Starting phenix.real_space_refine on Fri Dec 19 15:20:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jr1_36590/12_2025/8jr1_36590.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jr1_36590/12_2025/8jr1_36590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jr1_36590/12_2025/8jr1_36590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jr1_36590/12_2025/8jr1_36590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jr1_36590/12_2025/8jr1_36590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jr1_36590/12_2025/8jr1_36590.map" } resolution = 3.17 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= 0.014 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 Br 7 7.06 5 S 33 5.16 5 C 4712 2.51 5 N 1118 2.21 5 O 1212 1.98 5 F 7 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7089 Number of models: 1 Model: "" Number of chains: 17 Chain: "1" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "2" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "3" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "4" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "5" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "6" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "7" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "8" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "9" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "a" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1706 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 2 Chain: "4" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.27 Number of scatterers: 7089 At special positions: 0 Unit cell: (73, 98.55, 82.49, 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) Br 7 34.99 S 33 16.00 F 7 9.00 O 1212 8.00 N 1118 7.00 C 4712 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 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 337.1 milliseconds 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 1 sheets defined 87.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain '1' and resid 1 through 42 removed outlier: 4.180A pdb=" N ILE 1 5 " --> pdb=" O MET 1 1 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 76 removed outlier: 4.161A pdb=" N PHE 1 50 " --> pdb=" O GLN 1 46 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR 1 51 " --> pdb=" O GLY 1 47 " (cutoff:3.500A) Proline residue: 1 52 - end of helix removed outlier: 3.537A pdb=" N TYR 1 64 " --> pdb=" O VAL 1 60 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN 1 67 " --> pdb=" O ALA 1 63 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 42 removed outlier: 3.568A pdb=" N GLY 2 29 " --> pdb=" O GLY 2 25 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA 2 34 " --> pdb=" O VAL 2 30 " (cutoff:3.500A) Processing helix chain '2' and resid 45 through 77 removed outlier: 3.529A pdb=" N PHE 2 50 " --> pdb=" O GLN 2 46 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR 2 51 " --> pdb=" O GLY 2 47 " (cutoff:3.500A) Proline residue: 2 52 - end of helix removed outlier: 3.619A pdb=" N ALA 2 62 " --> pdb=" O GLY 2 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 42 removed outlier: 3.846A pdb=" N ALA 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER 3 37 " --> pdb=" O ASN 3 33 " (cutoff:3.500A) Processing helix chain '3' and resid 45 through 76 removed outlier: 4.776A pdb=" N THR 3 51 " --> pdb=" O GLY 3 47 " (cutoff:3.500A) Proline residue: 3 52 - end of helix removed outlier: 3.532A pdb=" N ILE 3 55 " --> pdb=" O THR 3 51 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA 3 62 " --> pdb=" O GLY 3 58 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA 3 63 " --> pdb=" O LEU 3 59 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR 3 64 " --> pdb=" O VAL 3 60 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN 3 67 " --> pdb=" O ALA 3 63 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 42 removed outlier: 3.530A pdb=" N ALA 4 34 " --> pdb=" O VAL 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 45 through 77 removed outlier: 4.762A pdb=" N THR 4 51 " --> pdb=" O GLY 4 47 " (cutoff:3.500A) Proline residue: 4 52 - end of helix removed outlier: 3.789A pdb=" N ILE 4 55 " --> pdb=" O THR 4 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR 4 56 " --> pdb=" O PRO 4 52 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA 4 63 " --> pdb=" O LEU 4 59 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN 4 67 " --> pdb=" O ALA 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 42 removed outlier: 3.557A pdb=" N ILE 5 26 " --> pdb=" O ILE 5 22 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 78 removed outlier: 3.927A pdb=" N PHE 5 50 " --> pdb=" O GLN 5 46 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR 5 51 " --> pdb=" O GLY 5 47 " (cutoff:3.500A) Proline residue: 5 52 - end of helix removed outlier: 3.824A pdb=" N ILE 5 55 " --> pdb=" O THR 5 51 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN 5 67 " --> pdb=" O ALA 5 63 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 42 removed outlier: 4.022A pdb=" N ALA 6 6 " --> pdb=" O ASP 6 2 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE 6 26 " --> pdb=" O ILE 6 22 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA 6 34 " --> pdb=" O VAL 6 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 6 35 " --> pdb=" O ALA 6 31 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 76 removed outlier: 3.972A pdb=" N PHE 6 50 " --> pdb=" O GLN 6 46 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR 6 51 " --> pdb=" O GLY 6 47 " (cutoff:3.500A) Proline residue: 6 52 - end of helix Processing helix chain '7' and resid 2 through 42 removed outlier: 3.826A pdb=" N ALA 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '7' and resid 45 through 77 removed outlier: 4.347A pdb=" N THR 7 51 " --> pdb=" O GLY 7 47 " (cutoff:3.500A) Proline residue: 7 52 - end of helix removed outlier: 3.841A pdb=" N ALA 7 63 " --> pdb=" O LEU 7 59 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 42 removed outlier: 3.532A pdb=" N ALA 8 34 " --> pdb=" O VAL 8 30 " (cutoff:3.500A) Processing helix chain '8' and resid 45 through 78 removed outlier: 3.810A pdb=" N PHE 8 50 " --> pdb=" O GLN 8 46 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR 8 51 " --> pdb=" O GLY 8 47 " (cutoff:3.500A) Proline residue: 8 52 - end of helix Processing helix chain '9' and resid 2 through 42 removed outlier: 3.532A pdb=" N ALA 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain '9' and resid 45 through 76 removed outlier: 4.384A pdb=" N THR 9 51 " --> pdb=" O GLY 9 47 " (cutoff:3.500A) Proline residue: 9 52 - end of helix removed outlier: 3.809A pdb=" N ASN 9 67 " --> pdb=" O ALA 9 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 27 through 51 removed outlier: 5.831A pdb=" N SER a 32 " --> pdb=" O ASP a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 79 Processing helix chain 'a' and resid 86 through 104 removed outlier: 3.773A pdb=" N ILE a 98 " --> pdb=" O ILE a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 107 No H-bonds generated for 'chain 'a' and resid 105 through 107' Processing helix chain 'a' and resid 128 through 151 removed outlier: 4.080A pdb=" N VAL a 132 " --> pdb=" O ASP a 128 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG a 151 " --> pdb=" O GLY a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 167 No H-bonds generated for 'chain 'a' and resid 165 through 167' Processing helix chain 'a' and resid 168 through 201 removed outlier: 4.103A pdb=" N GLU a 176 " --> pdb=" O ASN a 172 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL a 177 " --> pdb=" O LEU a 173 " (cutoff:3.500A) Proline residue: a 180 - end of helix removed outlier: 4.811A pdb=" N GLY a 194 " --> pdb=" O ASN a 190 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA a 199 " --> pdb=" O GLY a 195 " (cutoff:3.500A) Processing helix chain 'a' and resid 202 through 204 No H-bonds generated for 'chain 'a' and resid 202 through 204' Processing helix chain 'a' and resid 209 through 243 removed outlier: 3.844A pdb=" N LEU a 221 " --> pdb=" O LYS a 217 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE a 222 " --> pdb=" O ALA a 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 17 through 19 643 hydrogen bonds defined for protein. 1929 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 2202 1.36 - 1.50: 2083 1.50 - 1.65: 2894 1.65 - 1.80: 9 1.80 - 1.94: 63 Bond restraints: 7251 Sorted by residual: bond pdb=" C11 UTI 6 600 " pdb=" O13 UTI 6 600 " ideal model delta sigma weight residual 1.334 1.415 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C11 UTI 8 600 " pdb=" O13 UTI 8 600 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C11 UTI 5 600 " pdb=" O13 UTI 5 600 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C11 UTI 7 600 " pdb=" O13 UTI 7 600 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C11 UTI 9 600 " pdb=" O13 UTI 9 600 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 7246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 7839 1.78 - 3.56: 1725 3.56 - 5.34: 292 5.34 - 7.12: 20 7.12 - 8.91: 4 Bond angle restraints: 9880 Sorted by residual: angle pdb=" C MET 2 1 " pdb=" N ASP 2 2 " pdb=" CA ASP 2 2 " ideal model delta sigma weight residual 120.58 128.01 -7.43 1.32e+00 5.74e-01 3.17e+01 angle pdb=" C MET 7 1 " pdb=" N ASP 7 2 " pdb=" CA ASP 7 2 " ideal model delta sigma weight residual 120.09 126.64 -6.55 1.25e+00 6.40e-01 2.74e+01 angle pdb=" CA PHE 7 74 " pdb=" CB PHE 7 74 " pdb=" CG PHE 7 74 " ideal model delta sigma weight residual 113.80 118.60 -4.80 1.00e+00 1.00e+00 2.31e+01 angle pdb=" OE1 GLN 6 42 " pdb=" CD GLN 6 42 " pdb=" NE2 GLN 6 42 " ideal model delta sigma weight residual 122.60 117.83 4.77 1.00e+00 1.00e+00 2.27e+01 angle pdb=" OD1 ASN a 190 " pdb=" CG ASN a 190 " pdb=" ND2 ASN a 190 " ideal model delta sigma weight residual 122.60 117.96 4.64 1.00e+00 1.00e+00 2.15e+01 ... (remaining 9875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3796 17.85 - 35.71: 320 35.71 - 53.56: 57 53.56 - 71.42: 6 71.42 - 89.27: 6 Dihedral angle restraints: 4185 sinusoidal: 1613 harmonic: 2572 Sorted by residual: dihedral pdb=" CA ASP a 28 " pdb=" C ASP a 28 " pdb=" N THR a 29 " pdb=" CA THR a 29 " ideal model delta harmonic sigma weight residual 180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA HIS a 15 " pdb=" C HIS a 15 " pdb=" N HIS a 16 " pdb=" CA HIS a 16 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA THR a 27 " pdb=" C THR a 27 " pdb=" N ASP a 28 " pdb=" CA ASP a 28 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 4182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 858 0.084 - 0.169: 222 0.169 - 0.253: 45 0.253 - 0.337: 11 0.337 - 0.421: 1 Chirality restraints: 1137 Sorted by residual: chirality pdb=" C17 UTI a 600 " pdb=" C06 UTI a 600 " pdb=" C18 UTI a 600 " pdb=" C27 UTI a 600 " both_signs ideal model delta sigma weight residual False 2.42 2.84 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA ARG a 186 " pdb=" N ARG a 186 " pdb=" C ARG a 186 " pdb=" CB ARG a 186 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA PHE 9 54 " pdb=" N PHE 9 54 " pdb=" C PHE 9 54 " pdb=" CB PHE 9 54 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1134 not shown) Planarity restraints: 1228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 64 " -0.097 2.00e-02 2.50e+03 5.33e-02 5.67e+01 pdb=" CG TYR 3 64 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 64 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 64 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 64 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 64 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR 3 64 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR 3 64 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE a 239 " 0.079 2.00e-02 2.50e+03 5.60e-02 5.48e+01 pdb=" CG PHE a 239 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE a 239 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE a 239 " -0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE a 239 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE a 239 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE a 239 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 5 70 " -0.073 2.00e-02 2.50e+03 4.69e-02 3.84e+01 pdb=" CG PHE 5 70 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE 5 70 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE 5 70 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE 5 70 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE 5 70 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE 5 70 " -0.051 2.00e-02 2.50e+03 ... (remaining 1225 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 955 2.77 - 3.30: 7632 3.30 - 3.84: 11757 3.84 - 4.37: 14378 4.37 - 4.90: 24612 Nonbonded interactions: 59334 Sorted by model distance: nonbonded pdb=" OE2 GLU 5 61 " pdb=" N02 UTI 5 600 " model vdw 2.239 3.120 nonbonded pdb=" O THR 6 78 " pdb=" OG1 THR 6 78 " model vdw 2.328 3.040 nonbonded pdb=" O ALA 1 63 " pdb=" ND2 ASN 1 67 " model vdw 2.352 3.120 nonbonded pdb=" OE1 GLU 9 61 " pdb=" N02 UTI 9 600 " model vdw 2.391 3.120 nonbonded pdb=" ND2 ASN 4 33 " pdb=" O VAL 5 30 " model vdw 2.398 3.120 ... (remaining 59329 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 '1' selection = chain '2' selection = chain '3' selection = (chain '4' and resid 1 through 81) selection = (chain '5' and resid 1 through 81) selection = (chain '6' and resid 1 through 81) selection = (chain '7' and resid 1 through 81) selection = (chain '8' and resid 1 through 81) selection = (chain '9' and resid 1 through 81) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.120 Find NCS groups from input model: 0.110 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.012 0.081 7251 Z= 0.652 Angle : 1.493 8.905 9880 Z= 1.006 Chirality : 0.081 0.421 1137 Planarity : 0.012 0.093 1228 Dihedral : 13.752 89.269 2565 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.23), residues: 925 helix: -1.39 (0.16), residues: 758 sheet: None (None), residues: 0 loop : -2.18 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 72 TYR 0.097 0.008 TYR 3 64 PHE 0.085 0.011 PHE a 239 TRP 0.046 0.005 TRP a 20 HIS 0.005 0.002 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.01164 ( 7251) covalent geometry : angle 1.49337 ( 9880) hydrogen bonds : bond 0.18262 ( 643) hydrogen bonds : angle 8.94558 ( 1929) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 52 THR cc_start: 0.4866 (p) cc_final: 0.4418 (m) REVERT: a 81 MET cc_start: 0.7094 (mmm) cc_final: 0.6843 (mtp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0747 time to fit residues: 20.2867 Evaluate side-chains 158 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 4 46 GLN 8 42 GLN ** a 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.173381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123989 restraints weight = 7669.916| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.85 r_work: 0.3450 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7251 Z= 0.174 Angle : 0.676 8.787 9880 Z= 0.345 Chirality : 0.045 0.195 1137 Planarity : 0.006 0.052 1228 Dihedral : 8.126 82.022 1214 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.08 % Allowed : 11.15 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.28), residues: 925 helix: 1.06 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -1.33 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 48 TYR 0.034 0.003 TYR a 143 PHE 0.017 0.001 PHE a 192 TRP 0.009 0.001 TRP a 216 HIS 0.002 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7251) covalent geometry : angle 0.67608 ( 9880) hydrogen bonds : bond 0.04925 ( 643) hydrogen bonds : angle 4.66956 ( 1929) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 61 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: 4 61 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8594 (mm-30) REVERT: 4 71 MET cc_start: 0.8561 (tmm) cc_final: 0.7993 (tmm) REVERT: a 61 GLN cc_start: 0.7230 (tp40) cc_final: 0.6296 (tt0) REVERT: a 81 MET cc_start: 0.7246 (mmm) cc_final: 0.7036 (mtp) outliers start: 7 outliers final: 4 residues processed: 155 average time/residue: 0.0725 time to fit residues: 15.7010 Evaluate side-chains 134 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 227 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 70 GLN ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.173039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123341 restraints weight = 7651.255| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.84 r_work: 0.3442 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7251 Z= 0.168 Angle : 0.651 8.375 9880 Z= 0.321 Chirality : 0.044 0.189 1137 Planarity : 0.005 0.050 1228 Dihedral : 7.116 71.874 1214 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.01 % Allowed : 13.00 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.26 (0.28), residues: 925 helix: 1.95 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -0.48 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 48 TYR 0.033 0.002 TYR a 143 PHE 0.026 0.001 PHE a 138 TRP 0.007 0.001 TRP a 103 HIS 0.002 0.001 HIS a 164 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7251) covalent geometry : angle 0.65113 ( 9880) hydrogen bonds : bond 0.04525 ( 643) hydrogen bonds : angle 4.39209 ( 1929) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: 1 73 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8269 (tp) REVERT: 3 61 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: 4 71 MET cc_start: 0.8506 (tmm) cc_final: 0.7759 (tmm) REVERT: 5 71 MET cc_start: 0.8573 (tmm) cc_final: 0.8305 (tmm) REVERT: 8 42 GLN cc_start: 0.8004 (mt0) cc_final: 0.7547 (mt0) REVERT: 8 54 PHE cc_start: 0.8437 (m-80) cc_final: 0.8208 (m-80) REVERT: a 61 GLN cc_start: 0.7199 (tp40) cc_final: 0.6266 (tt0) REVERT: a 81 MET cc_start: 0.7237 (mmm) cc_final: 0.6965 (mtp) REVERT: a 104 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6849 (mt) REVERT: a 179 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7961 (mttt) REVERT: a 238 TYR cc_start: 0.8067 (m-10) cc_final: 0.7734 (m-80) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.0735 time to fit residues: 14.7336 Evaluate side-chains 140 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 73 LEU Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 42 GLN Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 90 LEU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 227 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/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-2.0-5913/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2038 > 50: distance: 27 - 31: 35.452 distance: 31 - 32: 38.943 distance: 32 - 33: 55.620 distance: 32 - 35: 21.175 distance: 33 - 34: 43.618 distance: 33 - 42: 23.097 distance: 35 - 36: 35.502 distance: 36 - 37: 28.190 distance: 36 - 38: 16.909 distance: 37 - 39: 29.911 distance: 38 - 40: 15.370 distance: 39 - 41: 33.420 distance: 40 - 41: 42.532 distance: 42 - 43: 57.505 distance: 43 - 44: 21.327 distance: 43 - 46: 45.009 distance: 44 - 45: 31.253 distance: 44 - 49: 30.617 distance: 45 - 78: 7.756 distance: 46 - 47: 45.223 distance: 46 - 48: 31.955 distance: 49 - 50: 12.363 distance: 49 - 55: 43.129 distance: 50 - 51: 36.392 distance: 50 - 53: 53.261 distance: 51 - 52: 23.977 distance: 51 - 56: 26.782 distance: 52 - 86: 45.102 distance: 53 - 54: 38.800 distance: 54 - 55: 17.619 distance: 56 - 57: 15.387 distance: 57 - 58: 43.505 distance: 57 - 60: 41.452 distance: 58 - 59: 23.611 distance: 58 - 67: 17.212 distance: 59 - 93: 39.296 distance: 60 - 61: 44.907 distance: 61 - 62: 51.929 distance: 61 - 63: 51.547 distance: 62 - 64: 41.994 distance: 63 - 65: 27.937 distance: 64 - 66: 11.701 distance: 65 - 66: 24.255 distance: 67 - 68: 8.258 distance: 68 - 69: 24.164 distance: 68 - 71: 50.120 distance: 69 - 70: 40.311 distance: 69 - 78: 20.700 distance: 70 - 100: 49.494 distance: 71 - 72: 36.615 distance: 72 - 73: 8.885 distance: 72 - 74: 25.610 distance: 73 - 75: 51.303 distance: 74 - 76: 29.389 distance: 75 - 77: 34.203 distance: 76 - 77: 30.438 distance: 78 - 79: 10.489 distance: 79 - 80: 51.900 distance: 79 - 82: 57.504 distance: 80 - 81: 41.800 distance: 80 - 86: 21.339 distance: 81 - 104: 41.738 distance: 82 - 83: 40.418 distance: 82 - 84: 14.170 distance: 83 - 85: 31.097 distance: 86 - 87: 23.991 distance: 87 - 88: 12.836 distance: 87 - 90: 50.215 distance: 88 - 89: 24.771 distance: 88 - 93: 35.007 distance: 89 - 112: 19.920 distance: 90 - 91: 56.172 distance: 90 - 92: 46.520 distance: 93 - 94: 45.419 distance: 94 - 95: 33.218 distance: 94 - 97: 43.313 distance: 95 - 96: 17.004 distance: 95 - 100: 33.930 distance: 96 - 119: 27.268 distance: 97 - 98: 43.953 distance: 97 - 99: 41.664 distance: 100 - 101: 28.286 distance: 101 - 102: 39.476 distance: 102 - 103: 31.646 distance: 102 - 104: 34.906 distance: 103 - 127: 18.136 distance: 104 - 105: 21.967 distance: 105 - 106: 30.536 distance: 105 - 108: 6.991 distance: 106 - 107: 15.984 distance: 106 - 112: 24.803 distance: 107 - 131: 32.944 distance: 108 - 109: 21.377 distance: 109 - 110: 25.537 distance: 109 - 111: 13.400