Starting phenix.real_space_refine on Fri Feb 14 18:02:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7klv_22919/02_2025/7klv_22919.cif Found real_map, /net/cci-nas-00/data/ceres_data/7klv_22919/02_2025/7klv_22919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7klv_22919/02_2025/7klv_22919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7klv_22919/02_2025/7klv_22919.map" model { file = "/net/cci-nas-00/data/ceres_data/7klv_22919/02_2025/7klv_22919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7klv_22919/02_2025/7klv_22919.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 522 atoms to isotropic. 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 K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 6233 2.51 5 N 1715 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.96, per 1000 atoms: 0.60 Number of scatterers: 9871 At special positions: 0 Unit cell: (121.378, 129.018, 90.8216, 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) K 2 19.00 S 44 16.00 P 6 15.00 Mg 2 11.99 O 1869 8.00 N 1715 7.00 C 6233 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 13 sheets defined 46.7% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.355A pdb=" N ARG A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.921A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 210 removed outlier: 3.505A pdb=" N SER A 207 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.527A pdb=" N PHE A 264 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 307 through 319 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 408 through 433 Processing helix chain 'A' and resid 433 through 455 removed outlier: 3.545A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.604A pdb=" N LYS A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.698A pdb=" N ALA A 516 " --> pdb=" O PRO A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 540 Processing helix chain 'A' and resid 550 through 557 removed outlier: 3.940A pdb=" N VAL A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 590 removed outlier: 4.313A pdb=" N GLU A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 648 through 658 removed outlier: 3.714A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 681 removed outlier: 3.885A pdb=" N LEU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 688 removed outlier: 4.063A pdb=" N ALA A 688 " --> pdb=" O ASP A 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 685 through 688' Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.960A pdb=" N LEU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 110 through 135 removed outlier: 4.300A pdb=" N ARG B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 178 through 186 removed outlier: 3.933A pdb=" N ALA B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 210 removed outlier: 3.557A pdb=" N SER B 207 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.598A pdb=" N PHE B 264 " --> pdb=" O CYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 408 through 433 removed outlier: 3.648A pdb=" N ASP B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.850A pdb=" N TYR B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.559A pdb=" N LYS B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 531 through 540 removed outlier: 3.626A pdb=" N THR B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 557 removed outlier: 3.733A pdb=" N VAL B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 590 Processing helix chain 'B' and resid 615 through 623 removed outlier: 3.760A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 Processing helix chain 'B' and resid 648 through 661 removed outlier: 3.653A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 681 removed outlier: 3.553A pdb=" N ASP B 670 " --> pdb=" O GLN B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 688 removed outlier: 4.204A pdb=" N ALA B 688 " --> pdb=" O ASP B 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 685 through 688' Processing helix chain 'B' and resid 689 through 701 removed outlier: 3.835A pdb=" N LEU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 3.519A pdb=" N ALA B 242 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 250 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 7.238A pdb=" N GLN A 91 " --> pdb=" O ILE B 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 4.155A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 233 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.915A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.915A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 removed outlier: 3.874A pdb=" N GLU A 471 " --> pdb=" O PHE A 526 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 596 through 599 removed outlier: 6.606A pdb=" N ASN A 596 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE A 644 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS A 598 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 327 through 333 removed outlier: 3.750A pdb=" N TYR B 327 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 471 through 472 removed outlier: 9.285A pdb=" N LEU B 525 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B 498 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N CYS B 527 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 500 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE B 497 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 597 through 599 removed outlier: 3.604A pdb=" N MET B 609 " --> pdb=" O GLU B 643 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3260 1.34 - 1.46: 2185 1.46 - 1.58: 4512 1.58 - 1.70: 6 1.70 - 1.82: 80 Bond restraints: 10043 Sorted by residual: bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.15e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" O5' ANP A 901 " pdb=" PA ANP A 901 " ideal model delta sigma weight residual 1.655 1.579 0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 10038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 13476 3.33 - 6.66: 64 6.66 - 10.00: 9 10.00 - 13.33: 2 13.33 - 16.66: 2 Bond angle restraints: 13553 Sorted by residual: angle pdb=" PB ANP A 901 " pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 126.95 110.29 16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 111.18 15.77 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O2B ANP B 901 " ideal model delta sigma weight residual 120.08 109.03 11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O1B ANP A 901 " pdb=" PB ANP A 901 " pdb=" O2B ANP A 901 " ideal model delta sigma weight residual 120.08 109.20 10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " pdb=" O2G ANP A 901 " ideal model delta sigma weight residual 101.05 109.65 -8.60 3.00e+00 1.11e-01 8.22e+00 ... (remaining 13548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5491 17.90 - 35.80: 554 35.80 - 53.70: 93 53.70 - 71.59: 30 71.59 - 89.49: 13 Dihedral angle restraints: 6181 sinusoidal: 2583 harmonic: 3598 Sorted by residual: dihedral pdb=" CA LEU A 539 " pdb=" C LEU A 539 " pdb=" N ARG A 540 " pdb=" CA ARG A 540 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG A 658 " pdb=" CD ARG A 658 " pdb=" NE ARG A 658 " pdb=" CZ ARG A 658 " ideal model delta sinusoidal sigma weight residual 90.00 134.96 -44.96 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CA GLU B 633 " pdb=" C GLU B 633 " pdb=" N ARG B 634 " pdb=" CA ARG B 634 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1280 0.056 - 0.111: 228 0.111 - 0.167: 18 0.167 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 1528 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1525 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 639 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO B 640 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 640 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 640 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 585 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.78e+00 pdb=" CG TRP B 585 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 585 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 585 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 585 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 585 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 585 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 585 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 621 " 0.008 2.00e-02 2.50e+03 9.18e-03 1.47e+00 pdb=" CG PHE A 621 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 621 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 621 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 621 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 621 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 621 " 0.001 2.00e-02 2.50e+03 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.61: 89 2.61 - 3.24: 9381 3.24 - 3.87: 18222 3.87 - 4.51: 24518 4.51 - 5.14: 40183 Nonbonded interactions: 92393 Sorted by model distance: nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 902 " model vdw 1.974 2.170 nonbonded pdb=" O3G ANP B 901 " pdb="MG MG B 902 " model vdw 2.000 2.170 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 902 " model vdw 2.025 2.170 nonbonded pdb=" O3G ANP A 901 " pdb="MG MG A 902 " model vdw 2.038 2.170 nonbonded pdb=" O1B ANP A 901 " pdb="MG MG A 902 " model vdw 2.050 2.170 ... (remaining 92388 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 704 or resid 901 through 903)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 704 or resid 901 through 903)) } 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.930 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.004 0.143 10043 Z= 0.230 Angle : 0.654 16.661 13553 Z= 0.320 Chirality : 0.042 0.279 1528 Planarity : 0.003 0.054 1720 Dihedral : 15.235 89.492 3843 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.09 % Allowed : 0.37 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1210 helix: 1.04 (0.24), residues: 510 sheet: 0.36 (0.39), residues: 189 loop : -1.42 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 585 HIS 0.004 0.001 HIS A 88 PHE 0.021 0.001 PHE A 621 TYR 0.008 0.001 TYR B 206 ARG 0.012 0.001 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.153 Fit side-chains REVERT: A 181 LYS cc_start: 0.8593 (mmmt) cc_final: 0.7953 (mtpp) REVERT: A 210 MET cc_start: 0.8400 (ttp) cc_final: 0.8127 (ptm) REVERT: A 309 TRP cc_start: 0.7420 (t-100) cc_final: 0.7109 (t-100) REVERT: A 490 MET cc_start: 0.8229 (ptp) cc_final: 0.7940 (ptp) REVERT: A 624 MET cc_start: 0.0541 (mtt) cc_final: 0.0311 (tpp) REVERT: A 689 MET cc_start: 0.8639 (ppp) cc_final: 0.7765 (ppp) REVERT: B 93 GLU cc_start: 0.8126 (tp30) cc_final: 0.7861 (tt0) REVERT: B 333 THR cc_start: 0.7945 (m) cc_final: 0.7616 (p) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2557 time to fit residues: 44.4497 Evaluate side-chains 88 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 279 ASN A 288 ASN B 279 ASN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086037 restraints weight = 17415.427| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.75 r_work: 0.2978 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10043 Z= 0.229 Angle : 0.566 8.939 13553 Z= 0.296 Chirality : 0.043 0.175 1528 Planarity : 0.004 0.032 1720 Dihedral : 6.659 57.906 1402 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.21 % Allowed : 7.38 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1210 helix: 1.26 (0.24), residues: 518 sheet: 0.38 (0.38), residues: 193 loop : -1.33 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 585 HIS 0.004 0.001 HIS A 88 PHE 0.012 0.001 PHE B 239 TYR 0.011 0.001 TYR B 437 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.081 Fit side-chains REVERT: A 181 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8051 (mtpp) REVERT: A 309 TRP cc_start: 0.7654 (t-100) cc_final: 0.7328 (t-100) REVERT: B 93 GLU cc_start: 0.8552 (tp30) cc_final: 0.8272 (tp30) REVERT: B 333 THR cc_start: 0.8307 (m) cc_final: 0.8079 (p) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.2414 time to fit residues: 35.3945 Evaluate side-chains 94 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 111 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 666 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.116222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086960 restraints weight = 17593.385| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.80 r_work: 0.2989 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10043 Z= 0.164 Angle : 0.511 8.943 13553 Z= 0.267 Chirality : 0.042 0.156 1528 Planarity : 0.003 0.028 1720 Dihedral : 6.126 59.688 1402 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.49 % Allowed : 9.71 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1210 helix: 1.52 (0.24), residues: 515 sheet: 0.40 (0.38), residues: 194 loop : -1.22 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 585 HIS 0.004 0.001 HIS B 620 PHE 0.010 0.001 PHE B 239 TYR 0.010 0.001 TYR B 206 ARG 0.002 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 1.200 Fit side-chains REVERT: A 181 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8065 (mtpp) REVERT: A 309 TRP cc_start: 0.7691 (t-100) cc_final: 0.7399 (t-100) REVERT: A 624 MET cc_start: 0.1335 (mtt) cc_final: 0.0788 (ttt) REVERT: B 93 GLU cc_start: 0.8570 (tp30) cc_final: 0.8291 (tp30) REVERT: B 333 THR cc_start: 0.8336 (m) cc_final: 0.8036 (p) REVERT: B 656 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: B 666 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8350 (tp40) outliers start: 16 outliers final: 12 residues processed: 106 average time/residue: 0.2577 time to fit residues: 37.7891 Evaluate side-chains 102 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.1648 > 50: distance: 42 - 70: 7.632 distance: 48 - 77: 7.954 distance: 57 - 88: 16.393 distance: 59 - 60: 3.911 distance: 60 - 61: 5.896 distance: 60 - 63: 5.175 distance: 61 - 62: 7.618 distance: 61 - 70: 5.941 distance: 62 - 96: 27.668 distance: 63 - 64: 4.234 distance: 64 - 65: 10.847 distance: 65 - 66: 4.563 distance: 66 - 67: 5.476 distance: 67 - 68: 4.225 distance: 67 - 69: 3.477 distance: 70 - 71: 14.485 distance: 71 - 72: 8.923 distance: 71 - 74: 14.836 distance: 72 - 73: 9.777 distance: 72 - 77: 10.912 distance: 73 - 103: 29.760 distance: 74 - 75: 7.027 distance: 74 - 76: 3.710 distance: 77 - 78: 7.579 distance: 78 - 79: 10.896 distance: 78 - 81: 9.476 distance: 79 - 80: 3.631 distance: 79 - 88: 6.008 distance: 80 - 110: 20.187 distance: 81 - 82: 6.837 distance: 82 - 83: 12.028 distance: 83 - 84: 11.876 distance: 84 - 85: 11.369 distance: 85 - 86: 16.518 distance: 85 - 87: 23.873 distance: 88 - 89: 12.125 distance: 89 - 90: 14.692 distance: 89 - 92: 16.933 distance: 90 - 91: 14.042 distance: 90 - 96: 30.377 distance: 91 - 117: 8.417 distance: 92 - 93: 12.955 distance: 93 - 94: 4.332 distance: 93 - 95: 4.566 distance: 96 - 97: 28.967 distance: 97 - 98: 23.551 distance: 97 - 100: 7.875 distance: 98 - 99: 8.250 distance: 98 - 103: 11.094 distance: 99 - 126: 18.572 distance: 100 - 101: 18.567 distance: 100 - 102: 17.735 distance: 103 - 104: 12.312 distance: 104 - 105: 5.322 distance: 104 - 107: 4.947 distance: 105 - 106: 10.685 distance: 105 - 110: 7.791 distance: 106 - 138: 7.598 distance: 107 - 108: 3.227 distance: 107 - 109: 22.589 distance: 110 - 111: 7.044 distance: 111 - 112: 3.310 distance: 111 - 114: 13.356 distance: 112 - 113: 6.468 distance: 112 - 117: 6.831 distance: 114 - 115: 17.571 distance: 114 - 116: 19.304 distance: 117 - 118: 8.750 distance: 118 - 119: 16.969 distance: 118 - 121: 18.774 distance: 119 - 120: 12.812 distance: 119 - 126: 5.315 distance: 121 - 122: 7.766 distance: 122 - 123: 4.885 distance: 123 - 124: 9.481 distance: 124 - 125: 7.789 distance: 126 - 127: 3.568 distance: 127 - 128: 9.928 distance: 127 - 130: 7.327 distance: 128 - 129: 8.911 distance: 128 - 138: 6.501 distance: 130 - 131: 7.385 distance: 131 - 132: 6.541 distance: 131 - 133: 5.735 distance: 132 - 134: 5.777 distance: 133 - 135: 6.516 distance: 135 - 136: 8.278 distance: 138 - 139: 5.158 distance: 139 - 140: 7.690 distance: 139 - 142: 10.469 distance: 140 - 141: 17.121 distance: 140 - 144: 10.909 distance: 142 - 143: 14.779