Starting phenix.real_space_refine on Fri Jul 3 14:42:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iej_35383/07_2026/8iej_35383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iej_35383/07_2026/8iej_35383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8iej_35383/07_2026/8iej_35383.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iej_35383/07_2026/8iej_35383.cif" model { file = "/net/cci-nas-00/data/ceres_data/8iej_35383/07_2026/8iej_35383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iej_35383/07_2026/8iej_35383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iej_35383/07_2026/8iej_35383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iej_35383/07_2026/8iej_35383.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1067 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 294 5.49 5 S 35 5.16 5 C 7937 2.51 5 N 2635 2.21 5 O 3181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14086 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "L" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "A" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 476 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "R" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1067 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 135} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'ASN:plan1': 4, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "A" 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} Chain: "M" 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 12108 SG CYS A 948 47.191 47.637 12.094 1.00216.57 S ATOM 12259 SG CYS A 968 47.274 50.753 11.972 1.00213.80 S ATOM 12285 SG CYS A 971 44.012 50.383 11.912 1.00208.87 S ATOM 12214 SG CYS A 963 43.787 45.876 27.411 1.00197.39 S ATOM 12386 SG CYS A 983 41.373 46.465 23.589 1.00200.37 S ATOM 12587 SG CYS M 922 63.805 58.535 26.486 1.00185.29 S ATOM 12606 SG CYS M 925 67.390 57.651 27.123 1.00189.09 S ATOM 12746 SG CYS M 942 64.428 55.921 29.187 1.00161.27 S ATOM 12772 SG CYS M 945 65.569 58.880 30.124 1.00148.39 S ATOM 12701 SG CYS M 937 53.818 64.915 26.888 1.00146.39 S ATOM 12879 SG CYS M 957 57.040 66.699 27.510 1.00142.03 S ATOM 12901 SG CYS M 960 54.070 68.660 26.301 1.00148.06 S Time building chain proxies: 2.57, per 1000 atoms: 0.18 Number of scatterers: 14086 At special positions: 0 Unit cell: (120.288, 121.362, 113.844, 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 4 29.99 S 35 16.00 P 294 15.00 O 3181 8.00 N 2635 7.00 C 7937 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 405.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 948 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 971 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 968 " pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 965 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 983 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 963 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 945 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 942 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 925 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 922 " pdb=" ZN M1002 " pdb="ZN ZN M1002 " - pdb=" ND1 HIS M 939 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 957 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 960 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 937 " Number of angles added : 9 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 13 sheets defined 62.2% alpha, 5.0% beta 140 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.473A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.542A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.874A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.786A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.535A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.425A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.605A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 55 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.557A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.171A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'A' and resid 942 through 947 Processing helix chain 'A' and resid 969 through 978 Processing helix chain 'M' and resid 916 through 920 Processing helix chain 'M' and resid 942 through 952 Processing helix chain 'R' and resid 3 through 19 Processing helix chain 'R' and resid 89 through 94 Processing helix chain 'R' and resid 101 through 115 Processing helix chain 'R' and resid 123 through 133 Processing helix chain 'R' and resid 133 through 149 removed outlier: 3.562A pdb=" N TRP R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.192A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.822A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.924A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.395A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'G' and resid 101 through 102 removed outlier: 6.791A pdb=" N THR G 101 " --> pdb=" O TYR L 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.809A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'A' and resid 966 through 967 removed outlier: 4.103A pdb=" N VAL A 959 " --> pdb=" O HIS A 996 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A 996 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 939 through 941 removed outlier: 3.727A pdb=" N HIS M 939 " --> pdb=" O LEU M 934 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 24 through 28 483 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 361 hydrogen bonds 718 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3044 1.33 - 1.45: 4483 1.45 - 1.57: 6786 1.57 - 1.69: 586 1.69 - 1.81: 48 Bond restraints: 14947 Sorted by residual: bond pdb=" C3' DG I -4 " pdb=" O3' DG I -4 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC J 8 " pdb=" O3' DC J 8 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.82e+00 bond pdb=" C3' DT J 64 " pdb=" C2' DT J 64 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DG I -22 " pdb=" C2' DG I -22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.95e+00 ... (remaining 14942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 21247 2.62 - 5.25: 204 5.25 - 7.87: 12 7.87 - 10.50: 1 10.50 - 13.12: 1 Bond angle restraints: 21465 Sorted by residual: angle pdb=" N ARG A 981 " pdb=" CA ARG A 981 " pdb=" C ARG A 981 " ideal model delta sigma weight residual 108.17 95.05 13.12 1.85e+00 2.92e-01 5.03e+01 angle pdb=" O4' DC I -26 " pdb=" C4' DC I -26 " pdb=" C3' DC I -26 " ideal model delta sigma weight residual 106.00 102.73 3.27 6.00e-01 2.78e+00 2.97e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 ... (remaining 21460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 6767 34.03 - 68.06: 1449 68.06 - 102.10: 15 102.10 - 136.13: 1 136.13 - 170.16: 3 Dihedral angle restraints: 8235 sinusoidal: 5233 harmonic: 3002 Sorted by residual: dihedral pdb=" CA ARG M 928 " pdb=" C ARG M 928 " pdb=" N LYS M 929 " pdb=" CA LYS M 929 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO R 28 " pdb=" C PRO R 28 " pdb=" N SER R 29 " pdb=" CA SER R 29 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 49.84 170.16 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1921 0.059 - 0.119: 467 0.119 - 0.178: 41 0.178 - 0.237: 2 0.237 - 0.296: 1 Chirality restraints: 2432 Sorted by residual: chirality pdb=" CA ARG A 981 " pdb=" N ARG A 981 " pdb=" C ARG A 981 " pdb=" CB ARG A 981 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' DT I 15 " pdb=" C4' DT I 15 " pdb=" O3' DT I 15 " pdb=" C2' DT I 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ARG A 979 " pdb=" N ARG A 979 " pdb=" C ARG A 979 " pdb=" CB ARG A 979 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 2429 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.025 2.00e-02 2.50e+03 3.06e-02 1.87e+01 pdb=" CG TYR D 83 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 36 " -0.020 2.00e-02 2.50e+03 1.82e-02 8.26e+00 pdb=" CG TRP R 36 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP R 36 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 36 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 36 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 36 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 17 " -0.026 2.00e-02 2.50e+03 1.15e-02 3.63e+00 pdb=" N9 DA I 17 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 17 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 17 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 17 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 17 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 17 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 17 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 17 " 0.001 2.00e-02 2.50e+03 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 3 2.12 - 2.81: 3438 2.81 - 3.51: 20074 3.51 - 4.20: 39166 4.20 - 4.90: 58629 Nonbonded interactions: 121310 Sorted by model distance: nonbonded pdb=" OH TYR A 999 " pdb=" NE2 HIS M 939 " model vdw 1.421 3.120 nonbonded pdb=" OH TYR A 999 " pdb=" CD2 HIS M 939 " model vdw 1.627 3.260 nonbonded pdb=" NH2 ARG A 954 " pdb=" SG CYS A 971 " model vdw 2.095 3.480 nonbonded pdb=" OH TYR C 50 " pdb=" OE1 GLN D 95 " model vdw 2.132 3.040 nonbonded pdb=" OG SER R 29 " pdb=" O ASN R 32 " model vdw 2.136 3.040 ... (remaining 121305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 942 through 952 or resid 954 through 972 or resid 975 thro \ ugh 976 or resid 979 through 992 or resid 994 through 1102)) selection = (chain 'M' and (resid 916 through 925 or (resid 926 and (name N or name CA or na \ me C or name O or name CB )) or resid 928 through 929 or (resid 930 and (name N \ or name CA or name C or name O or name CB )) or resid 931 through 946 or resid 9 \ 49 through 950 or resid 953 through 966 or resid 968 through 973 or (resid 974 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1001 through 10 \ 02)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 119 or resid 121 through 124)) selection = (chain 'H' and (resid 31 through 119 or resid 121 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 38 through 134) } ncs_group { reference = chain 'F' selection = (chain 'L' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) } 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=0.27 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 : 0.011 0.585 14963 Z= 0.689 Angle : 0.786 18.310 21474 Z= 0.638 Chirality : 0.049 0.296 2432 Planarity : 0.005 0.066 1710 Dihedral : 26.500 170.160 6293 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.32 % Allowed : 0.60 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.27), residues: 1008 helix: 2.04 (0.21), residues: 641 sheet: 0.59 (1.02), residues: 27 loop : -0.17 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 11 TYR 0.074 0.002 TYR D 83 PHE 0.020 0.002 PHE M 941 TRP 0.048 0.005 TRP R 36 HIS 0.006 0.001 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.55 (14947) covalent geometry : angle 0.76747 / 0.64 (21465) hydrogen bonds : bond 0.09008 / 5.89 ( 844) hydrogen bonds : angle 3.88644 / 2.76 ( 2146) metal coordination : bond 0.24229 / 14.96 ( 14) metal coordination : angle 8.34178 / 4.74 ( 9) Misc. bond : bond 0.29501 / 14.46 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 256 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.8421 (t0) cc_final: 0.8127 (p0) REVERT: C 72 ASP cc_start: 0.8554 (m-30) cc_final: 0.8333 (m-30) REVERT: C 90 ASP cc_start: 0.8660 (t70) cc_final: 0.8449 (t0) REVERT: D 68 ASP cc_start: 0.8827 (t70) cc_final: 0.8595 (t0) REVERT: G 24 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8961 (mm-40) REVERT: G 38 ASN cc_start: 0.8356 (t0) cc_final: 0.7963 (t0) REVERT: G 90 ASP cc_start: 0.8512 (t70) cc_final: 0.8301 (t70) REVERT: K 56 LYS cc_start: 0.9346 (ttmm) cc_final: 0.9120 (ttpp) REVERT: K 59 GLU cc_start: 0.8637 (pm20) cc_final: 0.8309 (pm20) REVERT: A 972 VAL cc_start: 0.9370 (m) cc_final: 0.9048 (m) REVERT: A 996 HIS cc_start: 0.6472 (t-90) cc_final: 0.6202 (t-90) REVERT: M 938 PHE cc_start: 0.9013 (m-80) cc_final: 0.8619 (m-80) REVERT: M 967 ASN cc_start: 0.9247 (m-40) cc_final: 0.8770 (m-40) REVERT: R 36 TRP cc_start: 0.6377 (m100) cc_final: 0.5977 (m100) outliers start: 11 outliers final: 8 residues processed: 265 average time/residue: 0.1308 time to fit residues: 48.4882 Evaluate side-chains 236 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain A residue 955 LYS Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 979 ARG Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain M residue 936 LYS Chi-restraints excluded: chain M residue 947 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 50.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN C 104 GLN G 73 ASN K 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.083380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.050017 restraints weight = 47473.674| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.56 r_work: 0.2613 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14963 Z= 0.188 Angle : 0.680 20.547 21474 Z= 0.383 Chirality : 0.046 0.278 2432 Planarity : 0.005 0.060 1710 Dihedral : 29.877 171.755 4379 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.92 % Allowed : 9.86 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.27), residues: 1008 helix: 2.16 (0.21), residues: 644 sheet: -0.18 (0.85), residues: 37 loop : -0.28 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 979 TYR 0.024 0.002 TYR D 42 PHE 0.024 0.002 PHE R 13 TRP 0.009 0.002 TRP R 36 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (14947) covalent geometry : angle 0.65364 / 0.38 (21465) hydrogen bonds : bond 0.04903 / 3.20 ( 844) hydrogen bonds : angle 3.38591 / 2.38 ( 2146) metal coordination : bond 0.01615 / 1.20 ( 14) metal coordination : angle 9.19629 / 5.23 ( 9) Misc. bond : bond 0.00754 / 0.38 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 250 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8885 (t70) cc_final: 0.8665 (t70) REVERT: D 68 ASP cc_start: 0.9386 (t70) cc_final: 0.9129 (t0) REVERT: E 59 GLU cc_start: 0.9059 (pm20) cc_final: 0.8802 (pm20) REVERT: G 13 LYS cc_start: 0.7378 (tptt) cc_final: 0.6928 (tppt) REVERT: G 36 LYS cc_start: 0.8947 (tmtt) cc_final: 0.8690 (tmtt) REVERT: G 38 ASN cc_start: 0.8467 (t0) cc_final: 0.8254 (t0) REVERT: G 90 ASP cc_start: 0.8771 (t70) cc_final: 0.8438 (t70) REVERT: H 42 TYR cc_start: 0.8890 (t80) cc_final: 0.8573 (t80) REVERT: K 56 LYS cc_start: 0.9385 (ttmm) cc_final: 0.9160 (ttpp) REVERT: K 59 GLU cc_start: 0.8897 (pm20) cc_final: 0.8489 (pm20) REVERT: A 962 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8300 (mtmm) REVERT: M 926 ASN cc_start: 0.9225 (m110) cc_final: 0.8817 (m110) REVERT: M 947 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9219 (tppt) REVERT: M 951 ASP cc_start: 0.9272 (m-30) cc_final: 0.8799 (p0) REVERT: M 967 ASN cc_start: 0.9254 (m-40) cc_final: 0.8758 (m-40) REVERT: R 36 TRP cc_start: 0.6168 (m100) cc_final: 0.5733 (m100) outliers start: 16 outliers final: 10 residues processed: 257 average time/residue: 0.1194 time to fit residues: 42.3927 Evaluate side-chains 248 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 237 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 955 LYS Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain M residue 936 LYS Chi-restraints excluded: chain M residue 947 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 40.0000 chunk 94 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN K 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.083498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.050256 restraints weight = 47705.800| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.56 r_work: 0.2613 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14963 Z= 0.171 Angle : 0.644 17.950 21474 Z= 0.365 Chirality : 0.044 0.258 2432 Planarity : 0.005 0.058 1710 Dihedral : 29.863 171.298 4375 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.56 % Allowed : 12.86 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.27), residues: 1008 helix: 2.21 (0.21), residues: 644 sheet: -0.06 (0.84), residues: 39 loop : -0.32 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 15 TYR 0.030 0.002 TYR D 83 PHE 0.015 0.001 PHE M 938 TRP 0.003 0.001 TRP R 36 HIS 0.010 0.001 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (14947) covalent geometry : angle 0.61929 / 0.36 (21465) hydrogen bonds : bond 0.04543 / 2.98 ( 844) hydrogen bonds : angle 3.21201 / 2.28 ( 2146) metal coordination : bond 0.00879 / 0.71 ( 14) metal coordination : angle 8.72682 / 4.97 ( 9) Misc. bond : bond 0.00373 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8858 (t70) cc_final: 0.8616 (t70) REVERT: D 68 ASP cc_start: 0.9391 (t70) cc_final: 0.9143 (t0) REVERT: D 108 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8999 (ttpp) REVERT: E 59 GLU cc_start: 0.9094 (pm20) cc_final: 0.8819 (pm20) REVERT: G 73 ASN cc_start: 0.8723 (t160) cc_final: 0.8399 (t0) REVERT: G 90 ASP cc_start: 0.8711 (t70) cc_final: 0.8370 (t0) REVERT: H 42 TYR cc_start: 0.8899 (t80) cc_final: 0.8525 (t80) REVERT: K 56 LYS cc_start: 0.9391 (ttmm) cc_final: 0.9160 (ttpp) REVERT: K 59 GLU cc_start: 0.8886 (pm20) cc_final: 0.8458 (pm20) REVERT: A 962 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8363 (mtmm) REVERT: A 996 HIS cc_start: 0.6950 (t-170) cc_final: 0.6602 (t-170) REVERT: M 936 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8723 (tptt) REVERT: M 938 PHE cc_start: 0.9268 (m-80) cc_final: 0.8813 (m-80) REVERT: M 947 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9227 (tppt) REVERT: M 951 ASP cc_start: 0.9228 (m-30) cc_final: 0.8748 (p0) REVERT: M 967 ASN cc_start: 0.9240 (m-40) cc_final: 0.8627 (m-40) REVERT: M 968 ASP cc_start: 0.9347 (m-30) cc_final: 0.8245 (t0) REVERT: R 12 ASP cc_start: 0.8450 (m-30) cc_final: 0.8111 (m-30) outliers start: 13 outliers final: 6 residues processed: 255 average time/residue: 0.1334 time to fit residues: 46.8806 Evaluate side-chains 247 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 238 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 936 LYS Chi-restraints excluded: chain M residue 947 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.084181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.051044 restraints weight = 47643.251| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.57 r_work: 0.2637 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14963 Z= 0.140 Angle : 0.633 15.962 21474 Z= 0.360 Chirality : 0.043 0.240 2432 Planarity : 0.005 0.115 1710 Dihedral : 29.811 171.028 4369 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.04 % Allowed : 13.22 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.27), residues: 1008 helix: 2.26 (0.21), residues: 642 sheet: 0.11 (0.86), residues: 39 loop : -0.44 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 11 TYR 0.039 0.002 TYR D 83 PHE 0.020 0.001 PHE R 13 TRP 0.014 0.003 TRP R 36 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (14947) covalent geometry : angle 0.60942 / 0.36 (21465) hydrogen bonds : bond 0.04202 / 2.74 ( 844) hydrogen bonds : angle 3.12160 / 2.22 ( 2146) metal coordination : bond 0.00626 / 0.54 ( 14) metal coordination : angle 8.32030 / 4.69 ( 9) Misc. bond : bond 0.00404 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9635 (OUTLIER) cc_final: 0.9396 (tt) REVERT: D 68 ASP cc_start: 0.9392 (t70) cc_final: 0.9140 (t0) REVERT: E 59 GLU cc_start: 0.9097 (pm20) cc_final: 0.8851 (pm20) REVERT: G 13 LYS cc_start: 0.7378 (tptt) cc_final: 0.6921 (tppt) REVERT: G 73 ASN cc_start: 0.8746 (t160) cc_final: 0.8306 (t0) REVERT: G 90 ASP cc_start: 0.8629 (t70) cc_final: 0.8256 (t0) REVERT: K 56 LYS cc_start: 0.9389 (ttmm) cc_final: 0.9140 (ttpp) REVERT: K 59 GLU cc_start: 0.8879 (pm20) cc_final: 0.8457 (pm20) REVERT: A 962 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8334 (mtmm) REVERT: A 996 HIS cc_start: 0.6921 (t-90) cc_final: 0.6683 (t-170) REVERT: M 938 PHE cc_start: 0.9240 (m-80) cc_final: 0.8701 (m-80) REVERT: M 947 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9214 (tppt) REVERT: M 951 ASP cc_start: 0.9201 (m-30) cc_final: 0.8740 (p0) REVERT: M 967 ASN cc_start: 0.9141 (m-40) cc_final: 0.8839 (m-40) REVERT: R 12 ASP cc_start: 0.8287 (m-30) cc_final: 0.8064 (m-30) REVERT: R 16 LEU cc_start: 0.6562 (pp) cc_final: 0.6308 (pp) REVERT: R 80 ASN cc_start: 0.8309 (t0) cc_final: 0.7383 (t0) outliers start: 17 outliers final: 11 residues processed: 268 average time/residue: 0.1427 time to fit residues: 53.1792 Evaluate side-chains 249 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 947 LYS Chi-restraints excluded: chain M residue 974 ILE Chi-restraints excluded: chain R residue 66 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 40.0000 chunk 73 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.083253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.050054 restraints weight = 47656.495| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.55 r_work: 0.2609 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14963 Z= 0.201 Angle : 0.673 19.301 21474 Z= 0.374 Chirality : 0.044 0.244 2432 Planarity : 0.005 0.090 1710 Dihedral : 29.895 171.040 4361 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.64 % Allowed : 14.54 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.27), residues: 1008 helix: 2.19 (0.21), residues: 644 sheet: 0.32 (0.89), residues: 39 loop : -0.35 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 11 TYR 0.060 0.002 TYR H 83 PHE 0.030 0.002 PHE R 13 TRP 0.012 0.002 TRP R 36 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (14947) covalent geometry : angle 0.64429 / 0.37 (21465) hydrogen bonds : bond 0.04623 / 3.03 ( 844) hydrogen bonds : angle 3.18734 / 2.26 ( 2146) metal coordination : bond 0.01002 / 0.73 ( 14) metal coordination : angle 9.59321 / 5.42 ( 9) Misc. bond : bond 0.00629 / 0.33 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9624 (mt) cc_final: 0.9397 (tt) REVERT: C 90 ASP cc_start: 0.8940 (t70) cc_final: 0.8622 (t0) REVERT: D 68 ASP cc_start: 0.9401 (t70) cc_final: 0.9158 (t0) REVERT: E 59 GLU cc_start: 0.9104 (pm20) cc_final: 0.8839 (pm20) REVERT: G 13 LYS cc_start: 0.7317 (tptt) cc_final: 0.6897 (tppt) REVERT: G 73 ASN cc_start: 0.8790 (t160) cc_final: 0.8373 (t0) REVERT: G 90 ASP cc_start: 0.8606 (t70) cc_final: 0.8229 (t0) REVERT: H 42 TYR cc_start: 0.8932 (t80) cc_final: 0.8533 (t80) REVERT: K 42 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7919 (ttt90) REVERT: K 56 LYS cc_start: 0.9413 (ttmm) cc_final: 0.9157 (ttpp) REVERT: K 59 GLU cc_start: 0.8890 (pm20) cc_final: 0.8447 (pm20) REVERT: A 962 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8373 (mtmm) REVERT: M 938 PHE cc_start: 0.9211 (m-80) cc_final: 0.8640 (m-80) REVERT: M 947 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9202 (tppt) REVERT: M 951 ASP cc_start: 0.9208 (m-30) cc_final: 0.8756 (p0) REVERT: M 967 ASN cc_start: 0.9181 (m-40) cc_final: 0.8786 (m-40) REVERT: M 968 ASP cc_start: 0.9412 (m-30) cc_final: 0.8314 (t0) REVERT: R 12 ASP cc_start: 0.8210 (m-30) cc_final: 0.7955 (m-30) REVERT: R 16 LEU cc_start: 0.6042 (pp) cc_final: 0.5538 (pp) outliers start: 22 outliers final: 15 residues processed: 256 average time/residue: 0.1409 time to fit residues: 49.9893 Evaluate side-chains 250 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 979 ARG Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 933 VAL Chi-restraints excluded: chain M residue 947 LYS Chi-restraints excluded: chain M residue 974 ILE Chi-restraints excluded: chain R residue 66 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4231 > 50: distance: 11 - 38: 14.223 distance: 18 - 49: 28.411 distance: 33 - 34: 7.804 distance: 33 - 36: 7.389 distance: 34 - 35: 17.627 distance: 34 - 38: 3.929 distance: 36 - 37: 7.177 distance: 38 - 39: 9.874 distance: 39 - 40: 9.760 distance: 39 - 42: 13.710 distance: 40 - 41: 21.928 distance: 40 - 49: 11.621 distance: 42 - 43: 8.350 distance: 43 - 44: 8.316 distance: 44 - 45: 4.087 distance: 45 - 46: 6.798 distance: 46 - 47: 7.023 distance: 46 - 48: 8.460 distance: 49 - 50: 16.031 distance: 50 - 51: 18.075 distance: 50 - 53: 12.458 distance: 51 - 52: 27.801 distance: 51 - 54: 9.873 distance: 54 - 55: 32.929 distance: 55 - 56: 10.313 distance: 56 - 57: 14.135 distance: 56 - 58: 14.949 distance: 58 - 59: 10.955 distance: 59 - 60: 8.468 distance: 59 - 62: 22.426 distance: 60 - 61: 19.518 distance: 60 - 66: 11.959 distance: 62 - 63: 25.276 distance: 63 - 64: 29.511 distance: 63 - 65: 4.682 distance: 66 - 67: 16.185 distance: 67 - 68: 20.782 distance: 67 - 70: 17.290 distance: 68 - 69: 17.516 distance: 68 - 75: 28.115 distance: 70 - 71: 27.685 distance: 71 - 72: 12.856 distance: 72 - 73: 16.077 distance: 72 - 74: 24.270 distance: 75 - 76: 34.923 distance: 76 - 77: 6.940 distance: 76 - 79: 23.088 distance: 77 - 78: 8.169 distance: 77 - 86: 4.920 distance: 79 - 80: 15.841 distance: 80 - 81: 13.931 distance: 80 - 82: 7.512 distance: 81 - 83: 12.166 distance: 82 - 84: 6.228 distance: 83 - 85: 9.617 distance: 84 - 85: 11.064 distance: 86 - 87: 6.454 distance: 86 - 92: 30.377 distance: 87 - 88: 7.614 distance: 87 - 90: 6.009 distance: 88 - 89: 9.654 distance: 88 - 93: 8.837 distance: 90 - 91: 22.705 distance: 91 - 92: 14.948 distance: 94 - 95: 5.184 distance: 94 - 97: 9.337 distance: 95 - 96: 9.652 distance: 95 - 100: 8.444 distance: 96 - 120: 13.032 distance: 97 - 98: 6.059 distance: 97 - 99: 6.112 distance: 100 - 101: 6.769 distance: 101 - 102: 3.727 distance: 102 - 104: 9.638 distance: 103 - 126: 10.340