unit cell: (82.062, 125.712, 174.6, 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 33 16.00 O 1857 8.00 N 1564 7.00 C 5897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.40 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 343 " Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 2.1 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 23 sheets defined 15.3% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 removed outlier: 3.928A pdb=" N GLU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.283A pdb=" N LEU A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.817A pdb=" N ASN A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 91 removed outlier: 3.930A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.747A pdb=" N GLU A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.610A pdb=" N LEU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 removed outlier: 4.251A pdb=" N VAL A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.938A pdb=" N ILE A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 4.275A pdb=" N ALA A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.543A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.558A pdb=" N ALA B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.803A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.789A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.869A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.640A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.606A pdb=" N LEU C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.724A pdb=" N SER D 31 " --> pdb=" O PRO D 28 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 199 through 203 removed outlier: 3.715A pdb=" N SER D 202 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.602A pdb=" N THR H 31 " --> pdb=" O GLY H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.947A pdb=" N GLN H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.989A pdb=" N VAL L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 134 Processing helix chain 'L' and resid 189 through 195 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.761A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.914A pdb=" N ARG C 24 " --> pdb=" O THR C 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 39 Processing sheet with id=AA6, first strand: chain 'C' and resid 34 through 39 Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 118 Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 150 Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.498A pdb=" N GLU D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY D 33 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 138 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 138 Processing sheet with id=AB5, first strand: chain 'D' and resid 165 through 168 removed outlier: 4.150A pdb=" N TYR D 208 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 2 through 5 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.734A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.734A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.630A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 185 " --> pdb=" O HIS H 168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.121A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.570A pdb=" N THR L 108 " --> pdb=" O TYR L 92 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 120 through 124 removed outlier: 5.933A pdb=" N TYR L 179 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 151 through 156 336 hydrogen bonds defined for protein. 864 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: 2.56 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.50 - 0.77: 1 0.77 - 1.04: 0 1.04 - 1.31: 1548 1.31 - 1.58: 7967 1.58 - 1.84: 46 Bond restraints: 9562 Sorted by residual: bond pdb=" CG PRO D 28 " pdb=" CD PRO D 28 " ideal model delta sigma weight residual 1.503 0.505 0.998 3.40e-02 8.65e+02 8.62e+02 bond pdb=" CG PRO C 204 " pdb=" CD PRO C 204 " ideal model delta sigma weight residual 1.503 1.060 0.443 3.40e-02 8.65e+02 1.70e+02 bond pdb=" N PRO D 28 " pdb=" CD PRO D 28 " ideal model delta sigma weight residual 1.473 1.589 -0.116 1.40e-02 5.10e+03 6.84e+01 bond pdb=" CB PRO D 28 " pdb=" CG PRO D 28 " ideal model delta sigma weight residual 1.492 1.844 -0.352 5.00e-02 4.00e+02 4.95e+01 bond pdb=" N PRO C 204 " pdb=" CD PRO C 204 " ideal model delta sigma weight residual 1.473 1.569 -0.096 1.40e-02 5.10e+03 4.73e+01 ... (remaining 9557 not shown) Histogram of bond angle deviations from ideal: 65.41 - 79.36: 1 79.36 - 93.30: 3 93.30 - 107.24: 323 107.24 - 121.19: 9690 121.19 - 135.13: 2987 Bond angle restraints: 13004 Sorted by residual: angle pdb=" N PRO D 28 " pdb=" CD PRO D 28 " pdb=" CG PRO D 28 " ideal model delta sigma weight residual 103.20 65.41 37.79 1.50e+00 4.44e-01 6.35e+02 angle pdb=" N PRO C 204 " pdb=" CD PRO C 204 " pdb=" CG PRO C 204 " ideal model delta sigma weight residual 103.20 81.48 21.72 1.50e+00 4.44e-01 2.10e+02 angle pdb=" CA PRO C 204 " pdb=" N PRO C 204 " pdb=" CD PRO C 204 " ideal model delta sigma weight residual 112.00 94.26 17.74 1.40e+00 5.10e-01 1.61e+02 angle pdb=" CA PRO D 28 " pdb=" CB PRO D 28 " pdb=" CG PRO D 28 " ideal model delta sigma weight residual 104.50 81.83 22.67 1.90e+00 2.77e-01 1.42e+02 angle pdb=" CA PRO C 81 " pdb=" N PRO C 81 " pdb=" CD PRO C 81 " ideal model delta sigma weight residual 112.00 96.12 15.88 1.40e+00 5.10e-01 1.29e+02 ... (remaining 12999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.00: 5008 21.00 - 42.01: 607 42.01 - 63.01: 88 63.01 - 84.01: 20 84.01 - 105.02: 6 Dihedral angle restraints: 5729 sinusoidal: 2221 harmonic: 3508 Sorted by residual: dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 210 " pdb=" CB CYS D 210 " ideal model delta sinusoidal sigma weight residual -86.00 -167.97 81.97 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 16.91 76.09 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS C 134 " pdb=" SG CYS C 134 " pdb=" SG CYS C 194 " pdb=" CB CYS C 194 " ideal model delta sinusoidal sigma weight residual -86.00 -161.05 75.05 1 1.00e+01 1.00e-02 7.12e+01 ... (remaining 5726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1453 0.131 - 0.263: 12 0.263 - 0.394: 2 0.394 - 0.525: 0 0.525 - 0.657: 1 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.77e+02 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA TRP D 50 " pdb=" N TRP D 50 " pdb=" C TRP D 50 " pdb=" CB TRP D 50 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1465 not shown) Planarity restraints: 1671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.081 2.00e-02 2.50e+03 6.71e-02 5.62e+01 pdb=" C7 NAG E 1 " 0.020 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.061 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.108 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 160 " 0.085 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO D 161 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 50 " 0.034 2.00e-02 2.50e+03 3.08e-02 2.37e+01 pdb=" CG TRP D 50 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP D 50 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP D 50 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 50 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 50 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP D 50 " 0.001 2.00e-02 2.50e+03 ... (remaining 1668 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 88 2.50 - 3.10: 6382 3.10 - 3.70: 13934 3.70 - 4.30: 18238 4.30 - 4.90: 30696 Nonbonded interactions: 69338 Sorted by model distance: nonbonded pdb=" NH1 ARG C 62 " pdb=" CG GLU C 80 " model vdw 1.895 3.520 nonbonded pdb=" OG1 THR B 345 " pdb=" OG SER D 109 " model vdw 2.105 2.440 nonbonded pdb=" O ILE C 106 " pdb=" OH TYR C 140 " model vdw 2.176 2.440 nonbonded pdb=" O SER C 121 " pdb=" NE2 GLN C 124 " model vdw 2.186 2.520 nonbonded pdb=" OG SER B 383 " pdb=" OG SER H 100 " model vdw 2.198 2.440 ... (remaining 69333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ through 20 or resid 23 or resid 26 through 27 or resid 29 through 31 or resid 3 \ 4 through 43 or resid 45 or resid 47 through 50 or resid 52 through 53 or resid \ 55 or resid 58 or resid 60 through 77 or resid 79 or resid 82 through 83 or resi \ d 85 through 91 or resid 94 or resid 97 through 99 or resid 101 through 213)) selection = (chain 'L' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ through 20 or resid 23 or resid 26 through 27 or resid 29 or resid 32 through 3 \ 3 or resid 39 through 48 or resid 50 or resid 52 through 55 or resid 57 through \ 58 or resid 60 or resid 63 or resid 65 through 82 or resid 84 or resid 87 throug \ h 88 or resid 90 through 96 or resid 100 or resid 103 through 105 or resid 107 t \ hrough 219)) } 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=0.00 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: 1.020 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: 4.000 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.800 Find NCS groups from input model: 0.430 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 : 0.013 0.998 9562 Z= 0.944 Angle : 0.949 37.787 13004 Z= 0.526 Chirality : 0.051 0.657 1468 Planarity : 0.008 0.122 1670 Dihedral : 17.592 105.017 3459 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.21 % Rotamer: Outliers : 0.10 % Allowed : 37.69 % Favored : 62.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.89 (0.24), residues: 1209 helix: -0.33 (0.49), residues: 104 sheet: 0.37 (0.27), residues: 418 loop : -1.29 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP D 50 HIS 0.005 0.001 HIS A 52 PHE 0.025 0.001 PHE L 145 TYR 0.041 0.001 TYR L 102 ARG 0.003 0.000 ARG L 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8274 (mp) cc_final: 0.7734 (tp) REVERT: B 489 TYR cc_start: 0.6882 (m-80) cc_final: 0.6449 (m-80) REVERT: C 117 ILE cc_start: 0.9102 (tt) cc_final: 0.8880 (tt) REVERT: C 154 LEU cc_start: 0.9124 (tp) cc_final: 0.8874 (pt) REVERT: D 48 MET cc_start: 0.6484 (mmm) cc_final: 0.6169 (tpp) REVERT: D 138 LEU cc_start: 0.7749 (tp) cc_final: 0.7006 (mp) REVERT: D 168 TRP cc_start: 0.7187 (m100) cc_final: 0.6603 (m100) REVERT: D 210 CYS cc_start: 0.4075 (t) cc_final: 0.2355 (t) REVERT: H 158 TRP cc_start: 0.7154 (m100) cc_final: 0.6662 (m100) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 0.2162 time to fit residues: 60.5495 Evaluate side-chains 128 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 30.0000 chunk 90 optimal weight: 0.0570 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 overall best weight: 3.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN C 6 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN H 204 HIS L 43 GLN ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9562 Z= 0.301 Angle : 0.690 7.585 13004 Z= 0.348 Chirality : 0.045 0.167 1468 Planarity : 0.006 0.083 1670 Dihedral : 6.507 56.955 1372 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.95 % Favored : 92.97 % Rotamer: Outliers : 0.39 % Allowed : 5.62 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % 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: -0.92 (0.25), residues: 1209 helix: -0.32 (0.47), residues: 118 sheet: 0.33 (0.27), residues: 418 loop : -1.31 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 50 HIS 0.008 0.001 HIS H 168 PHE 0.019 0.002 PHE C 98 TYR 0.016 0.002 TYR L 98 ARG 0.004 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 165 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 460 ASN cc_start: 0.8716 (t0) cc_final: 0.8443 (m-40) REVERT: C 118 PHE cc_start: 0.7248 (m-80) cc_final: 0.6780 (m-80) REVERT: D 30 THR cc_start: 0.8190 (p) cc_final: 0.7950 (t) REVERT: D 48 MET cc_start: 0.6544 (mmm) cc_final: 0.5441 (tpp) REVERT: D 70 MET cc_start: 0.7901 (mtp) cc_final: 0.7638 (mtm) REVERT: D 138 LEU cc_start: 0.7373 (tp) cc_final: 0.6876 (mp) REVERT: D 168 TRP cc_start: 0.7481 (m100) cc_final: 0.6733 (m100) REVERT: D 210 CYS cc_start: 0.4194 (t) cc_final: 0.2661 (t) REVERT: H 158 TRP cc_start: 0.6822 (m100) cc_final: 0.6553 (m100) outliers start: 4 outliers final: 2 residues processed: 169 average time/residue: 0.1922 time to fit residues: 46.6247 Evaluate side-chains 106 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN L 43 GLN ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9562 Z= 0.282 Angle : 0.653 9.496 13004 Z= 0.328 Chirality : 0.044 0.167 1468 Planarity : 0.005 0.062 1670 Dihedral : 5.562 33.973 1372 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.95 % Favored : 92.97 % Rotamer: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.00 (0.24), residues: 1209 helix: -0.29 (0.47), residues: 119 sheet: 0.20 (0.26), residues: 419 loop : -1.33 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 50 HIS 0.006 0.001 HIS H 168 PHE 0.015 0.002 PHE B 456 TYR 0.018 0.002 TYR B 396 ARG 0.009 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 460 ASN cc_start: 0.8751 (t0) cc_final: 0.8542 (m-40) REVERT: B 516 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7193 (tm-30) REVERT: C 118 PHE cc_start: 0.7248 (m-80) cc_final: 0.6670 (m-80) REVERT: D 48 MET cc_start: 0.6400 (mmm) cc_final: 0.5648 (tpp) REVERT: D 168 TRP cc_start: 0.7474 (m100) cc_final: 0.6754 (m100) REVERT: D 210 CYS cc_start: 0.4447 (t) cc_final: 0.3103 (t) REVERT: H 180 TYR cc_start: 0.7632 (m-10) cc_final: 0.7286 (m-10) outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 0.1949 time to fit residues: 42.2367 Evaluate side-chains 96 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 57.9356 > 50: distance: 4 - 7: 6.009 distance: 7 - 8: 9.474 distance: 8 - 9: 3.687 distance: 9 - 10: 29.781 distance: 9 - 16: 4.350 distance: 11 - 12: 31.471 distance: 12 - 13: 26.867 distance: 13 - 14: 7.735 distance: 13 - 15: 26.801 distance: 16 - 17: 19.456 distance: 17 - 18: 18.598 distance: 17 - 20: 15.056 distance: 18 - 19: 14.822 distance: 18 - 23: 19.832 distance: 20 - 21: 39.840 distance: 20 - 22: 34.254 distance: 23 - 24: 7.823 distance: 24 - 25: 30.709 distance: 24 - 27: 15.830 distance: 25 - 26: 41.600 distance: 25 - 32: 21.702 distance: 27 - 28: 24.352 distance: 28 - 29: 31.691 distance: 29 - 30: 18.474 distance: 30 - 31: 12.768 distance: 32 - 33: 19.611 distance: 33 - 34: 17.981 distance: 33 - 36: 40.617 distance: 34 - 35: 36.153 distance: 34 - 41: 31.825 distance: 36 - 37: 41.677 distance: 37 - 38: 47.009 distance: 38 - 39: 47.930 distance: 39 - 40: 36.589 distance: 41 - 42: 15.166 distance: 41 - 47: 30.961 distance: 42 - 43: 18.354 distance: 42 - 45: 26.179 distance: 43 - 44: 28.831 distance: 43 - 48: 13.313 distance: 45 - 46: 34.441 distance: 46 - 47: 44.659 distance: 48 - 49: 10.861 distance: 49 - 50: 9.379 distance: 50 - 51: 12.937 distance: 50 - 52: 7.707 distance: 52 - 53: 13.114 distance: 53 - 54: 13.807 distance: 53 - 56: 28.112 distance: 54 - 55: 10.714 distance: 54 - 57: 33.057 distance: 57 - 58: 26.765 distance: 58 - 59: 12.998 distance: 58 - 61: 42.250 distance: 59 - 60: 6.796 distance: 59 - 63: 48.239 distance: 61 - 62: 24.231 distance: 63 - 64: 22.504 distance: 63 - 105: 29.386 distance: 64 - 65: 26.757 distance: 64 - 67: 7.084 distance: 65 - 66: 50.107 distance: 65 - 70: 11.854 distance: 66 - 102: 21.229 distance: 67 - 68: 29.220 distance: 67 - 69: 5.919 distance: 70 - 71: 12.282 distance: 71 - 72: 21.399 distance: 71 - 74: 46.481 distance: 72 - 73: 13.230 distance: 72 - 79: 10.523 distance: 74 - 75: 15.102 distance: 75 - 76: 24.271 distance: 76 - 77: 15.586 distance: 77 - 78: 21.229