Starting phenix.real_space_refine on Fri May 16 08:51:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sn9_40617/05_2025/8sn9_40617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn9_40617/05_2025/8sn9_40617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sn9_40617/05_2025/8sn9_40617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn9_40617/05_2025/8sn9_40617.map" model { file = "/net/cci-nas-00/data/ceres_data/8sn9_40617/05_2025/8sn9_40617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn9_40617/05_2025/8sn9_40617.cif" } resolution = 3.9 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= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8264 2.51 5 N 2710 2.21 5 O 3288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14591 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 682 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 53.370 71.554 45.709 1.00 90.47 S ATOM 12446 SG CYS K 51 52.485 67.970 44.923 1.00 88.01 S ATOM 12470 SG CYS K 54 52.408 70.634 42.129 1.00 89.07 S ATOM 12187 SG CYS K 16 43.387 65.421 52.089 1.00 95.41 S ATOM 12205 SG CYS K 19 43.026 62.019 53.804 1.00 88.88 S ATOM 12335 SG CYS K 36 44.943 64.767 55.368 1.00 85.82 S ATOM 12357 SG CYS K 39 46.383 62.853 52.270 1.00 90.71 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 10.41, per 1000 atoms: 0.71 Number of scatterers: 14591 At special positions: 0 Unit cell: (130.144, 130.144, 124.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 33 16.00 P 294 15.00 O 3288 8.00 N 2710 7.00 C 8264 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=0, symmetry=0 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " Number of angles added : 9 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 13 sheets defined 61.6% alpha, 5.5% beta 136 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 7.11 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.817A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.578A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.946A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.931A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.717A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.619A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.849A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.670A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.752A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.743A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.866A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.553A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.577A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.893A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.782A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.811A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.550A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 68 removed outlier: 3.806A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 4.081A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.591A pdb=" N ASP L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.652A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 146 removed outlier: 3.925A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.585A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.806A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.783A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.563A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.747A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16 492 hydrogen bonds defined for protein. 1453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3546 1.34 - 1.46: 4319 1.46 - 1.58: 6962 1.58 - 1.70: 586 1.70 - 1.82: 49 Bond restraints: 15462 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 1.523 1.502 0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" CB MET H 59 " pdb=" CG MET H 59 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 ... (remaining 15457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 21543 1.53 - 3.07: 564 3.07 - 4.60: 31 4.60 - 6.13: 16 6.13 - 7.67: 2 Bond angle restraints: 22156 Sorted by residual: angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 105.03 7.67 3.00e+00 1.11e-01 6.53e+00 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 122.46 126.05 -3.59 1.41e+00 5.03e-01 6.47e+00 angle pdb=" C ALA L 19 " pdb=" N GLN L 20 " pdb=" CA GLN L 20 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.24e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 118.86 -5.68 2.37e+00 1.78e-01 5.75e+00 angle pdb=" CG ARG L 15 " pdb=" CD ARG L 15 " pdb=" NE ARG L 15 " ideal model delta sigma weight residual 112.00 116.98 -4.98 2.20e+00 2.07e-01 5.12e+00 ... (remaining 22151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 7251 36.00 - 71.99: 1335 71.99 - 107.99: 14 107.99 - 143.99: 0 143.99 - 179.99: 2 Dihedral angle restraints: 8602 sinusoidal: 5466 harmonic: 3136 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 40.01 179.99 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 70.83 149.17 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CG ARG D 92 " pdb=" CD ARG D 92 " pdb=" NE ARG D 92 " pdb=" CZ ARG D 92 " ideal model delta sinusoidal sigma weight residual 180.00 135.58 44.42 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 8599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1768 0.032 - 0.064: 560 0.064 - 0.096: 131 0.096 - 0.128: 48 0.128 - 0.160: 7 Chirality restraints: 2514 Sorted by residual: chirality pdb=" CB VAL K 58 " pdb=" CA VAL K 58 " pdb=" CG1 VAL K 58 " pdb=" CG2 VAL K 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2511 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " -0.009 2.00e-02 2.50e+03 1.38e-02 3.81e+00 pdb=" CG TYR F 88 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.025 2.00e-02 2.50e+03 1.06e-02 3.07e+00 pdb=" N9 DA I -35 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.024 2.00e-02 2.50e+03 9.63e-03 2.78e+00 pdb=" N9 DG I 47 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 164 2.63 - 3.20: 12082 3.20 - 3.77: 25513 3.77 - 4.33: 32901 4.33 - 4.90: 48665 Nonbonded interactions: 119325 Sorted by model distance: nonbonded pdb=" OG SER L 22 " pdb=" OG1 THR L 36 " model vdw 2.063 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.106 2.496 nonbonded pdb=" NH2 ARG B 35 " pdb=" OP2 DG J 8 " model vdw 2.192 3.120 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.200 3.040 nonbonded pdb=" OG SER D 64 " pdb=" O GLY F 101 " model vdw 2.226 3.040 ... (remaining 119320 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.25 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: 1.990 Set stop_for_unknowns flag: 0.010 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 44.690 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 0.035 15472 Z= 0.159 Angle : 0.557 7.668 22171 Z= 0.322 Chirality : 0.035 0.160 2514 Planarity : 0.003 0.040 1792 Dihedral : 25.887 179.987 6570 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.88 (0.26), residues: 1056 helix: 2.33 (0.21), residues: 640 sheet: 1.42 (0.81), residues: 48 loop : -0.80 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 93 HIS 0.002 0.001 HIS D 82 PHE 0.010 0.001 PHE L 69 TYR 0.033 0.002 TYR F 88 ARG 0.014 0.000 ARG L 15 Details of bonding type rmsd link_TRANS : bond 0.00058 ( 2) link_TRANS : angle 0.24804 ( 6) hydrogen bonds : bond 0.10647 ( 841) hydrogen bonds : angle 3.84937 ( 2147) metal coordination : bond 0.00697 ( 8) metal coordination : angle 3.45337 ( 9) covalent geometry : bond 0.00349 (15462) covalent geometry : angle 0.55309 (22156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8580 (tppt) REVERT: D 83 TYR cc_start: 0.8301 (m-80) cc_final: 0.7966 (m-80) REVERT: D 116 LYS cc_start: 0.9178 (ttpp) cc_final: 0.8815 (tttt) REVERT: D 120 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8480 (tttp) REVERT: G 30 VAL cc_start: 0.9252 (t) cc_final: 0.9023 (m) REVERT: H 35 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8135 (mt-10) REVERT: K 41 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7631 (mm-40) REVERT: K 49 LEU cc_start: 0.8683 (tp) cc_final: 0.8430 (tp) REVERT: K 57 ARG cc_start: 0.7490 (mtp-110) cc_final: 0.6992 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2899 time to fit residues: 73.4090 Evaluate side-chains 150 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 0.0570 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.142269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110042 restraints weight = 34476.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111862 restraints weight = 82896.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112783 restraints weight = 31136.084| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15472 Z= 0.177 Angle : 0.593 11.512 22171 Z= 0.335 Chirality : 0.036 0.183 2514 Planarity : 0.004 0.035 1792 Dihedral : 28.896 179.477 4410 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.65 % Allowed : 9.99 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.88 (0.26), residues: 1056 helix: 2.39 (0.20), residues: 644 sheet: 1.22 (0.80), residues: 48 loop : -0.91 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 141 HIS 0.003 0.001 HIS L 32 PHE 0.008 0.001 PHE H 70 TYR 0.028 0.002 TYR H 83 ARG 0.008 0.000 ARG M 42 Details of bonding type rmsd link_TRANS : bond 0.00133 ( 2) link_TRANS : angle 0.36562 ( 6) hydrogen bonds : bond 0.04997 ( 841) hydrogen bonds : angle 3.29374 ( 2147) metal coordination : bond 0.00787 ( 8) metal coordination : angle 4.46612 ( 9) covalent geometry : bond 0.00400 (15462) covalent geometry : angle 0.58618 (22156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8671 (tptt) REVERT: D 51 ASP cc_start: 0.7971 (t0) cc_final: 0.7696 (t0) REVERT: D 83 TYR cc_start: 0.8575 (m-80) cc_final: 0.7933 (m-10) REVERT: D 116 LYS cc_start: 0.9152 (ttpp) cc_final: 0.8781 (tttt) REVERT: D 120 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8418 (tttp) REVERT: K 49 LEU cc_start: 0.8662 (tp) cc_final: 0.8454 (tp) REVERT: L 97 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8285 (tp) outliers start: 6 outliers final: 4 residues processed: 160 average time/residue: 0.2807 time to fit residues: 63.8668 Evaluate side-chains 159 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 114 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105278 restraints weight = 27019.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105258 restraints weight = 51384.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106028 restraints weight = 35800.529| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15472 Z= 0.154 Angle : 0.569 10.732 22171 Z= 0.323 Chirality : 0.035 0.227 2514 Planarity : 0.004 0.034 1792 Dihedral : 28.776 179.577 4410 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.41 % Allowed : 12.05 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.93 (0.26), residues: 1056 helix: 2.45 (0.21), residues: 648 sheet: 0.79 (0.78), residues: 48 loop : -0.89 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 141 HIS 0.007 0.001 HIS K 65 PHE 0.008 0.001 PHE D 65 TYR 0.024 0.002 TYR H 83 ARG 0.009 0.000 ARG M 42 Details of bonding type rmsd link_TRANS : bond 0.00116 ( 2) link_TRANS : angle 0.29489 ( 6) hydrogen bonds : bond 0.04478 ( 841) hydrogen bonds : angle 3.08809 ( 2147) metal coordination : bond 0.00592 ( 8) metal coordination : angle 3.58995 ( 9) covalent geometry : bond 0.00341 (15462) covalent geometry : angle 0.56458 (22156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8723 (tptt) REVERT: D 51 ASP cc_start: 0.7954 (t0) cc_final: 0.7622 (t0) REVERT: D 83 TYR cc_start: 0.8481 (m-10) cc_final: 0.7940 (m-10) REVERT: D 116 LYS cc_start: 0.9174 (ttpp) cc_final: 0.8797 (tttt) REVERT: H 51 ASP cc_start: 0.8630 (p0) cc_final: 0.8419 (p0) REVERT: K 49 LEU cc_start: 0.8623 (tp) cc_final: 0.8405 (tp) outliers start: 13 outliers final: 8 residues processed: 157 average time/residue: 0.3202 time to fit residues: 70.3626 Evaluate side-chains 158 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 89 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 145)---------------| | r_work = 0.2888 r_free = 0.2888 target = 0.083182 restraints weight = 41860.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.083950 restraints weight = 28653.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.083339 restraints weight = 21482.540| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 15472 Z= 0.316 Angle : 0.689 11.779 22171 Z= 0.384 Chirality : 0.041 0.226 2514 Planarity : 0.004 0.035 1792 Dihedral : 29.026 178.725 4410 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.85 % Allowed : 14.44 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.43 (0.26), residues: 1056 helix: 2.06 (0.20), residues: 645 sheet: 0.76 (0.80), residues: 48 loop : -1.12 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 141 HIS 0.005 0.001 HIS D 82 PHE 0.016 0.002 PHE L 62 TYR 0.024 0.002 TYR H 83 ARG 0.007 0.001 ARG C 99 Details of bonding type rmsd link_TRANS : bond 0.00344 ( 2) link_TRANS : angle 0.56407 ( 6) hydrogen bonds : bond 0.06172 ( 841) hydrogen bonds : angle 3.65505 ( 2147) metal coordination : bond 0.00916 ( 8) metal coordination : angle 3.70114 ( 9) covalent geometry : bond 0.00751 (15462) covalent geometry : angle 0.68489 (22156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8760 (mptt) REVERT: D 51 ASP cc_start: 0.8216 (t0) cc_final: 0.7984 (t0) REVERT: D 116 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8838 (tttt) REVERT: L 147 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.3425 (pmm) outliers start: 17 outliers final: 10 residues processed: 156 average time/residue: 0.2986 time to fit residues: 65.6316 Evaluate side-chains 153 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 104 optimal weight: 0.0040 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 0.0970 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096119 restraints weight = 48465.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091824 restraints weight = 39275.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.091696 restraints weight = 33019.103| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15472 Z= 0.144 Angle : 0.579 12.466 22171 Z= 0.325 Chirality : 0.035 0.242 2514 Planarity : 0.004 0.035 1792 Dihedral : 28.797 179.790 4410 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.65 % Allowed : 16.29 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.82 (0.26), residues: 1056 helix: 2.39 (0.20), residues: 648 sheet: 0.60 (0.77), residues: 48 loop : -0.98 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 141 HIS 0.002 0.001 HIS M 68 PHE 0.016 0.001 PHE L 62 TYR 0.027 0.002 TYR H 83 ARG 0.007 0.000 ARG M 42 Details of bonding type rmsd link_TRANS : bond 0.00094 ( 2) link_TRANS : angle 0.58284 ( 6) hydrogen bonds : bond 0.04367 ( 841) hydrogen bonds : angle 3.04559 ( 2147) metal coordination : bond 0.00614 ( 8) metal coordination : angle 3.80337 ( 9) covalent geometry : bond 0.00306 (15462) covalent geometry : angle 0.57424 (22156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8790 (mptt) REVERT: D 59 MET cc_start: 0.8772 (tpp) cc_final: 0.8531 (tpp) REVERT: D 71 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7505 (tm-30) REVERT: D 83 TYR cc_start: 0.8639 (m-10) cc_final: 0.8365 (m-10) REVERT: D 116 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8689 (tttt) REVERT: D 120 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8413 (tttt) REVERT: H 42 TYR cc_start: 0.8146 (t80) cc_final: 0.7143 (t80) REVERT: K 49 LEU cc_start: 0.8412 (tp) cc_final: 0.8100 (tp) REVERT: L 147 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.3360 (pmm) REVERT: M 42 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7494 (ptp90) outliers start: 6 outliers final: 4 residues processed: 160 average time/residue: 0.3076 time to fit residues: 69.0969 Evaluate side-chains 155 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN L 77 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.139683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.090759 restraints weight = 54506.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085058 restraints weight = 44308.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.085439 restraints weight = 38291.120| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15472 Z= 0.252 Angle : 0.643 13.069 22171 Z= 0.357 Chirality : 0.038 0.212 2514 Planarity : 0.004 0.033 1792 Dihedral : 28.983 179.028 4410 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.52 % Allowed : 15.85 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.53 (0.26), residues: 1056 helix: 2.18 (0.20), residues: 654 sheet: 0.33 (0.79), residues: 48 loop : -1.18 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 61 HIS 0.004 0.001 HIS F 75 PHE 0.012 0.001 PHE L 62 TYR 0.027 0.002 TYR H 83 ARG 0.007 0.000 ARG C 99 Details of bonding type rmsd link_TRANS : bond 0.00270 ( 2) link_TRANS : angle 0.49612 ( 6) hydrogen bonds : bond 0.05560 ( 841) hydrogen bonds : angle 3.43456 ( 2147) metal coordination : bond 0.00777 ( 8) metal coordination : angle 3.74653 ( 9) covalent geometry : bond 0.00593 (15462) covalent geometry : angle 0.63839 (22156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8931 (mptt) REVERT: D 83 TYR cc_start: 0.8824 (m-10) cc_final: 0.8397 (m-10) REVERT: D 116 LYS cc_start: 0.9153 (ttpp) cc_final: 0.8793 (tttt) REVERT: F 84 MET cc_start: 0.8442 (mmm) cc_final: 0.7977 (mmm) REVERT: H 33 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7552 (mtp-110) REVERT: L 147 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.3767 (pmm) outliers start: 14 outliers final: 9 residues processed: 153 average time/residue: 0.3049 time to fit residues: 65.0494 Evaluate side-chains 154 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 52.1338 > 50: distance: 13 - 105: 4.735 distance: 28 - 90: 4.423 distance: 31 - 87: 17.405 distance: 39 - 68: 10.099 distance: 42 - 65: 7.937 distance: 56 - 58: 17.536 distance: 58 - 59: 16.596 distance: 59 - 60: 8.156 distance: 59 - 62: 6.956 distance: 60 - 61: 11.521 distance: 60 - 65: 9.899 distance: 62 - 63: 14.599 distance: 62 - 64: 10.622 distance: 65 - 66: 4.232 distance: 66 - 67: 8.041 distance: 66 - 69: 13.493 distance: 67 - 68: 18.571 distance: 67 - 76: 18.397 distance: 69 - 70: 8.057 distance: 70 - 72: 4.735 distance: 71 - 73: 5.020 distance: 72 - 74: 5.363 distance: 76 - 77: 7.504 distance: 77 - 78: 9.906 distance: 77 - 80: 8.897 distance: 78 - 79: 9.731 distance: 78 - 87: 6.160 distance: 80 - 81: 10.843 distance: 81 - 82: 8.422 distance: 81 - 83: 10.604 distance: 82 - 84: 4.731 distance: 84 - 86: 3.018 distance: 85 - 86: 4.539 distance: 87 - 88: 7.653 distance: 88 - 89: 8.209 distance: 88 - 91: 9.213 distance: 89 - 90: 7.189 distance: 89 - 95: 10.264 distance: 91 - 92: 9.138 distance: 92 - 93: 7.749 distance: 92 - 94: 10.027 distance: 95 - 96: 8.711 distance: 95 - 192: 13.260 distance: 96 - 97: 3.189 distance: 96 - 99: 4.711 distance: 97 - 98: 7.325 distance: 97 - 102: 5.445 distance: 98 - 189: 6.592 distance: 99 - 100: 4.735 distance: 99 - 101: 6.045 distance: 102 - 103: 3.311 distance: 103 - 106: 3.645 distance: 104 - 110: 8.339 distance: 106 - 107: 3.483 distance: 107 - 109: 3.493 distance: 110 - 111: 10.919 distance: 110 - 177: 7.958 distance: 111 - 112: 38.964 distance: 111 - 114: 6.062 distance: 112 - 113: 41.821 distance: 112 - 120: 52.134 distance: 113 - 174: 18.466 distance: 114 - 115: 10.949 distance: 115 - 116: 11.110 distance: 115 - 117: 10.095 distance: 116 - 118: 5.334 distance: 117 - 119: 3.549 distance: 118 - 119: 6.359 distance: 120 - 121: 43.923 distance: 121 - 122: 33.192 distance: 121 - 124: 35.208 distance: 122 - 123: 10.643 distance: 122 - 131: 13.746 distance: 124 - 125: 13.769 distance: 125 - 126: 9.094 distance: 125 - 127: 12.353 distance: 126 - 128: 7.735 distance: 127 - 129: 8.530 distance: 131 - 132: 3.824 distance: 132 - 133: 10.966 distance: 132 - 135: 4.487 distance: 133 - 134: 11.461 distance: 133 - 138: 12.221 distance: 136 - 137: 3.333 distance: 138 - 139: 9.070 distance: 139 - 140: 5.071 distance: 139 - 142: 4.408 distance: 140 - 145: 3.534 distance: 142 - 143: 6.853 distance: 142 - 144: 8.159