Starting phenix.real_space_refine on Thu Jul 2 23:19:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k7n_9942/07_2026/6k7n_9942.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7n_9942/07_2026/6k7n_9942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6k7n_9942/07_2026/6k7n_9942.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k7n_9942/07_2026/6k7n_9942.cif" model { file = "/net/cci-nas-00/data/ceres_data/6k7n_9942/07_2026/6k7n_9942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7n_9942/07_2026/6k7n_9942.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k7n_9942/07_2026/6k7n_9942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7n_9942/07_2026/6k7n_9942.map" } resolution = 2.84 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 56 5.16 5 C 6834 2.51 5 N 1745 2.21 5 O 1903 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 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: 10544 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7821 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 952} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {' MG': 1, 'ALF': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.77, per 1000 atoms: 0.26 Number of scatterers: 10544 At special positions: 0 Unit cell: (68.89, 109.56, 165.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 56 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1903 8.00 N 1745 7.00 C 6834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 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 ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 308.2 milliseconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 48.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 131 Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.616A pdb=" N ASP A 273 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 288 through 324 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.119A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.787A pdb=" N PHE A 465 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 570 through 588 removed outlier: 5.569A pdb=" N ILE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 617 removed outlier: 4.154A pdb=" N GLU A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 685 removed outlier: 4.588A pdb=" N ASN A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 742 through 751 removed outlier: 3.925A pdb=" N LEU A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 777 Processing helix chain 'A' and resid 787 through 797 removed outlier: 4.622A pdb=" N SER A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N MET A 793 " --> pdb=" O ASN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 823 through 831 removed outlier: 4.252A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 856 Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.657A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 881 Processing helix chain 'A' and resid 887 through 896 removed outlier: 3.993A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 919 removed outlier: 3.615A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 3.832A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1020 through 1024 removed outlier: 3.577A pdb=" N SER A1024 " --> pdb=" O PRO A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1033 through 1062 removed outlier: 3.655A pdb=" N TRP A1037 " --> pdb=" O SER A1033 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.155A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A1062 " --> pdb=" O LYS A1058 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 74 Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.530A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 removed outlier: 3.964A pdb=" N ILE C 253 " --> pdb=" O ASN C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 253' Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.985A pdb=" N VAL A 263 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 7.785A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 782 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 406 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE A 784 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER A 408 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A 669 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER A 408 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS A 759 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 729 " --> pdb=" O CYS A 759 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 728 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 425 removed outlier: 7.201A pdb=" N MET A 419 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS A 647 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE A 421 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU A 645 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 423 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 641 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 517 Processing sheet with id=AA7, first strand: chain 'A' and resid 545 through 547 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.944A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.343A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 295 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 162 through 163 removed outlier: 3.573A pdb=" N LYS C 166 " --> pdb=" O ASN C 163 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1368 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: 2.18 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1846 1.32 - 1.44: 2834 1.44 - 1.57: 6020 1.57 - 1.69: 1 1.69 - 1.82: 89 Bond restraints: 10790 Sorted by residual: bond pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.684 1.791 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.792 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" F4 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.686 1.793 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.790 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C ILE C 62 " pdb=" N PRO C 63 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.36e-02 5.41e+03 1.09e+01 ... (remaining 10785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.21: 14642 14.21 - 28.42: 5 28.42 - 42.63: 0 42.63 - 56.84: 0 56.84 - 71.05: 2 Bond angle restraints: 14649 Sorted by residual: angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F2 ALF A1301 " ideal model delta sigma weight residual 108.68 179.73 -71.05 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 109.63 177.39 -67.76 3.00e+00 1.11e-01 5.10e+02 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 110.21 88.85 21.36 3.00e+00 1.11e-01 5.07e+01 angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.69 89.52 20.17 3.00e+00 1.11e-01 4.52e+01 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.59 90.70 18.89 3.00e+00 1.11e-01 3.96e+01 ... (remaining 14644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5610 17.76 - 35.52: 627 35.52 - 53.28: 108 53.28 - 71.03: 19 71.03 - 88.79: 9 Dihedral angle restraints: 6373 sinusoidal: 2556 harmonic: 3817 Sorted by residual: dihedral pdb=" CA ARG A 479 " pdb=" C ARG A 479 " pdb=" N GLU A 480 " pdb=" CA GLU A 480 " ideal model delta harmonic sigma weight residual 180.00 146.31 33.69 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA THR A 535 " pdb=" C THR A 535 " pdb=" N SER A 536 " pdb=" CA SER A 536 " ideal model delta harmonic sigma weight residual -180.00 -146.87 -33.13 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA THR C 100 " pdb=" C THR C 100 " pdb=" N PRO C 101 " pdb=" CA PRO C 101 " ideal model delta harmonic sigma weight residual 0.00 32.24 -32.24 0 5.00e+00 4.00e-02 4.16e+01 ... (remaining 6370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1380 0.094 - 0.187: 276 0.187 - 0.281: 20 0.281 - 0.375: 1 0.375 - 0.468: 1 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CB ILE A 694 " pdb=" CA ILE A 694 " pdb=" CG1 ILE A 694 " pdb=" CG2 ILE A 694 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CG LEU A 854 " pdb=" CB LEU A 854 " pdb=" CD1 LEU A 854 " pdb=" CD2 LEU A 854 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB ILE A 784 " pdb=" CA ILE A 784 " pdb=" CG1 ILE A 784 " pdb=" CG2 ILE A 784 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1675 not shown) Planarity restraints: 1831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.265 2.00e-02 2.50e+03 2.26e-01 6.40e+02 pdb=" C7 NAG C 402 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.391 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.220 2.00e-02 2.50e+03 1.83e-01 4.17e+02 pdb=" C7 NAG C 401 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.058 2.00e-02 2.50e+03 5.08e-02 3.22e+01 pdb=" C7 NAG B 1 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.012 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.084 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.047 2.00e-02 2.50e+03 ... (remaining 1828 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 111 2.62 - 3.19: 8625 3.19 - 3.76: 17111 3.76 - 4.33: 24221 4.33 - 4.90: 38949 Nonbonded interactions: 89017 Sorted by model distance: nonbonded pdb=" F3 ALF A1301 " pdb="MG MG A1303 " model vdw 2.046 2.120 nonbonded pdb=" OD2 ASP A 409 " pdb="MG MG A1303 " model vdw 2.233 2.170 nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.243 3.040 nonbonded pdb=" OG SER A 767 " pdb=" OG SER A 792 " model vdw 2.293 3.040 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.297 3.040 ... (remaining 89012 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.900 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 0.107 10798 Z= 0.534 Angle : 1.543 71.046 14670 Z= 0.736 Chirality : 0.072 0.468 1678 Planarity : 0.011 0.226 1828 Dihedral : 15.241 88.793 3902 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.99 % Rotamer: Outliers : 0.44 % Allowed : 8.54 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.24 % 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: -3.74 (0.19), residues: 1298 helix: -2.16 (0.16), residues: 560 sheet: -1.53 (0.39), residues: 144 loop : -3.03 (0.21), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 214 TYR 0.031 0.004 TYR C 297 PHE 0.031 0.004 PHE C 179 TRP 0.026 0.004 TRP A 143 HIS 0.024 0.003 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.01283 / 0.53 (10790) covalent geometry : angle 1.53291 / 0.73 (14649) SS BOND : bond 0.00708 / 0.36 ( 3) SS BOND : angle 2.77414 / 1.32 ( 6) hydrogen bonds : bond 0.11587 / 7.63 ( 472) hydrogen bonds : angle 6.91537 / 4.84 ( 1368) link_ALPHA1-4 : bond 0.01223 / 0.64 ( 1) link_ALPHA1-4 : angle 3.42058 / 1.81 ( 3) link_BETA1-4 : bond 0.00316 / 0.17 ( 1) link_BETA1-4 : angle 2.87276 / 1.59 ( 3) link_NAG-ASN : bond 0.01278 / 0.63 ( 3) link_NAG-ASN : angle 6.81563 / 3.50 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.6781 (tpt90) cc_final: 0.6262 (ttp-110) REVERT: A 119 GLU cc_start: 0.7207 (pt0) cc_final: 0.7004 (pt0) REVERT: A 127 ASP cc_start: 0.6730 (t0) cc_final: 0.5991 (p0) REVERT: A 180 MET cc_start: 0.3435 (tpp) cc_final: 0.2468 (tpt) REVERT: A 213 MET cc_start: 0.4081 (ttt) cc_final: 0.3549 (ptp) REVERT: A 469 MET cc_start: 0.0611 (pmm) cc_final: -0.0974 (mpp) REVERT: A 693 MET cc_start: 0.3923 (mtp) cc_final: 0.3220 (mmt) REVERT: A 771 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6437 (mt-10) REVERT: A 875 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.7374 (mtt90) REVERT: A 901 ARG cc_start: 0.7153 (ttp-110) cc_final: 0.6915 (ttm110) REVERT: C 184 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7385 (mt-10) REVERT: C 278 ARG cc_start: 0.7618 (ptp-170) cc_final: 0.7410 (ptm160) outliers start: 5 outliers final: 2 residues processed: 123 average time/residue: 0.5837 time to fit residues: 77.1690 Evaluate side-chains 93 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain C residue 83 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 chunk 129 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 227 HIS A 234 ASN A 433 GLN A 454 ASN A 605 GLN A 612 GLN A 765 GLN A 936 HIS A 967 ASN C 176 ASN C 222 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.209929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.153978 restraints weight = 10163.290| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.57 r_work: 0.3101 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10798 Z= 0.137 Angle : 0.693 13.105 14670 Z= 0.357 Chirality : 0.045 0.179 1678 Planarity : 0.006 0.067 1828 Dihedral : 6.778 45.316 1428 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.18 % Allowed : 13.25 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.21 (0.22), residues: 1298 helix: -0.54 (0.20), residues: 575 sheet: -1.18 (0.39), residues: 158 loop : -2.53 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 481 TYR 0.025 0.002 TYR A 611 PHE 0.017 0.001 PHE A 968 TRP 0.022 0.002 TRP A 876 HIS 0.014 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (10790) covalent geometry : angle 0.67861 / 0.35 (14649) SS BOND : bond 0.00178 / 0.09 ( 3) SS BOND : angle 0.93778 / 0.51 ( 6) hydrogen bonds : bond 0.04914 / 3.17 ( 472) hydrogen bonds : angle 5.59525 / 3.91 ( 1368) link_ALPHA1-4 : bond 0.00372 / 0.20 ( 1) link_ALPHA1-4 : angle 2.72678 / 1.39 ( 3) link_BETA1-4 : bond 0.00201 / 0.11 ( 1) link_BETA1-4 : angle 1.25094 / 0.67 ( 3) link_NAG-ASN : bond 0.00219 / 0.11 ( 3) link_NAG-ASN : angle 5.41451 / 2.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7348 (tpt90) cc_final: 0.6610 (ttp-110) REVERT: A 79 SER cc_start: 0.8743 (p) cc_final: 0.8485 (m) REVERT: A 180 MET cc_start: 0.3516 (tpp) cc_final: 0.2221 (tpt) REVERT: A 654 GLU cc_start: 0.7190 (mp0) cc_final: 0.6969 (mp0) REVERT: A 693 MET cc_start: 0.3863 (mtp) cc_final: 0.3135 (mmt) REVERT: A 771 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6989 (mt-10) REVERT: A 904 ASN cc_start: 0.8581 (m-40) cc_final: 0.8347 (m-40) REVERT: A 915 SER cc_start: 0.7274 (t) cc_final: 0.7067 (m) REVERT: C 184 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8066 (mt-10) REVERT: C 195 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8475 (pp) REVERT: C 242 MET cc_start: 0.8540 (mmm) cc_final: 0.8198 (mmp) REVERT: C 278 ARG cc_start: 0.7982 (ptp-170) cc_final: 0.7675 (ptm160) outliers start: 25 outliers final: 9 residues processed: 125 average time/residue: 0.5476 time to fit residues: 74.3681 Evaluate side-chains 104 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 346 ILE 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: 66.7006 > 50: distance: 28 - 32: 17.103 distance: 32 - 33: 30.768 distance: 33 - 34: 17.909 distance: 33 - 36: 43.581 distance: 34 - 35: 15.626 distance: 34 - 40: 15.638 distance: 36 - 37: 35.246 distance: 37 - 38: 16.192 distance: 38 - 39: 6.564 distance: 40 - 41: 46.298 distance: 41 - 42: 66.547 distance: 41 - 44: 51.360 distance: 42 - 43: 55.893 distance: 42 - 50: 62.611 distance: 44 - 45: 31.143 distance: 45 - 46: 39.520 distance: 45 - 47: 24.184 distance: 46 - 48: 38.184 distance: 47 - 49: 39.819 distance: 48 - 49: 27.683 distance: 50 - 51: 41.054 distance: 51 - 52: 60.622 distance: 51 - 54: 36.008 distance: 52 - 53: 53.250 distance: 52 - 62: 11.695 distance: 54 - 55: 21.727 distance: 55 - 56: 13.226 distance: 55 - 57: 13.319 distance: 56 - 58: 12.010 distance: 57 - 59: 5.889 distance: 58 - 60: 8.717 distance: 59 - 60: 4.324 distance: 60 - 61: 14.386 distance: 62 - 63: 36.215 distance: 63 - 64: 24.640 distance: 63 - 66: 31.141 distance: 64 - 65: 36.073 distance: 64 - 71: 49.336 distance: 66 - 67: 13.091 distance: 67 - 68: 20.450 distance: 68 - 69: 25.006 distance: 68 - 70: 17.209 distance: 71 - 72: 39.936 distance: 71 - 77: 36.886 distance: 72 - 73: 15.045 distance: 72 - 75: 25.938 distance: 73 - 74: 22.068 distance: 73 - 78: 29.307 distance: 75 - 76: 21.585 distance: 76 - 77: 19.821 distance: 78 - 79: 32.823 distance: 79 - 80: 24.754 distance: 79 - 82: 27.514 distance: 80 - 81: 12.983 distance: 80 - 85: 29.506 distance: 82 - 83: 28.925 distance: 82 - 84: 22.421 distance: 85 - 86: 31.387 distance: 86 - 87: 43.575 distance: 86 - 89: 8.609 distance: 87 - 88: 19.714 distance: 87 - 93: 35.422 distance: 89 - 90: 42.194 distance: 90 - 91: 35.426 distance: 90 - 92: 25.373 distance: 93 - 94: 31.395 distance: 94 - 95: 37.787 distance: 94 - 97: 20.921 distance: 95 - 96: 28.613 distance: 95 - 100: 22.304 distance: 97 - 98: 21.156 distance: 97 - 99: 23.269 distance: 100 - 101: 24.337 distance: 101 - 102: 47.132 distance: 101 - 104: 37.186 distance: 102 - 103: 32.500 distance: 102 - 105: 34.971 distance: 105 - 106: 23.828 distance: 106 - 107: 27.387 distance: 106 - 109: 22.171 distance: 107 - 108: 18.332 distance: 107 - 110: 16.299