Starting phenix.real_space_refine on Fri Jul 3 21:58:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q62_13850/07_2026/7q62_13850.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q62_13850/07_2026/7q62_13850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q62_13850/07_2026/7q62_13850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q62_13850/07_2026/7q62_13850.map" model { file = "/net/cci-nas-00/data/ceres_data/7q62_13850/07_2026/7q62_13850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q62_13850/07_2026/7q62_13850.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7q62_13850/07_2026/7q62_13850.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q62_13850/07_2026/7q62_13850.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 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 75 5.16 5 C 10356 2.51 5 N 2653 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16186 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9560 Classifications: {'peptide': 1223} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1159} Chain breaks: 3 Chain: "B" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6486 Classifications: {'peptide': 822} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 772} Chain breaks: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.12, per 1000 atoms: 0.19 Number of scatterers: 16186 At special positions: 0 Unit cell: (106.108, 122.93, 142.34, 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 75 16.00 O 3102 8.00 N 2653 7.00 C 10356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.02 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.11 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.02 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 78 " distance=2.02 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 291 " distance=2.04 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 589 " - pdb=" SG CYS B 769 " distance=2.02 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 694 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B 845 " - pdb=" SG CYS B 881 " distance=2.03 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 Links applied NAG-ASN " NAG A1501 " - " ASN A 120 " " NAG A1502 " - " ASN A 328 " " NAG A1503 " - " ASN A 609 " " NAG A1504 " - " ASN A 857 " " NAG A1505 " - " ASN A 867 " " NAG B1501 " - " ASN B 120 " " NAG B1502 " - " ASN B 328 " " NAG B1503 " - " ASN B 609 " " NAG B1504 " - " ASN B 857 " " NAG B1505 " - " ASN B 867 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 786.6 milliseconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 34 sheets defined 12.2% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 406 through 409 removed outlier: 4.133A pdb=" N ASN A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 597 through 602 removed outlier: 4.008A pdb=" N LEU A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 597 through 602' Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 670 through 679 removed outlier: 3.674A pdb=" N VAL A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 963 removed outlier: 3.704A pdb=" N LEU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 979 removed outlier: 4.343A pdb=" N VAL A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 990 removed outlier: 4.265A pdb=" N TYR A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 990 " --> pdb=" O GLN A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1010 Processing helix chain 'A' and resid 1011 through 1014 Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1056 through 1070 removed outlier: 3.845A pdb=" N LYS A1064 " --> pdb=" O GLN A1060 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TRP A1065 " --> pdb=" O ASP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1104 removed outlier: 3.612A pdb=" N LEU A1097 " --> pdb=" O ASP A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 removed outlier: 4.294A pdb=" N MET A1108 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A1109 " --> pdb=" O LEU A1106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1105 through 1109' Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 4.331A pdb=" N ASN A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A1127 " --> pdb=" O CYS A1123 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1129 " --> pdb=" O LYS A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1148 removed outlier: 3.796A pdb=" N ILE A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1162 removed outlier: 3.946A pdb=" N LYS A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN A1159 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A1162 " --> pdb=" O LYS A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1207 removed outlier: 3.702A pdb=" N LYS A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1227 removed outlier: 4.039A pdb=" N LYS A1227 " --> pdb=" O ALA A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1255 removed outlier: 3.552A pdb=" N ALA A1255 " --> pdb=" O TYR A1251 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 481 removed outlier: 3.824A pdb=" N ALA B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 478 through 481' Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.807A pdb=" N LYS B 511 " --> pdb=" O ASN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 602 removed outlier: 3.719A pdb=" N LEU B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 624 through 628 removed outlier: 3.697A pdb=" N ALA B 628 " --> pdb=" O TYR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 82 removed outlier: 8.244A pdb=" N LYS A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.797A pdb=" N PHE A 52 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU A 67 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 54 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.759A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 346 removed outlier: 4.038A pdb=" N GLU A 345 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LYS A 360 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 455 Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 507 removed outlier: 5.308A pdb=" N LEU A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A 495 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 487 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB3, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB4, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB5, first strand: chain 'A' and resid 790 through 795 Processing sheet with id=AB6, first strand: chain 'A' and resid 800 through 801 removed outlier: 7.081A pdb=" N VAL A 800 " --> pdb=" O LYS A 904 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 908 through 918 Processing sheet with id=AB8, first strand: chain 'A' and resid 921 through 930 Processing sheet with id=AB9, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.599A pdb=" N TYR A1172 " --> pdb=" O ILE A1165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 75 through 82 removed outlier: 8.101A pdb=" N LYS B 38 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.814A pdb=" N LEU B 56 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS B 64 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 121 through 126 Processing sheet with id=AC4, first strand: chain 'B' and resid 130 through 131 removed outlier: 7.626A pdb=" N SER B 156 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU B 172 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 158 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN B 170 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 160 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 219 through 223 Processing sheet with id=AC6, first strand: chain 'B' and resid 229 through 230 removed outlier: 6.230A pdb=" N LEU B 229 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS B 310 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN B 311 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS B 261 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 340 through 346 removed outlier: 5.431A pdb=" N MET B 342 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ARG B 364 " --> pdb=" O MET B 342 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 344 " --> pdb=" O ARG B 362 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 362 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 346 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AC9, first strand: chain 'B' and resid 451 through 455 Processing sheet with id=AD1, first strand: chain 'B' and resid 498 through 507 removed outlier: 5.152A pdb=" N LEU B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY B 495 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER B 488 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE B 539 " --> pdb=" O SER B 488 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 563 through 567 Processing sheet with id=AD3, first strand: chain 'B' and resid 742 through 743 Processing sheet with id=AD4, first strand: chain 'B' and resid 592 through 595 Processing sheet with id=AD5, first strand: chain 'B' and resid 729 through 730 removed outlier: 5.938A pdb=" N VAL B 800 " --> pdb=" O LYS B 904 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD7, first strand: chain 'B' and resid 790 through 795 640 hydrogen bonds defined for protein. 1758 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: 4.32 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5061 1.34 - 1.46: 4006 1.46 - 1.59: 7390 1.59 - 1.71: 0 1.71 - 1.84: 110 Bond restraints: 16567 Sorted by residual: bond pdb=" CD GLU B 596 " pdb=" OE1 GLU B 596 " ideal model delta sigma weight residual 1.249 1.326 -0.077 1.90e-02 2.77e+03 1.66e+01 bond pdb=" CD GLU A 596 " pdb=" OE1 GLU A 596 " ideal model delta sigma weight residual 1.249 1.321 -0.072 1.90e-02 2.77e+03 1.45e+01 bond pdb=" N ILE A1318 " pdb=" CA ILE A1318 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.61e+00 bond pdb=" N GLY A1031 " pdb=" CA GLY A1031 " ideal model delta sigma weight residual 1.449 1.478 -0.028 9.80e-03 1.04e+04 8.41e+00 bond pdb=" C1 NAG A1504 " pdb=" O5 NAG A1504 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.36e+00 ... (remaining 16562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.50: 22455 7.50 - 15.00: 56 15.00 - 22.51: 1 22.51 - 30.01: 0 30.01 - 37.51: 2 Bond angle restraints: 22514 Sorted by residual: angle pdb=" CA CYS A 279 " pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " ideal model delta sigma weight residual 114.40 151.91 -37.51 2.30e+00 1.89e-01 2.66e+02 angle pdb=" CA CYS A 259 " pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " ideal model delta sigma weight residual 114.40 151.66 -37.26 2.30e+00 1.89e-01 2.62e+02 angle pdb=" N CYS A 259 " pdb=" CA CYS A 259 " pdb=" C CYS A 259 " ideal model delta sigma weight residual 108.99 122.76 -13.77 1.57e+00 4.06e-01 7.69e+01 angle pdb=" N CYS A 279 " pdb=" CA CYS A 279 " pdb=" C CYS A 279 " ideal model delta sigma weight residual 108.79 119.95 -11.16 1.53e+00 4.27e-01 5.32e+01 angle pdb=" C ASN B 103 " pdb=" N ASN B 104 " pdb=" CA ASN B 104 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 ... (remaining 22509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8939 17.69 - 35.38: 717 35.38 - 53.07: 129 53.07 - 70.76: 37 70.76 - 88.45: 34 Dihedral angle restraints: 9856 sinusoidal: 3916 harmonic: 5940 Sorted by residual: dihedral pdb=" CB CYS A 633 " pdb=" SG CYS A 633 " pdb=" SG CYS A 694 " pdb=" CB CYS A 694 " ideal model delta sinusoidal sigma weight residual -86.00 -173.78 87.78 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual -86.00 -2.50 -83.50 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CA GLU A 835 " pdb=" C GLU A 835 " pdb=" N SER A 836 " pdb=" CA SER A 836 " ideal model delta harmonic sigma weight residual 180.00 140.64 39.36 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 9853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2446 0.139 - 0.277: 93 0.277 - 0.416: 10 0.416 - 0.554: 3 0.554 - 0.693: 1 Chirality restraints: 2553 Sorted by residual: chirality pdb=" C1 NAG A1504 " pdb=" ND2 ASN A 857 " pdb=" C2 NAG A1504 " pdb=" O5 NAG A1504 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA CYS A 259 " pdb=" N CYS A 259 " pdb=" C CYS A 259 " pdb=" CB CYS A 259 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CA CYS A 279 " pdb=" N CYS A 279 " pdb=" C CYS A 279 " pdb=" CB CYS A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 2550 not shown) Planarity restraints: 2899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 837 " 0.029 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP A 837 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A 837 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 837 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 837 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 837 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 837 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 837 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 837 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 837 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 44 " 0.057 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A 45 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 609 " 0.027 2.00e-02 2.50e+03 2.64e-02 8.73e+00 pdb=" CG ASN B 609 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 609 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 609 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG B1503 " 0.030 2.00e-02 2.50e+03 ... (remaining 2896 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4033 2.80 - 3.33: 13141 3.33 - 3.85: 26931 3.85 - 4.38: 29959 4.38 - 4.90: 52543 Nonbonded interactions: 126607 Sorted by model distance: nonbonded pdb=" OD1 ASP A 127 " pdb=" OH TYR A 131 " model vdw 2.276 3.040 nonbonded pdb=" O ALA B 827 " pdb=" OH TYR B 832 " model vdw 2.327 3.040 nonbonded pdb=" O ALA A 827 " pdb=" OH TYR A 832 " model vdw 2.333 3.040 nonbonded pdb=" OD1 ASP B 127 " pdb=" OH TYR B 131 " model vdw 2.337 3.040 nonbonded pdb=" OG1 THR A1238 " pdb=" OE1 GLN A1239 " model vdw 2.341 3.040 ... (remaining 126602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.620 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.050 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.006 0.092 16595 Z= 0.269 Angle : 1.163 37.509 22580 Z= 0.576 Chirality : 0.067 0.693 2553 Planarity : 0.008 0.105 2889 Dihedral : 14.536 88.447 5990 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.68 % Favored : 95.17 % Rotamer: Outliers : 0.06 % Allowed : 0.67 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.17), residues: 2031 helix: -2.90 (0.26), residues: 204 sheet: -0.24 (0.17), residues: 917 loop : -1.65 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 774 TYR 0.049 0.003 TYR B 306 PHE 0.030 0.003 PHE A1286 TRP 0.069 0.003 TRP A 837 HIS 0.007 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.27 (16567) covalent geometry : angle 1.13339 / 0.57 (22514) SS BOND : bond 0.01958 / 1.01 ( 18) SS BOND : angle 2.47744 / 1.51 ( 36) hydrogen bonds : bond 0.09654 / 6.69 ( 628) hydrogen bonds : angle 6.67293 / 4.64 ( 1758) link_NAG-ASN : bond 0.01558 / 0.78 ( 10) link_NAG-ASN : angle 6.78288 / 4.37 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.550 Fit side-chains REVERT: A 266 TRP cc_start: 0.6368 (m-10) cc_final: 0.6051 (m-90) REVERT: A 394 ASP cc_start: 0.7664 (p0) cc_final: 0.7412 (p0) REVERT: A 578 GLU cc_start: 0.7945 (tt0) cc_final: 0.7547 (tt0) REVERT: A 985 LEU cc_start: 0.9067 (mm) cc_final: 0.8834 (mm) REVERT: A 1015 MET cc_start: 0.7157 (pmm) cc_final: 0.6045 (tmm) REVERT: A 1065 TRP cc_start: 0.6221 (m100) cc_final: 0.5448 (m100) REVERT: A 1173 TRP cc_start: 0.6464 (m-90) cc_final: 0.5897 (m-90) REVERT: A 1297 MET cc_start: 0.7573 (pmm) cc_final: 0.7273 (pmm) REVERT: B 298 MET cc_start: 0.7018 (ppp) cc_final: 0.6725 (ppp) REVERT: B 306 TYR cc_start: 0.7928 (t80) cc_final: 0.7713 (t80) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.0989 time to fit residues: 28.9059 Evaluate side-chains 133 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 HIS B 22 ASN B 164 ASN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.116539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083206 restraints weight = 42266.932| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.91 r_work: 0.3333 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16595 Z= 0.133 Angle : 0.707 17.835 22580 Z= 0.345 Chirality : 0.047 0.500 2553 Planarity : 0.005 0.057 2889 Dihedral : 5.245 31.983 2192 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 0.56 % Allowed : 6.94 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.18), residues: 2031 helix: -1.74 (0.29), residues: 217 sheet: -0.09 (0.17), residues: 904 loop : -1.21 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 774 TYR 0.019 0.001 TYR B 435 PHE 0.039 0.001 PHE A1286 TRP 0.040 0.002 TRP A 837 HIS 0.002 0.000 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16567) covalent geometry : angle 0.67132 / 0.33 (22514) SS BOND : bond 0.00477 / 0.29 ( 18) SS BOND : angle 2.95073 / 1.51 ( 36) hydrogen bonds : bond 0.03513 / 2.37 ( 628) hydrogen bonds : angle 5.51810 / 3.85 ( 1758) link_NAG-ASN : bond 0.01506 / 0.78 ( 10) link_NAG-ASN : angle 5.26046 / 3.36 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6289 (m-10) cc_final: 0.5964 (m-90) REVERT: A 394 ASP cc_start: 0.8046 (p0) cc_final: 0.7745 (p0) REVERT: A 578 GLU cc_start: 0.8543 (tt0) cc_final: 0.7945 (tt0) REVERT: A 619 TRP cc_start: 0.6571 (p90) cc_final: 0.5847 (p-90) REVERT: A 766 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8817 (ppp) REVERT: A 837 TRP cc_start: 0.4269 (m-90) cc_final: 0.3843 (m-90) REVERT: A 985 LEU cc_start: 0.9062 (mm) cc_final: 0.8784 (mm) REVERT: A 1065 TRP cc_start: 0.6004 (m100) cc_final: 0.5335 (m100) REVERT: A 1142 TYR cc_start: 0.8953 (t80) cc_final: 0.8670 (t80) REVERT: B 157 MET cc_start: 0.8264 (ppp) cc_final: 0.7664 (ppp) REVERT: B 298 MET cc_start: 0.7319 (ppp) cc_final: 0.6915 (ppp) REVERT: B 551 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7996 (tp-100) outliers start: 10 outliers final: 5 residues processed: 157 average time/residue: 0.1138 time to fit residues: 28.7981 Evaluate side-chains 143 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 472 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.5287 > 50: distance: 14 - 109: 14.589 distance: 17 - 106: 24.839 distance: 27 - 97: 8.435 distance: 30 - 94: 9.606 distance: 64 - 70: 5.404 distance: 70 - 71: 4.634 distance: 70 - 209: 6.080 distance: 71 - 72: 6.294 distance: 71 - 74: 12.197 distance: 72 - 73: 9.525 distance: 72 - 77: 3.078 distance: 73 - 206: 7.319 distance: 74 - 75: 19.770 distance: 74 - 76: 22.228 distance: 77 - 78: 4.391 distance: 78 - 79: 3.191 distance: 78 - 81: 9.431 distance: 79 - 80: 5.205 distance: 79 - 86: 6.053 distance: 81 - 82: 11.525 distance: 82 - 83: 6.373 distance: 83 - 84: 12.322 distance: 84 - 85: 7.357 distance: 86 - 87: 4.476 distance: 86 - 195: 8.701 distance: 87 - 88: 5.489 distance: 88 - 89: 5.073 distance: 88 - 94: 3.283 distance: 89 - 192: 9.965 distance: 90 - 91: 4.909 distance: 90 - 92: 11.142 distance: 91 - 93: 8.903 distance: 94 - 95: 3.790 distance: 95 - 96: 4.601 distance: 95 - 98: 6.349 distance: 96 - 97: 8.382 distance: 96 - 100: 11.054 distance: 98 - 99: 8.525 distance: 99 - 191: 14.097 distance: 100 - 101: 8.403 distance: 101 - 102: 12.743 distance: 101 - 104: 6.392 distance: 102 - 103: 19.503 distance: 104 - 105: 13.617 distance: 106 - 107: 11.011 distance: 107 - 108: 9.076 distance: 107 - 110: 4.799 distance: 108 - 109: 10.715 distance: 108 - 117: 12.631 distance: 110 - 111: 13.755 distance: 112 - 113: 21.359 distance: 113 - 114: 28.888 distance: 114 - 115: 8.125 distance: 114 - 116: 21.231 distance: 117 - 118: 13.799 distance: 118 - 119: 24.307 distance: 118 - 121: 12.320 distance: 119 - 120: 19.762 distance: 119 - 129: 38.756 distance: 121 - 122: 9.678 distance: 122 - 123: 18.354 distance: 122 - 124: 18.795 distance: 123 - 125: 3.601 distance: 124 - 126: 6.817 distance: 125 - 127: 13.052 distance: 126 - 127: 20.648 distance: 127 - 128: 11.199 distance: 129 - 130: 9.621 distance: 130 - 131: 4.590 distance: 130 - 133: 3.684 distance: 131 - 132: 4.063 distance: 131 - 136: 12.732 distance: 133 - 134: 6.438 distance: 133 - 135: 5.909 distance: 136 - 137: 15.803 distance: 137 - 138: 13.576 distance: 137 - 140: 7.515 distance: 138 - 139: 3.795 distance: 140 - 141: 9.623 distance: 141 - 142: 13.203 distance: 141 - 143: 28.479 distance: 142 - 144: 15.255 distance: 143 - 145: 17.319 distance: 144 - 146: 19.254 distance: 145 - 146: 29.140 distance: 146 - 147: 3.461 distance: 149 - 150: 16.799 distance: 150 - 151: 12.423 distance: 150 - 152: 12.746