Starting phenix.real_space_refine on Wed Mar 12 09:46:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ln8_0927/03_2025/6ln8_0927.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ln8_0927/03_2025/6ln8_0927.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/6ln8_0927/03_2025/6ln8_0927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ln8_0927/03_2025/6ln8_0927.map" model { file = "/net/cci-nas-00/data/ceres_data/6ln8_0927/03_2025/6ln8_0927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ln8_0927/03_2025/6ln8_0927.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= 0.007 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 Mg 1 5.21 5 S 57 5.16 5 Be 1 3.05 5 C 4932 2.51 5 N 1294 2.21 5 O 1451 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7739 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7734 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 957} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.04, per 1000 atoms: 0.65 Number of scatterers: 7739 At special positions: 0 Unit cell: (88.395, 92.13, 145.665, 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 57 16.00 Mg 1 11.99 F 3 9.00 O 1451 8.00 N 1294 7.00 C 4932 6.00 Be 1 4.00 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: 2.12 Conformation dependent library (CDL) restraints added in 874.7 milliseconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 54.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.713A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.677A pdb=" N GLU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 77 Processing helix chain 'A' and resid 84 through 118 removed outlier: 5.083A pdb=" N GLU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 3.638A pdb=" N ALA A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 247 through 276 Processing helix chain 'A' and resid 290 through 306 removed outlier: 4.320A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 328 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.632A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.929A pdb=" N ASN A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 4.468A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 537 through 552 Processing helix chain 'A' and resid 581 through 586 removed outlier: 4.090A pdb=" N LYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 removed outlier: 3.735A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 661 through 672 Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.739A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 723 through 730 Processing helix chain 'A' and resid 739 through 781 removed outlier: 3.872A pdb=" N VAL A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.938A pdb=" N TRP A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP A 799 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 807 through 809 No H-bonds generated for 'chain 'A' and resid 807 through 809' Processing helix chain 'A' and resid 814 through 818 removed outlier: 4.042A pdb=" N LYS A 818 " --> pdb=" O ILE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 857 removed outlier: 3.844A pdb=" N ILE A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 873 through 877 removed outlier: 3.601A pdb=" N LYS A 876 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.471A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 951 through 956 removed outlier: 3.599A pdb=" N ILE A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.981A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1030 Proline residue: A1024 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141 removed outlier: 12.144A pdb=" N MET A 126 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N ALA A 154 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS A 218 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE A 168 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET A 220 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.479A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG A 174 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 213 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.205A pdb=" N GLY A 716 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU A 734 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA A 718 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 697 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 717 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY A 701 " --> pdb=" O MET A 719 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.768A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 19.639A pdb=" N CYS A 524 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 17.183A pdb=" N PHE A 367 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 14.582A pdb=" N HIS A 526 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N LEU A 369 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG A 528 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ARG A 371 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.768A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.642A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.736A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS A 524 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 592 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N HIS A 526 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY A 594 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N ARG A 528 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 12.816A pdb=" N VAL A 596 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.768A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.642A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.736A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 493 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A 487 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 495 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 483 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 428 439 hydrogen bonds defined for protein. 1269 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: 2.74 Time building geometry restraints manager: 2.48 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: 2532 1.34 - 1.46: 1398 1.46 - 1.58: 3862 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7880 Sorted by residual: bond pdb=" F2 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" F3 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.533 -0.057 2.00e-02 2.50e+03 8.06e+00 bond pdb=" C ASP A 398 " pdb=" O ASP A 398 " ideal model delta sigma weight residual 1.234 1.247 -0.013 1.30e-02 5.92e+03 9.31e-01 bond pdb=" CA ILE A 307 " pdb=" CB ILE A 307 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.55e-02 4.16e+03 6.89e-01 ... (remaining 7875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 10644 2.78 - 5.56: 46 5.56 - 8.34: 1 8.34 - 11.12: 1 11.12 - 13.90: 1 Bond angle restraints: 10693 Sorted by residual: angle pdb=" F2 BEF A2001 " pdb="BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 119.96 106.06 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 120.12 109.98 10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N ASP A 398 " pdb=" CA ASP A 398 " pdb=" C ASP A 398 " ideal model delta sigma weight residual 112.13 107.72 4.41 1.37e+00 5.33e-01 1.04e+01 angle pdb=" N THR A 358 " pdb=" CA THR A 358 " pdb=" C THR A 358 " ideal model delta sigma weight residual 110.53 106.96 3.57 1.29e+00 6.01e-01 7.65e+00 angle pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " pdb=" F2 BEF A2001 " ideal model delta sigma weight residual 119.91 112.30 7.61 3.00e+00 1.11e-01 6.44e+00 ... (remaining 10688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4279 16.00 - 32.01: 397 32.01 - 48.01: 89 48.01 - 64.01: 7 64.01 - 80.01: 5 Dihedral angle restraints: 4777 sinusoidal: 1882 harmonic: 2895 Sorted by residual: dihedral pdb=" CA LEU A 947 " pdb=" C LEU A 947 " pdb=" N TYR A 948 " pdb=" CA TYR A 948 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR A 357 " pdb=" C THR A 357 " pdb=" N THR A 358 " pdb=" CA THR A 358 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.98e+00 dihedral pdb=" CB MET A 908 " pdb=" CG MET A 908 " pdb=" SD MET A 908 " pdb=" CE MET A 908 " ideal model delta sinusoidal sigma weight residual 60.00 112.21 -52.21 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 4774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 735 0.027 - 0.055: 345 0.055 - 0.082: 102 0.082 - 0.110: 60 0.110 - 0.137: 17 Chirality restraints: 1259 Sorted by residual: chirality pdb=" CA ILE A 307 " pdb=" N ILE A 307 " pdb=" C ILE A 307 " pdb=" CB ILE A 307 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 621 " pdb=" N ILE A 621 " pdb=" C ILE A 621 " pdb=" CB ILE A 621 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 150 " pdb=" N ILE A 150 " pdb=" C ILE A 150 " pdb=" CB ILE A 150 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1256 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 975 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 796 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C LEU A 796 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU A 796 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 797 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 952 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 953 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 953 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 953 " 0.021 5.00e-02 4.00e+02 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 61 2.62 - 3.19: 7035 3.19 - 3.76: 12017 3.76 - 4.33: 16964 4.33 - 4.90: 28144 Nonbonded interactions: 64221 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.051 2.170 nonbonded pdb=" F1 BEF A2001 " pdb="MG MG A2002 " model vdw 2.059 2.120 nonbonded pdb=" OD2 ASP A 351 " pdb=" F1 BEF A2001 " model vdw 2.085 2.990 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.097 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.101 2.170 ... (remaining 64216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.500 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.860 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.003 0.084 7880 Z= 0.209 Angle : 0.562 13.901 10693 Z= 0.320 Chirality : 0.039 0.137 1259 Planarity : 0.004 0.041 1362 Dihedral : 12.814 80.014 2901 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: -2.71 (0.22), residues: 997 helix: -1.61 (0.20), residues: 506 sheet: -1.80 (0.43), residues: 105 loop : -1.82 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 927 HIS 0.001 0.000 HIS A 15 PHE 0.016 0.001 PHE A 759 TYR 0.015 0.001 TYR A 836 ARG 0.002 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.880 Fit side-chains REVERT: A 63 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7612 (mtm-85) REVERT: A 128 LYS cc_start: 0.8284 (mttt) cc_final: 0.8037 (mtmm) REVERT: A 140 ILE cc_start: 0.8162 (pt) cc_final: 0.7732 (pt) REVERT: A 545 MET cc_start: 0.7955 (mmm) cc_final: 0.7627 (tpp) REVERT: A 586 TYR cc_start: 0.6963 (m-10) cc_final: 0.6597 (m-80) REVERT: A 732 MET cc_start: 0.8480 (ttm) cc_final: 0.8260 (ttt) REVERT: A 816 MET cc_start: 0.7378 (mmm) cc_final: 0.6963 (mmm) REVERT: A 1028 TRP cc_start: 0.7329 (t60) cc_final: 0.6918 (t60) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2665 time to fit residues: 49.1555 Evaluate side-chains 113 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 177 GLN A 428 ASN A 582 ASN A 615 GLN A 671 ASN A 682 HIS A 868 GLN A 943 HIS A 965 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.172891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131154 restraints weight = 8298.003| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.80 r_work: 0.3251 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7880 Z= 0.296 Angle : 0.550 5.511 10693 Z= 0.289 Chirality : 0.043 0.152 1259 Planarity : 0.005 0.042 1362 Dihedral : 4.072 16.866 1061 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.17 % Allowed : 11.24 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 997 helix: -0.30 (0.22), residues: 518 sheet: -1.64 (0.42), residues: 105 loop : -1.13 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 831 HIS 0.003 0.001 HIS A 15 PHE 0.024 0.002 PHE A 759 TYR 0.016 0.002 TYR A 762 ARG 0.006 0.001 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.790 Fit side-chains REVERT: A 63 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7551 (mtm-85) REVERT: A 140 ILE cc_start: 0.8169 (pt) cc_final: 0.7745 (pt) REVERT: A 143 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7858 (mtmm) REVERT: A 297 LYS cc_start: 0.6847 (mtpp) cc_final: 0.6561 (mttp) REVERT: A 518 GLU cc_start: 0.8336 (pp20) cc_final: 0.7775 (pp20) REVERT: A 536 MET cc_start: 0.7436 (ttm) cc_final: 0.6909 (ttm) REVERT: A 586 TYR cc_start: 0.7069 (m-10) cc_final: 0.6690 (m-80) REVERT: A 816 MET cc_start: 0.8134 (mmm) cc_final: 0.7728 (mmm) REVERT: A 1028 TRP cc_start: 0.7592 (t60) cc_final: 0.6974 (t60) outliers start: 10 outliers final: 9 residues processed: 125 average time/residue: 0.2397 time to fit residues: 39.1174 Evaluate side-chains 116 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 0.2980 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 29 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.175957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133425 restraints weight = 8332.411| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.80 r_work: 0.3309 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7880 Z= 0.149 Angle : 0.471 6.173 10693 Z= 0.246 Chirality : 0.040 0.139 1259 Planarity : 0.004 0.049 1362 Dihedral : 3.815 17.185 1061 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.76 % Allowed : 13.47 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 997 helix: 0.42 (0.23), residues: 520 sheet: -1.44 (0.43), residues: 103 loop : -0.81 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 927 HIS 0.002 0.000 HIS A 871 PHE 0.025 0.001 PHE A 759 TYR 0.014 0.001 TYR A 990 ARG 0.003 0.000 ARG A 655 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.995 Fit side-chains REVERT: A 120 LYS cc_start: 0.7387 (mttp) cc_final: 0.7024 (mmtp) REVERT: A 140 ILE cc_start: 0.8137 (pt) cc_final: 0.7716 (pt) REVERT: A 143 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7824 (mtmm) REVERT: A 297 LYS cc_start: 0.6859 (mtpp) cc_final: 0.6632 (mttp) REVERT: A 518 GLU cc_start: 0.8313 (pp20) cc_final: 0.7792 (pp20) REVERT: A 542 GLN cc_start: 0.7155 (pp30) cc_final: 0.6934 (pp30) REVERT: A 549 ARG cc_start: 0.7556 (mpp80) cc_final: 0.7255 (mtt90) REVERT: A 586 TYR cc_start: 0.7117 (m-10) cc_final: 0.6800 (m-80) REVERT: A 714 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: A 816 MET cc_start: 0.8069 (mmm) cc_final: 0.7710 (mmm) REVERT: A 1028 TRP cc_start: 0.7590 (t60) cc_final: 0.7015 (t60) outliers start: 15 outliers final: 8 residues processed: 129 average time/residue: 0.2807 time to fit residues: 47.2582 Evaluate side-chains 115 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 54.9953 > 50: distance: 14 - 40: 12.980 distance: 19 - 51: 4.412 distance: 30 - 59: 4.773 distance: 36 - 40: 9.674 distance: 37 - 64: 11.004 distance: 40 - 41: 5.145 distance: 41 - 42: 8.451 distance: 41 - 44: 5.006 distance: 42 - 43: 8.242 distance: 42 - 51: 5.323 distance: 43 - 73: 8.809 distance: 44 - 45: 8.542 distance: 46 - 47: 10.231 distance: 47 - 48: 12.588 distance: 48 - 49: 8.544 distance: 51 - 52: 5.939 distance: 52 - 53: 12.043 distance: 52 - 55: 9.671 distance: 53 - 54: 9.190 distance: 53 - 59: 14.514 distance: 54 - 81: 27.384 distance: 55 - 56: 6.403 distance: 56 - 57: 9.153 distance: 56 - 58: 7.107 distance: 60 - 61: 7.497 distance: 60 - 63: 4.549 distance: 61 - 62: 8.794 distance: 61 - 64: 5.394 distance: 62 - 86: 5.892 distance: 64 - 65: 8.282 distance: 65 - 66: 3.369 distance: 65 - 68: 3.629 distance: 66 - 67: 7.803 distance: 66 - 73: 14.980 distance: 67 - 94: 18.335 distance: 68 - 69: 5.000 distance: 69 - 70: 9.345 distance: 70 - 71: 3.011 distance: 70 - 72: 6.063 distance: 73 - 74: 14.868 distance: 74 - 75: 11.364 distance: 74 - 77: 11.120 distance: 75 - 76: 39.017 distance: 75 - 81: 27.497 distance: 77 - 78: 16.586 distance: 78 - 79: 15.864 distance: 78 - 80: 17.021 distance: 81 - 82: 18.646 distance: 82 - 83: 12.500 distance: 82 - 85: 20.191 distance: 83 - 84: 20.614 distance: 83 - 86: 8.562 distance: 86 - 87: 12.965 distance: 87 - 88: 14.743 distance: 87 - 90: 4.670 distance: 88 - 89: 23.174 distance: 88 - 94: 9.239 distance: 90 - 91: 15.073 distance: 90 - 92: 10.320 distance: 91 - 93: 8.844 distance: 94 - 95: 8.025 distance: 95 - 96: 8.171 distance: 95 - 98: 8.817 distance: 96 - 97: 17.938 distance: 98 - 99: 5.444 distance: 99 - 100: 12.507 distance: 100 - 101: 3.615 distance: 100 - 102: 10.439 distance: 104 - 107: 7.136 distance: 105 - 106: 18.665 distance: 105 - 108: 4.105 distance: 108 - 109: 6.737 distance: 109 - 110: 4.113 distance: 109 - 112: 3.715 distance: 110 - 111: 3.136 distance: 110 - 116: 9.937 distance: 112 - 113: 11.286 distance: 113 - 114: 13.970 distance: 113 - 115: 13.203