Starting phenix.real_space_refine on Sun May 11 01:12:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjq_31627/05_2025/7fjq_31627.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjq_31627/05_2025/7fjq_31627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fjq_31627/05_2025/7fjq_31627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjq_31627/05_2025/7fjq_31627.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjq_31627/05_2025/7fjq_31627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjq_31627/05_2025/7fjq_31627.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4570 2.51 5 N 1203 2.21 5 O 1269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7072 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 67, 'TRANS': 905} Chain breaks: 9 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 534 Unresolved non-hydrogen dihedrals: 372 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 260 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'SPM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.58, per 1000 atoms: 0.65 Number of scatterers: 7086 At special positions: 0 Unit cell: (77.9509, 96.6152, 138.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1269 8.00 N 1203 7.00 C 4570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 317 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 42.4% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.623A pdb=" N MET A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 257 through 287 removed outlier: 4.197A pdb=" N SER A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.736A pdb=" N VAL A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.850A pdb=" N VAL A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.534A pdb=" N GLN A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 3.782A pdb=" N ASN A 502 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 505 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 removed outlier: 3.610A pdb=" N ALA A 554 " --> pdb=" O PRO A 550 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 4.178A pdb=" N LYS A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 577' Processing helix chain 'A' and resid 577 through 582 removed outlier: 4.523A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 662 removed outlier: 3.535A pdb=" N GLY A 662 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 709 through 713 removed outlier: 3.935A pdb=" N VAL A 712 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.838A pdb=" N ILE A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 737 " --> pdb=" O THR A 733 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 738 " --> pdb=" O PRO A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 765 removed outlier: 3.705A pdb=" N THR A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 834 Processing helix chain 'A' and resid 840 through 844 Processing helix chain 'A' and resid 858 through 866 removed outlier: 3.719A pdb=" N LEU A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS A 864 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 889 removed outlier: 4.390A pdb=" N LYS A 887 " --> pdb=" O CYS A 883 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 888 " --> pdb=" O GLY A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.607A pdb=" N ILE A 920 " --> pdb=" O VAL A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 950 removed outlier: 3.522A pdb=" N TYR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 979 removed outlier: 3.923A pdb=" N VAL A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1025 Processing helix chain 'A' and resid 1044 through 1065 removed outlier: 3.943A pdb=" N THR A1048 " --> pdb=" O ASN A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1077 Processing helix chain 'A' and resid 1078 through 1098 Processing helix chain 'A' and resid 1104 through 1108 removed outlier: 3.969A pdb=" N ALA A1107 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A1108 " --> pdb=" O PRO A1105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1104 through 1108' Processing helix chain 'A' and resid 1116 through 1140 Processing helix chain 'A' and resid 1157 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.643A pdb=" N LEU A 392 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 493 through 495 Processing sheet with id=AA3, first strand: chain 'A' and resid 792 through 794 removed outlier: 4.689A pdb=" N LEU A 773 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 823 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 850 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA A 746 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N PHE A 851 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET A 748 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N MET A 875 " --> pdb=" O ILE A 893 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 530 removed outlier: 5.417A pdb=" N VAL A 525 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG A 725 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A 527 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU A 718 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER A 692 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 641 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG A 636 " --> pdb=" O PRO A 629 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER A 638 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG A 627 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA A 642 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER A 623 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 562 through 564 removed outlier: 3.730A pdb=" N LEU A 564 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 783 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: 2.24 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1025 1.25 - 1.39: 1712 1.39 - 1.53: 3693 1.53 - 1.67: 728 1.67 - 1.81: 65 Bond restraints: 7223 Sorted by residual: bond pdb=" CA TYR A 256 " pdb=" C TYR A 256 " ideal model delta sigma weight residual 1.523 1.308 0.215 1.34e-02 5.57e+03 2.57e+02 bond pdb=" CA HIS A 255 " pdb=" C HIS A 255 " ideal model delta sigma weight residual 1.523 1.347 0.176 1.34e-02 5.57e+03 1.73e+02 bond pdb=" CA ALA A 965 " pdb=" C ALA A 965 " ideal model delta sigma weight residual 1.524 1.363 0.161 1.27e-02 6.20e+03 1.60e+02 bond pdb=" C LEU A 964 " pdb=" O LEU A 964 " ideal model delta sigma weight residual 1.237 1.106 0.131 1.17e-02 7.31e+03 1.25e+02 bond pdb=" CA SER A 941 " pdb=" C SER A 941 " ideal model delta sigma weight residual 1.524 1.386 0.138 1.27e-02 6.20e+03 1.17e+02 ... (remaining 7218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 9458 4.92 - 9.84: 372 9.84 - 14.77: 31 14.77 - 19.69: 6 19.69 - 24.61: 3 Bond angle restraints: 9870 Sorted by residual: angle pdb=" N PRO A1172 " pdb=" CA PRO A1172 " pdb=" C PRO A1172 " ideal model delta sigma weight residual 110.70 86.09 24.61 1.22e+00 6.72e-01 4.07e+02 angle pdb=" N LYS A1117 " pdb=" CA LYS A1117 " pdb=" C LYS A1117 " ideal model delta sigma weight residual 111.71 98.66 13.05 1.15e+00 7.56e-01 1.29e+02 angle pdb=" N ILE A 441 " pdb=" CA ILE A 441 " pdb=" C ILE A 441 " ideal model delta sigma weight residual 111.56 101.88 9.68 8.60e-01 1.35e+00 1.27e+02 angle pdb=" N TRP A 258 " pdb=" CA TRP A 258 " pdb=" C TRP A 258 " ideal model delta sigma weight residual 111.11 123.97 -12.86 1.20e+00 6.94e-01 1.15e+02 angle pdb=" N LEU A1042 " pdb=" CA LEU A1042 " pdb=" C LEU A1042 " ideal model delta sigma weight residual 109.81 133.44 -23.63 2.21e+00 2.05e-01 1.14e+02 ... (remaining 9865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 3961 16.85 - 33.69: 266 33.69 - 50.53: 93 50.53 - 67.37: 17 67.37 - 84.22: 4 Dihedral angle restraints: 4341 sinusoidal: 1536 harmonic: 2805 Sorted by residual: dihedral pdb=" C LEU A1042 " pdb=" N LEU A1042 " pdb=" CA LEU A1042 " pdb=" CB LEU A1042 " ideal model delta harmonic sigma weight residual -122.60 -152.07 29.47 0 2.50e+00 1.60e-01 1.39e+02 dihedral pdb=" N LEU A1042 " pdb=" C LEU A1042 " pdb=" CA LEU A1042 " pdb=" CB LEU A1042 " ideal model delta harmonic sigma weight residual 122.80 151.73 -28.93 0 2.50e+00 1.60e-01 1.34e+02 dihedral pdb=" N GLN A 944 " pdb=" C GLN A 944 " pdb=" CA GLN A 944 " pdb=" CB GLN A 944 " ideal model delta harmonic sigma weight residual 122.80 147.79 -24.99 0 2.50e+00 1.60e-01 1.00e+02 ... (remaining 4338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.265: 1108 0.265 - 0.530: 82 0.530 - 0.795: 26 0.795 - 1.060: 4 1.060 - 1.325: 2 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CA LEU A1042 " pdb=" N LEU A1042 " pdb=" C LEU A1042 " pdb=" CB LEU A1042 " both_signs ideal model delta sigma weight residual False 2.51 1.19 1.33 2.00e-01 2.50e+01 4.39e+01 chirality pdb=" CA GLN A 944 " pdb=" N GLN A 944 " pdb=" C GLN A 944 " pdb=" CB GLN A 944 " both_signs ideal model delta sigma weight residual False 2.51 1.44 1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA LYS A 935 " pdb=" N LYS A 935 " pdb=" C LYS A 935 " pdb=" CB LYS A 935 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 1219 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 966 " -0.040 2.00e-02 2.50e+03 7.67e-02 5.88e+01 pdb=" C ILE A 966 " 0.133 2.00e-02 2.50e+03 pdb=" O ILE A 966 " -0.047 2.00e-02 2.50e+03 pdb=" N ASP A 967 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 967 " -0.039 2.00e-02 2.50e+03 7.29e-02 5.31e+01 pdb=" C ASP A 967 " 0.126 2.00e-02 2.50e+03 pdb=" O ASP A 967 " -0.045 2.00e-02 2.50e+03 pdb=" N LEU A 968 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 969 " 0.032 2.00e-02 2.50e+03 6.23e-02 3.89e+01 pdb=" C VAL A 969 " -0.108 2.00e-02 2.50e+03 pdb=" O VAL A 969 " 0.039 2.00e-02 2.50e+03 pdb=" N ILE A 970 " 0.036 2.00e-02 2.50e+03 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 147 2.56 - 3.15: 5519 3.15 - 3.73: 10784 3.73 - 4.32: 14168 4.32 - 4.90: 22826 Nonbonded interactions: 53444 Sorted by model distance: nonbonded pdb=" CB HIS A 255 " pdb=" N TYR A 256 " model vdw 1.980 2.816 nonbonded pdb=" CB TYR A 256 " pdb=" N TYR A 257 " model vdw 2.063 2.816 nonbonded pdb=" N SER A1055 " pdb=" OG SER A1055 " model vdw 2.181 2.496 nonbonded pdb=" O TYR A 256 " pdb=" N TRP A 258 " model vdw 2.204 3.120 nonbonded pdb=" O TYR A 256 " pdb=" C TYR A 257 " model vdw 2.294 3.270 ... (remaining 53439 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.150 Find NCS groups from input model: 0.070 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.019 0.215 7224 Z= 1.371 Angle : 2.025 24.610 9872 Z= 1.333 Chirality : 0.171 1.325 1222 Planarity : 0.014 0.144 1250 Dihedral : 13.671 84.216 2522 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 1.68 % Allowed : 10.18 % Favored : 88.14 % Rotamer: Outliers : 6.77 % Allowed : 9.94 % Favored : 83.29 % Cbeta Deviations : 4.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.67 (0.24), residues: 953 helix: -1.36 (0.25), residues: 398 sheet: -2.71 (0.50), residues: 71 loop : -3.45 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1171 HIS 0.009 0.001 HIS A 255 PHE 0.066 0.004 PHE A 945 TYR 0.035 0.003 TYR A 940 ARG 0.003 0.001 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.24116 ( 275) hydrogen bonds : angle 9.55292 ( 783) SS BOND : bond 0.00208 ( 1) SS BOND : angle 1.03296 ( 2) covalent geometry : bond 0.01897 ( 7223) covalent geometry : angle 2.02513 ( 9870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ILE cc_start: 0.8701 (pp) cc_final: 0.8493 (mm) REVERT: A 854 MET cc_start: 0.8812 (mmm) cc_final: 0.8491 (mmm) REVERT: A 918 MET cc_start: 0.8317 (ptp) cc_final: 0.7981 (ptp) REVERT: A 937 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (mmt) REVERT: A 941 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.9060 (t) REVERT: A 942 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 1008 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7960 (tt0) outliers start: 49 outliers final: 25 residues processed: 156 average time/residue: 0.1568 time to fit residues: 33.6906 Evaluate side-chains 95 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1080 PRO Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.0170 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 497 HIS A 870 GLN A1047 ASN ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.176328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111350 restraints weight = 10629.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112292 restraints weight = 7126.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113385 restraints weight = 5790.955| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7224 Z= 0.158 Angle : 0.818 11.373 9872 Z= 0.411 Chirality : 0.049 0.311 1222 Planarity : 0.008 0.136 1250 Dihedral : 9.159 56.297 1091 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.65 % Favored : 89.82 % Rotamer: Outliers : 4.97 % Allowed : 14.78 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -3.29 (0.25), residues: 953 helix: -1.27 (0.26), residues: 385 sheet: -2.13 (0.50), residues: 74 loop : -3.03 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1171 HIS 0.005 0.001 HIS A 255 PHE 0.017 0.002 PHE A 963 TYR 0.025 0.002 TYR A 936 ARG 0.007 0.001 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.06157 ( 275) hydrogen bonds : angle 6.08551 ( 783) SS BOND : bond 0.00470 ( 1) SS BOND : angle 0.78858 ( 2) covalent geometry : bond 0.00347 ( 7223) covalent geometry : angle 0.81828 ( 9870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 501 ILE cc_start: 0.9094 (mt) cc_final: 0.8883 (mt) REVERT: A 542 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6096 (pp20) REVERT: A 875 MET cc_start: 0.8232 (tpt) cc_final: 0.8013 (tpt) REVERT: A 937 MET cc_start: 0.8636 (tpp) cc_final: 0.8206 (mmm) REVERT: A 1047 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7735 (t0) REVERT: A 1093 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8499 (p) REVERT: A 1133 MET cc_start: 0.7347 (mmm) cc_final: 0.6950 (mmp) outliers start: 36 outliers final: 15 residues processed: 103 average time/residue: 0.1714 time to fit residues: 24.6800 Evaluate side-chains 83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1067 LYS Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.0980 chunk 1 optimal weight: 40.0000 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 26 optimal weight: 50.0000 chunk 95 optimal weight: 0.0170 chunk 2 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.178467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114327 restraints weight = 10758.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114424 restraints weight = 6912.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116016 restraints weight = 5413.377| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7224 Z= 0.131 Angle : 0.730 11.092 9872 Z= 0.360 Chirality : 0.046 0.283 1222 Planarity : 0.006 0.072 1250 Dihedral : 7.633 59.097 1057 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.44 % Favored : 90.03 % Rotamer: Outliers : 4.28 % Allowed : 16.57 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.87 (0.26), residues: 953 helix: -0.87 (0.26), residues: 395 sheet: -1.39 (0.57), residues: 66 loop : -2.96 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1028 HIS 0.002 0.000 HIS A 198 PHE 0.017 0.001 PHE A 963 TYR 0.015 0.001 TYR A 936 ARG 0.005 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 275) hydrogen bonds : angle 5.33548 ( 783) SS BOND : bond 0.00496 ( 1) SS BOND : angle 0.55946 ( 2) covalent geometry : bond 0.00277 ( 7223) covalent geometry : angle 0.73023 ( 9870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.781 Fit side-chains REVERT: A 235 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: A 276 TYR cc_start: 0.7213 (t80) cc_final: 0.6754 (t80) REVERT: A 542 GLU cc_start: 0.6520 (tm-30) cc_final: 0.5986 (pp20) REVERT: A 612 LEU cc_start: 0.2620 (OUTLIER) cc_final: 0.2360 (tp) REVERT: A 637 MET cc_start: 0.8212 (tmm) cc_final: 0.7641 (ttt) REVERT: A 1133 MET cc_start: 0.7389 (mmm) cc_final: 0.7037 (mmp) REVERT: A 1140 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6169 (mp10) outliers start: 31 outliers final: 11 residues processed: 98 average time/residue: 0.1396 time to fit residues: 20.3917 Evaluate side-chains 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1140 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 54.3436 > 50: distance: 26 - 34: 5.065 distance: 27 - 49: 3.701 distance: 34 - 35: 14.450 distance: 34 - 40: 24.037 distance: 35 - 36: 18.478 distance: 35 - 38: 22.327 distance: 36 - 37: 38.740 distance: 36 - 41: 5.676 distance: 37 - 60: 36.016 distance: 38 - 39: 4.762 distance: 39 - 40: 12.696 distance: 41 - 42: 15.066 distance: 42 - 43: 12.735 distance: 42 - 45: 31.908 distance: 43 - 44: 25.107 distance: 43 - 49: 7.205 distance: 45 - 46: 12.914 distance: 46 - 47: 13.690 distance: 46 - 48: 16.148 distance: 49 - 50: 7.553 distance: 50 - 51: 9.573 distance: 50 - 53: 10.544 distance: 51 - 52: 10.079 distance: 51 - 60: 9.029 distance: 52 - 76: 17.522 distance: 53 - 54: 8.974 distance: 54 - 55: 3.330 distance: 55 - 56: 4.163 distance: 60 - 61: 13.554 distance: 61 - 62: 8.497 distance: 61 - 64: 5.162 distance: 62 - 63: 5.213 distance: 62 - 68: 16.501 distance: 63 - 84: 26.166 distance: 64 - 65: 11.797 distance: 64 - 66: 25.316 distance: 65 - 67: 16.264 distance: 68 - 69: 13.180 distance: 69 - 70: 13.582 distance: 69 - 72: 16.625 distance: 70 - 71: 10.393 distance: 70 - 76: 10.977 distance: 72 - 73: 26.443 distance: 73 - 74: 20.378 distance: 73 - 75: 18.197 distance: 76 - 77: 10.531 distance: 77 - 78: 3.549 distance: 77 - 80: 5.838 distance: 78 - 79: 17.381 distance: 78 - 84: 28.282 distance: 80 - 81: 14.020 distance: 81 - 82: 20.446 distance: 81 - 83: 38.049 distance: 84 - 85: 25.204 distance: 85 - 86: 19.959 distance: 86 - 87: 12.427 distance: 86 - 88: 22.796 distance: 88 - 89: 14.059 distance: 89 - 90: 29.449 distance: 90 - 91: 14.948 distance: 90 - 92: 10.936 distance: 92 - 93: 22.065 distance: 93 - 94: 4.106 distance: 93 - 96: 19.984 distance: 94 - 95: 15.567 distance: 94 - 101: 21.155 distance: 96 - 97: 18.801 distance: 97 - 98: 27.369 distance: 98 - 99: 18.345 distance: 99 - 100: 16.082 distance: 101 - 102: 16.361 distance: 102 - 103: 23.966 distance: 102 - 105: 11.576 distance: 103 - 104: 4.800 distance: 103 - 109: 20.515 distance: 105 - 106: 14.723 distance: 106 - 107: 15.683 distance: 106 - 108: 27.525