Starting phenix.real_space_refine on Sat Aug 23 03:28:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddm_46776/08_2025/9ddm_46776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddm_46776/08_2025/9ddm_46776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ddm_46776/08_2025/9ddm_46776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddm_46776/08_2025/9ddm_46776.map" model { file = "/net/cci-nas-00/data/ceres_data/9ddm_46776/08_2025/9ddm_46776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddm_46776/08_2025/9ddm_46776.cif" } resolution = 2.94 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 6211 2.51 5 N 1640 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9582 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1745 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain: "B" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1737 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1730 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain: "D" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1698 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1743 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain: "F" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 234 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 245 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "Y" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 251 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 30} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Time building chain proxies: 2.21, per 1000 atoms: 0.23 Number of scatterers: 9582 At special positions: 0 Unit cell: (91.3, 87.98, 114.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1690 8.00 N 1640 7.00 C 6211 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: 0.69 Conformation dependent library (CDL) restraints added in 438.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 92.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 14 through 57 Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.664A pdb=" N LEU A 76 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.660A pdb=" N ALA A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 124 removed outlier: 4.506A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 157 removed outlier: 3.663A pdb=" N LEU A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 163 through 223 removed outlier: 3.650A pdb=" N VAL A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 3.683A pdb=" N ILE A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Proline residue: A 187 - end of helix Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 14 through 58 removed outlier: 4.111A pdb=" N LYS B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 removed outlier: 3.835A pdb=" N GLY B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 97 removed outlier: 3.887A pdb=" N ASN B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 124 removed outlier: 3.543A pdb=" N VAL B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 157 Proline residue: B 138 - end of helix removed outlier: 3.576A pdb=" N ALA B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 222 Proline residue: B 169 - end of helix Proline residue: B 187 - end of helix removed outlier: 4.702A pdb=" N ASN B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.634A pdb=" N LEU C 9 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 12 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 57 Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.715A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 97 Processing helix chain 'C' and resid 100 through 124 removed outlier: 3.527A pdb=" N GLY C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 157 removed outlier: 3.892A pdb=" N LEU C 130 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 163 through 184 removed outlier: 3.682A pdb=" N VAL C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Proline residue: C 169 - end of helix removed outlier: 3.842A pdb=" N ILE C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 223 removed outlier: 3.631A pdb=" N GLN C 197 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 13 Processing helix chain 'D' and resid 14 through 57 removed outlier: 3.537A pdb=" N LYS D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.516A pdb=" N GLY D 71 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 Processing helix chain 'D' and resid 100 through 124 removed outlier: 3.679A pdb=" N GLU D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 157 removed outlier: 3.767A pdb=" N LEU D 130 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 3.939A pdb=" N ALA D 155 " --> pdb=" O HIS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 223 removed outlier: 3.681A pdb=" N VAL D 167 " --> pdb=" O THR D 163 " (cutoff:3.500A) Proline residue: D 169 - end of helix Proline residue: D 187 - end of helix removed outlier: 4.026A pdb=" N ASN D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 Processing helix chain 'E' and resid 14 through 57 removed outlier: 3.712A pdb=" N ARG E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 71 removed outlier: 3.907A pdb=" N GLY E 71 " --> pdb=" O GLN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 98 removed outlier: 3.841A pdb=" N ARG E 95 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 98 " --> pdb=" O HIS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 124 removed outlier: 4.087A pdb=" N ASN E 122 " --> pdb=" O ARG E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 159 removed outlier: 3.825A pdb=" N LEU E 130 " --> pdb=" O HIS E 126 " (cutoff:3.500A) Proline residue: E 138 - end of helix removed outlier: 3.888A pdb=" N VAL E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 167 through 225 removed outlier: 3.510A pdb=" N THR E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Proline residue: E 187 - end of helix Processing helix chain 'F' and resid 5 through 32 removed outlier: 3.936A pdb=" N ASP F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 33 Processing helix chain 'Y' and resid 18 through 40 Proline residue: Y 37 - end of helix Processing helix chain 'Z' and resid 19 through 35 removed outlier: 4.184A pdb=" N ASP Z 23 " --> pdb=" O VAL Z 19 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2571 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: 1.57 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2779 1.34 - 1.46: 1407 1.46 - 1.58: 5495 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9763 Sorted by residual: bond pdb=" N ILE C 186 " pdb=" CA ILE C 186 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.05e+01 bond pdb=" N HIS B 99 " pdb=" CA HIS B 99 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.21e-02 6.83e+03 9.06e+00 bond pdb=" N ASN D 75 " pdb=" CA ASN D 75 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.12e-02 7.97e+03 8.94e+00 bond pdb=" N LYS A 72 " pdb=" CA LYS A 72 " ideal model delta sigma weight residual 1.459 1.486 -0.027 9.10e-03 1.21e+04 8.91e+00 bond pdb=" CZ ARG E 38 " pdb=" NH2 ARG E 38 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.85e+00 ... (remaining 9758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 7844 1.32 - 2.65: 3967 2.65 - 3.97: 1225 3.97 - 5.29: 157 5.29 - 6.62: 10 Bond angle restraints: 13203 Sorted by residual: angle pdb=" C ASP D 8 " pdb=" N LEU D 9 " pdb=" CA LEU D 9 " ideal model delta sigma weight residual 120.54 125.93 -5.39 1.35e+00 5.49e-01 1.60e+01 angle pdb=" CB HIS E 94 " pdb=" CG HIS E 94 " pdb=" CD2 HIS E 94 " ideal model delta sigma weight residual 131.20 126.01 5.19 1.30e+00 5.92e-01 1.60e+01 angle pdb=" C ALA B 185 " pdb=" N ILE B 186 " pdb=" CA ILE B 186 " ideal model delta sigma weight residual 120.43 124.27 -3.84 9.60e-01 1.09e+00 1.60e+01 angle pdb=" OE1 GLN D 37 " pdb=" CD GLN D 37 " pdb=" NE2 GLN D 37 " ideal model delta sigma weight residual 122.60 118.61 3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" OE1 GLN C 165 " pdb=" CD GLN C 165 " pdb=" NE2 GLN C 165 " ideal model delta sigma weight residual 122.60 118.63 3.97 1.00e+00 1.00e+00 1.58e+01 ... (remaining 13198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5382 17.76 - 35.53: 356 35.53 - 53.29: 54 53.29 - 71.05: 22 71.05 - 88.81: 10 Dihedral angle restraints: 5824 sinusoidal: 2287 harmonic: 3537 Sorted by residual: dihedral pdb=" CA SER E 98 " pdb=" C SER E 98 " pdb=" N HIS E 99 " pdb=" CA HIS E 99 " ideal model delta harmonic sigma weight residual -180.00 -152.30 -27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ASN E 97 " pdb=" C ASN E 97 " pdb=" N SER E 98 " pdb=" CA SER E 98 " ideal model delta harmonic sigma weight residual -180.00 -154.52 -25.48 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA GLU A 124 " pdb=" C GLU A 124 " pdb=" N THR A 125 " pdb=" CA THR A 125 " ideal model delta harmonic sigma weight residual -180.00 -154.91 -25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 5821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 865 0.061 - 0.121: 446 0.121 - 0.181: 181 0.181 - 0.242: 35 0.242 - 0.302: 9 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA ILE B 136 " pdb=" N ILE B 136 " pdb=" C ILE B 136 " pdb=" CB ILE B 136 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA PRO A 128 " pdb=" N PRO A 128 " pdb=" C PRO A 128 " pdb=" CB PRO A 128 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLN B 67 " pdb=" N GLN B 67 " pdb=" C GLN B 67 " pdb=" CB GLN B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1533 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 66 " -0.076 2.00e-02 2.50e+03 4.06e-02 3.29e+01 pdb=" CG TYR E 66 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR E 66 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 66 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR E 66 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR E 66 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR E 66 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 66 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 26 " -0.064 2.00e-02 2.50e+03 3.95e-02 2.73e+01 pdb=" CG PHE G 26 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE G 26 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE G 26 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE G 26 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 26 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE G 26 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.067 2.00e-02 2.50e+03 3.60e-02 2.60e+01 pdb=" CG TYR A 139 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.053 2.00e-02 2.50e+03 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 4021 2.96 - 3.45: 10842 3.45 - 3.93: 15793 3.93 - 4.42: 15947 4.42 - 4.90: 29173 Nonbonded interactions: 75776 Sorted by model distance: nonbonded pdb=" CD1 LEU A 9 " pdb=" CD1 ILE A 176 " model vdw 2.478 3.880 nonbonded pdb=" OD1 ASP E 54 " pdb=" N LYS E 55 " model vdw 2.522 3.120 nonbonded pdb=" O LYS E 55 " pdb=" OG SER E 58 " model vdw 2.578 3.040 nonbonded pdb=" OG1 THR B 77 " pdb=" OE1 GLU B 119 " model vdw 2.591 3.040 nonbonded pdb=" OG1 THR A 145 " pdb=" OG1 THR A 178 " model vdw 2.594 3.040 ... (remaining 75771 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 8 through 223) selection = (chain 'B' and resid 8 through 223) selection = (chain 'C' and resid 8 through 223) selection = chain 'D' selection = (chain 'E' and resid 8 through 223) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 4 through 33) } 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: 1.090 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.440 Find NCS groups from input model: 0.140 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 0.040 9763 Z= 0.701 Angle : 1.616 6.618 13203 Z= 1.128 Chirality : 0.081 0.302 1536 Planarity : 0.014 0.127 1664 Dihedral : 13.350 88.814 3524 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.40 % Allowed : 6.34 % Favored : 93.26 % 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 aren not related in a simple way. whole: 0.12 (0.22), residues: 1203 helix: 0.23 (0.14), residues: 1056 sheet: None (None), residues: 0 loop : 0.03 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 110 TYR 0.076 0.015 TYR E 66 PHE 0.064 0.012 PHE G 26 TRP 0.060 0.013 TRP B 147 HIS 0.015 0.002 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.01144 ( 9763) covalent geometry : angle 1.61618 (13203) hydrogen bonds : bond 0.17374 ( 860) hydrogen bonds : angle 6.72367 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 373 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.9049 (tt0) cc_final: 0.8742 (tm-30) REVERT: B 66 TYR cc_start: 0.9008 (t80) cc_final: 0.8690 (t80) REVERT: B 67 GLN cc_start: 0.9123 (pt0) cc_final: 0.8775 (pp30) REVERT: B 80 GLU cc_start: 0.8683 (tt0) cc_final: 0.8011 (tp30) REVERT: B 102 GLU cc_start: 0.8508 (mp0) cc_final: 0.8223 (pm20) REVERT: B 106 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8158 (mt-10) REVERT: B 166 MET cc_start: 0.9284 (mtp) cc_final: 0.9035 (mtp) REVERT: B 222 PHE cc_start: 0.8711 (m-80) cc_final: 0.8468 (m-10) REVERT: C 21 MET cc_start: 0.8952 (mmm) cc_final: 0.8689 (mpp) REVERT: C 67 GLN cc_start: 0.9334 (pt0) cc_final: 0.9131 (pt0) REVERT: C 68 GLU cc_start: 0.9163 (tt0) cc_final: 0.8854 (tt0) REVERT: C 88 LYS cc_start: 0.8783 (tttm) cc_final: 0.8463 (ttmm) REVERT: C 118 ARG cc_start: 0.8636 (ttm170) cc_final: 0.8398 (ttm110) REVERT: C 161 GLN cc_start: 0.8534 (tp40) cc_final: 0.8280 (pp30) REVERT: C 204 LEU cc_start: 0.8980 (tt) cc_final: 0.8694 (tm) REVERT: C 207 ASP cc_start: 0.9000 (t0) cc_final: 0.8689 (t0) REVERT: D 47 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.8151 (mtp180) REVERT: D 53 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8269 (mm-30) REVERT: D 70 GLN cc_start: 0.9120 (mm110) cc_final: 0.8579 (mm-40) REVERT: D 122 ASN cc_start: 0.9198 (t0) cc_final: 0.8968 (t0) REVERT: D 173 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8569 (mt-10) REVERT: D 208 ASN cc_start: 0.8688 (t0) cc_final: 0.8334 (t0) REVERT: D 220 GLN cc_start: 0.7779 (tp-100) cc_final: 0.7464 (tp-100) REVERT: E 8 ASP cc_start: 0.8393 (p0) cc_final: 0.7896 (p0) REVERT: E 18 LYS cc_start: 0.8500 (mttp) cc_final: 0.8287 (mttp) REVERT: E 37 GLN cc_start: 0.8852 (tt0) cc_final: 0.8638 (tt0) REVERT: E 61 GLU cc_start: 0.9244 (mp0) cc_final: 0.8994 (mp0) REVERT: E 66 TYR cc_start: 0.8767 (t80) cc_final: 0.7836 (t80) REVERT: E 68 GLU cc_start: 0.9328 (tm-30) cc_final: 0.8949 (tm-30) REVERT: E 81 GLN cc_start: 0.8610 (tp40) cc_final: 0.8285 (tp-100) REVERT: E 88 LYS cc_start: 0.8961 (ttmm) cc_final: 0.8574 (ttmm) REVERT: E 89 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7976 (tp30) REVERT: E 94 HIS cc_start: 0.7966 (t70) cc_final: 0.7755 (t-90) REVERT: E 110 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8284 (ttp80) REVERT: E 207 ASP cc_start: 0.8970 (t70) cc_final: 0.8565 (t0) REVERT: E 211 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8892 (mm-30) REVERT: E 220 GLN cc_start: 0.7245 (tm-30) cc_final: 0.7026 (tm-30) REVERT: G 8 ASN cc_start: 0.8233 (m-40) cc_final: 0.7773 (m110) REVERT: G 12 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8540 (mppt) outliers start: 4 outliers final: 2 residues processed: 374 average time/residue: 0.7242 time to fit residues: 285.1571 Evaluate side-chains 260 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain Z residue 23 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN C 70 GLN C 99 HIS C 197 GLN D 37 GLN D 94 HIS D 99 HIS D 197 GLN E 205 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.102066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.073305 restraints weight = 16413.055| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.08 r_work: 0.2869 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9763 Z= 0.177 Angle : 0.651 8.245 13203 Z= 0.342 Chirality : 0.041 0.175 1536 Planarity : 0.005 0.042 1664 Dihedral : 4.186 25.647 1310 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 4.02 % Allowed : 18.71 % Favored : 77.26 % 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 aren not related in a simple way. whole: 3.01 (0.23), residues: 1203 helix: 2.22 (0.15), residues: 1069 sheet: None (None), residues: 0 loop : 0.20 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 47 TYR 0.026 0.002 TYR A 66 PHE 0.017 0.002 PHE G 26 TRP 0.009 0.001 TRP D 147 HIS 0.007 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9763) covalent geometry : angle 0.65098 (13203) hydrogen bonds : bond 0.05786 ( 860) hydrogen bonds : angle 4.06015 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7096 (pmt) REVERT: A 53 GLU cc_start: 0.9136 (tt0) cc_final: 0.8779 (tm-30) REVERT: A 70 GLN cc_start: 0.9171 (mt0) cc_final: 0.8878 (mp10) REVERT: A 88 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8661 (tppt) REVERT: A 210 MET cc_start: 0.8923 (ttm) cc_final: 0.8624 (mtp) REVERT: B 66 TYR cc_start: 0.8792 (t80) cc_final: 0.8592 (t80) REVERT: B 67 GLN cc_start: 0.9326 (pt0) cc_final: 0.8855 (pp30) REVERT: B 166 MET cc_start: 0.9273 (mtp) cc_final: 0.8977 (mtp) REVERT: B 203 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8502 (tm-30) REVERT: B 222 PHE cc_start: 0.8692 (m-80) cc_final: 0.8416 (m-10) REVERT: C 21 MET cc_start: 0.8716 (mmm) cc_final: 0.8502 (mpp) REVERT: C 64 ARG cc_start: 0.9043 (ttm110) cc_final: 0.8474 (tpp80) REVERT: C 67 GLN cc_start: 0.9244 (pt0) cc_final: 0.9005 (pt0) REVERT: C 88 LYS cc_start: 0.8674 (tttm) cc_final: 0.8435 (ttmm) REVERT: C 102 GLU cc_start: 0.8407 (pm20) cc_final: 0.7926 (pm20) REVERT: C 159 VAL cc_start: 0.8042 (t) cc_final: 0.7813 (p) REVERT: C 207 ASP cc_start: 0.8864 (t0) cc_final: 0.8502 (t0) REVERT: D 53 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8344 (mm-30) REVERT: D 70 GLN cc_start: 0.8993 (mm110) cc_final: 0.8630 (mm-40) REVERT: D 74 ASP cc_start: 0.6799 (p0) cc_final: 0.6409 (p0) REVERT: D 165 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8381 (mp10) REVERT: D 173 GLU cc_start: 0.8648 (mt-10) cc_final: 0.7673 (tp30) REVERT: D 208 ASN cc_start: 0.8204 (t0) cc_final: 0.7845 (t0) REVERT: D 220 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7296 (tp-100) REVERT: E 66 TYR cc_start: 0.8750 (t80) cc_final: 0.7907 (t80) REVERT: E 84 TYR cc_start: 0.8406 (t80) cc_final: 0.8003 (t80) REVERT: E 166 MET cc_start: 0.9306 (mmm) cc_final: 0.8867 (mpp) REVERT: E 207 ASP cc_start: 0.8896 (t70) cc_final: 0.8441 (t0) REVERT: E 211 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8712 (mm-30) REVERT: G 12 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8024 (mppt) outliers start: 40 outliers final: 11 residues processed: 288 average time/residue: 0.6211 time to fit residues: 190.2855 Evaluate side-chains 249 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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: 70.1407 > 50: distance: 1 - 30: 22.758 distance: 8 - 38: 31.329 distance: 15 - 48: 30.202 distance: 21 - 30: 23.194 distance: 22 - 59: 35.969 distance: 30 - 31: 11.266 distance: 31 - 32: 39.034 distance: 31 - 34: 13.367 distance: 32 - 33: 25.190 distance: 32 - 38: 51.469 distance: 35 - 36: 5.204 distance: 38 - 39: 25.575 distance: 39 - 40: 33.022 distance: 39 - 42: 56.879 distance: 40 - 41: 30.279 distance: 40 - 48: 11.745 distance: 42 - 43: 18.730 distance: 43 - 44: 10.050 distance: 43 - 45: 20.817 distance: 44 - 46: 22.269 distance: 45 - 47: 6.517 distance: 48 - 49: 28.846 distance: 49 - 50: 40.387 distance: 49 - 52: 36.296 distance: 50 - 51: 56.009 distance: 52 - 53: 25.614 distance: 53 - 54: 6.415 distance: 54 - 55: 19.648 distance: 55 - 56: 26.587 distance: 56 - 57: 12.986 distance: 56 - 58: 49.705 distance: 59 - 60: 40.900 distance: 60 - 61: 55.463 distance: 60 - 63: 57.344 distance: 61 - 64: 40.302 distance: 64 - 65: 40.607 distance: 65 - 66: 38.470 distance: 66 - 72: 23.361 distance: 68 - 69: 38.770 distance: 69 - 71: 40.113 distance: 72 - 73: 34.384 distance: 73 - 74: 32.819 distance: 73 - 76: 55.768 distance: 74 - 75: 29.811 distance: 74 - 78: 13.566 distance: 76 - 77: 10.165 distance: 78 - 79: 17.241 distance: 79 - 80: 44.592 distance: 79 - 82: 49.883 distance: 80 - 81: 8.326 distance: 80 - 88: 19.232 distance: 83 - 84: 55.855 distance: 83 - 85: 68.388 distance: 84 - 86: 40.990 distance: 85 - 87: 20.654 distance: 86 - 87: 44.142 distance: 88 - 89: 15.262 distance: 89 - 90: 57.034 distance: 90 - 93: 39.684 distance: 93 - 94: 41.087 distance: 93 - 99: 40.569 distance: 94 - 95: 38.731 distance: 95 - 96: 49.165 distance: 96 - 121: 29.663 distance: 97 - 98: 43.307 distance: 98 - 99: 39.666 distance: 100 - 101: 6.781 distance: 101 - 102: 15.912 distance: 101 - 104: 24.077 distance: 102 - 103: 43.494 distance: 102 - 109: 27.486 distance: 103 - 128: 17.872 distance: 104 - 105: 28.696 distance: 105 - 106: 39.978 distance: 106 - 107: 13.520 distance: 106 - 108: 14.935