Starting phenix.real_space_refine on Fri Aug 22 21:52:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2b_45153/08_2025/9c2b_45153.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2b_45153/08_2025/9c2b_45153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c2b_45153/08_2025/9c2b_45153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2b_45153/08_2025/9c2b_45153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c2b_45153/08_2025/9c2b_45153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2b_45153/08_2025/9c2b_45153.map" } resolution = 2.42 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= 0.001 sd= 0.030 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 P 9 5.49 5 Mg 3 5.21 5 S 42 5.16 5 C 5178 2.51 5 N 1350 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 8208 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2576 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2576 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2576 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Time building chain proxies: 2.39, per 1000 atoms: 0.29 Number of scatterers: 8208 At special positions: 0 Unit cell: (90.832, 88.8856, 118.082, 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) S 42 16.00 P 9 15.00 Mg 3 11.99 O 1626 8.00 N 1350 7.00 C 5178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 502 " - " ASN A 242 " " NAG B 502 " - " ASN B 242 " " NAG C 403 " - " ASN C 242 " " NAG D 1 " - " ASN A 153 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN B 153 " " NAG G 1 " - " ASN B 184 " " NAG H 1 " - " ASN C 153 " " NAG I 1 " - " ASN C 184 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 302.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 30.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 210 through 217 removed outlier: 3.565A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.691A pdb=" N GLU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 327 through 356 Processing helix chain 'B' and resid 28 through 47 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 210 through 217 removed outlier: 3.564A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.691A pdb=" N GLU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 327 through 356 Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.565A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.690A pdb=" N GLU C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 60 current: chain 'A' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 99 through 118 current: chain 'A' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 157 through 165 current: chain 'A' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 277 current: chain 'A' and resid 302 through 326 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 60 current: chain 'B' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 99 through 118 current: chain 'B' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 157 through 165 current: chain 'B' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 277 current: chain 'B' and resid 302 through 326 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 76 Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 60 current: chain 'C' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 99 through 118 current: chain 'C' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 157 through 165 current: chain 'C' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 277 current: chain 'C' and resid 302 through 326 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 76 241 hydrogen bonds defined for protein. 606 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: 0.87 Time building geometry restraints manager: 1.14 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: 2523 1.34 - 1.46: 1934 1.46 - 1.58: 3754 1.58 - 1.70: 12 1.70 - 1.82: 51 Bond restraints: 8274 Sorted by residual: bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.435 -0.047 1.00e-02 1.00e+04 2.17e+01 bond pdb=" C4 ATP A 500 " pdb=" C5 ATP A 500 " ideal model delta sigma weight residual 1.388 1.434 -0.046 1.00e-02 1.00e+04 2.13e+01 bond pdb=" C4 ATP B 500 " pdb=" C5 ATP B 500 " ideal model delta sigma weight residual 1.388 1.434 -0.046 1.00e-02 1.00e+04 2.09e+01 bond pdb=" C4 ATP A 500 " pdb=" N9 ATP A 500 " ideal model delta sigma weight residual 1.374 1.334 0.040 1.00e-02 1.00e+04 1.57e+01 bond pdb=" C8 ATP B 500 " pdb=" N7 ATP B 500 " ideal model delta sigma weight residual 1.310 1.349 -0.039 1.00e-02 1.00e+04 1.54e+01 ... (remaining 8269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 11195 3.69 - 7.39: 52 7.39 - 11.08: 3 11.08 - 14.78: 0 14.78 - 18.47: 6 Bond angle restraints: 11256 Sorted by residual: angle pdb=" PB ATP A 500 " pdb=" O3B ATP A 500 " pdb=" PG ATP A 500 " ideal model delta sigma weight residual 139.87 121.40 18.47 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PB ATP B 500 " pdb=" O3B ATP B 500 " pdb=" PG ATP B 500 " ideal model delta sigma weight residual 139.87 121.44 18.43 1.00e+00 1.00e+00 3.40e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 121.74 15.09 1.00e+00 1.00e+00 2.28e+02 angle pdb=" PA ATP A 500 " pdb=" O3A ATP A 500 " pdb=" PB ATP A 500 " ideal model delta sigma weight residual 136.83 121.79 15.04 1.00e+00 1.00e+00 2.26e+02 ... (remaining 11251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 4551 21.12 - 42.24: 419 42.24 - 63.35: 94 63.35 - 84.47: 21 84.47 - 105.59: 21 Dihedral angle restraints: 5106 sinusoidal: 2298 harmonic: 2808 Sorted by residual: dihedral pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N LYS B 309 " pdb=" CA LYS B 309 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA PHE C 308 " pdb=" C PHE C 308 " pdb=" N LYS C 309 " pdb=" CA LYS C 309 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA PHE A 308 " pdb=" C PHE A 308 " pdb=" N LYS A 309 " pdb=" CA LYS A 309 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 866 0.052 - 0.103: 289 0.103 - 0.155: 120 0.155 - 0.206: 18 0.206 - 0.258: 9 Chirality restraints: 1302 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.82e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.72e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.68e+01 ... (remaining 1299 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.085 2.00e-02 2.50e+03 7.04e-02 6.20e+01 pdb=" C7 NAG D 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.111 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.085 2.00e-02 2.50e+03 7.01e-02 6.14e+01 pdb=" C7 NAG F 1 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.111 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.085 2.00e-02 2.50e+03 7.00e-02 6.13e+01 pdb=" C7 NAG H 1 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.111 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.012 2.00e-02 2.50e+03 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 393 2.71 - 3.26: 7929 3.26 - 3.80: 14664 3.80 - 4.35: 18955 4.35 - 4.90: 29682 Nonbonded interactions: 71623 Sorted by model distance: nonbonded pdb=" O1G ATP B 500 " pdb="MG MG C 402 " model vdw 2.161 2.170 nonbonded pdb=" O1G ATP A 500 " pdb="MG MG B 501 " model vdw 2.161 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1G ATP C 401 " model vdw 2.162 2.170 nonbonded pdb=" O HOH A 608 " pdb=" O HOH A 645 " model vdw 2.218 3.040 nonbonded pdb=" O HOH B 608 " pdb=" O HOH B 645 " model vdw 2.226 3.040 ... (remaining 71618 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 356) selection = (chain 'B' and resid 27 through 356) selection = (chain 'C' and resid 27 through 356) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 4.050 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.740 Find NCS groups from input model: 0.120 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.007 0.053 8304 Z= 0.446 Angle : 0.991 18.470 11334 Z= 0.707 Chirality : 0.063 0.258 1302 Planarity : 0.007 0.070 1395 Dihedral : 18.261 105.589 3276 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.27 (0.27), residues: 984 helix: -0.27 (0.33), residues: 273 sheet: 0.47 (0.28), residues: 309 loop : 0.52 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.019 0.002 TYR B 51 PHE 0.013 0.002 PHE A 276 TRP 0.010 0.002 TRP C 85 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00697 ( 8274) covalent geometry : angle 0.97577 (11256) SS BOND : bond 0.00273 ( 12) SS BOND : angle 1.10238 ( 24) hydrogen bonds : bond 0.16394 ( 241) hydrogen bonds : angle 6.24701 ( 606) link_BETA1-4 : bond 0.00290 ( 9) link_BETA1-4 : angle 1.38228 ( 27) link_NAG-ASN : bond 0.00904 ( 9) link_NAG-ASN : angle 3.45262 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: C 215 LYS cc_start: 0.8178 (tttp) cc_final: 0.7892 (ttmm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.7017 time to fit residues: 94.2319 Evaluate side-chains 115 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110076 restraints weight = 7424.395| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.68 r_work: 0.3177 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 8304 Z= 0.313 Angle : 0.717 7.714 11334 Z= 0.366 Chirality : 0.051 0.184 1302 Planarity : 0.005 0.046 1395 Dihedral : 13.503 85.615 1530 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.14 % Allowed : 17.03 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.96 (0.27), residues: 984 helix: 1.12 (0.33), residues: 273 sheet: 0.56 (0.27), residues: 324 loop : 0.56 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 180 TYR 0.020 0.002 TYR C 90 PHE 0.020 0.003 PHE A 289 TRP 0.016 0.003 TRP A 85 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 8274) covalent geometry : angle 0.69275 (11256) SS BOND : bond 0.00493 ( 12) SS BOND : angle 1.63971 ( 24) hydrogen bonds : bond 0.04494 ( 241) hydrogen bonds : angle 4.99122 ( 606) link_BETA1-4 : bond 0.00494 ( 9) link_BETA1-4 : angle 1.95477 ( 27) link_NAG-ASN : bond 0.00393 ( 9) link_NAG-ASN : angle 3.08823 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.221 Fit side-chains REVERT: A 138 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8349 (tttt) REVERT: A 215 LYS cc_start: 0.8438 (tttt) cc_final: 0.8130 (ttmm) REVERT: A 275 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: B 138 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8270 (tttt) REVERT: B 215 LYS cc_start: 0.8500 (tttp) cc_final: 0.8100 (ttmm) REVERT: B 275 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: C 138 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8256 (tttt) REVERT: C 215 LYS cc_start: 0.8438 (tttp) cc_final: 0.8097 (ttmm) outliers start: 26 outliers final: 5 residues processed: 137 average time/residue: 0.5618 time to fit residues: 81.4041 Evaluate side-chains 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 275 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.162137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114389 restraints weight = 7352.132| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.67 r_work: 0.3237 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8304 Z= 0.138 Angle : 0.569 6.282 11334 Z= 0.285 Chirality : 0.046 0.234 1302 Planarity : 0.004 0.044 1395 Dihedral : 11.162 89.500 1530 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.78 % Allowed : 18.00 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.17 (0.28), residues: 984 helix: 1.50 (0.34), residues: 273 sheet: 0.52 (0.27), residues: 324 loop : 0.68 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 180 TYR 0.016 0.002 TYR C 90 PHE 0.010 0.001 PHE B 289 TRP 0.008 0.001 TRP C 259 HIS 0.002 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8274) covalent geometry : angle 0.54170 (11256) SS BOND : bond 0.00287 ( 12) SS BOND : angle 1.13331 ( 24) hydrogen bonds : bond 0.03169 ( 241) hydrogen bonds : angle 4.58910 ( 606) link_BETA1-4 : bond 0.00488 ( 9) link_BETA1-4 : angle 2.00688 ( 27) link_NAG-ASN : bond 0.00811 ( 9) link_NAG-ASN : angle 2.89530 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.222 Fit side-chains REVERT: A 52 GLU cc_start: 0.7986 (tp30) cc_final: 0.7655 (mt-10) REVERT: A 275 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: B 138 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8208 (tttt) REVERT: B 215 LYS cc_start: 0.8409 (tttp) cc_final: 0.8030 (ttmm) REVERT: B 275 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: B 332 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6191 (mpm) REVERT: C 52 GLU cc_start: 0.8002 (tp30) cc_final: 0.7614 (mt-10) REVERT: C 148 LYS cc_start: 0.8374 (mppt) cc_final: 0.7742 (mmtt) REVERT: C 215 LYS cc_start: 0.8374 (tttp) cc_final: 0.8046 (ttmm) outliers start: 23 outliers final: 7 residues processed: 140 average time/residue: 0.5617 time to fit residues: 83.2513 Evaluate side-chains 132 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 68.7715 > 50: distance: 95 - 151: 28.939 distance: 101 - 108: 25.018 distance: 108 - 109: 25.226 distance: 109 - 110: 29.157 distance: 109 - 112: 42.424 distance: 110 - 111: 40.568 distance: 110 - 118: 59.892 distance: 111 - 136: 40.606 distance: 112 - 113: 53.972 distance: 113 - 114: 52.449 distance: 113 - 115: 40.047 distance: 114 - 116: 46.733 distance: 115 - 117: 42.719 distance: 116 - 117: 32.264 distance: 118 - 119: 19.480 distance: 119 - 120: 36.878 distance: 119 - 122: 30.684 distance: 120 - 121: 33.217 distance: 120 - 125: 59.008 distance: 121 - 146: 37.545 distance: 122 - 123: 30.472 distance: 122 - 124: 21.575 distance: 125 - 126: 33.867 distance: 126 - 127: 32.442 distance: 126 - 129: 43.530 distance: 127 - 128: 34.037 distance: 127 - 136: 28.321 distance: 129 - 130: 24.991 distance: 130 - 131: 31.738 distance: 131 - 132: 51.555 distance: 132 - 133: 18.006 distance: 133 - 134: 17.328 distance: 133 - 135: 14.423 distance: 136 - 137: 11.141 distance: 137 - 138: 37.233 distance: 137 - 140: 19.157 distance: 138 - 139: 27.965 distance: 138 - 146: 21.896 distance: 140 - 141: 52.537 distance: 141 - 142: 22.250 distance: 141 - 143: 24.269 distance: 142 - 144: 28.343 distance: 143 - 145: 29.985 distance: 146 - 147: 42.866 distance: 147 - 148: 40.444 distance: 147 - 150: 54.733 distance: 148 - 152: 22.779 distance: 150 - 151: 39.670 distance: 152 - 153: 44.861 distance: 153 - 154: 5.916 distance: 153 - 156: 40.743 distance: 154 - 155: 48.286 distance: 154 - 163: 43.140 distance: 156 - 157: 55.959 distance: 157 - 158: 30.946 distance: 158 - 159: 54.640 distance: 159 - 160: 42.031 distance: 160 - 161: 26.158 distance: 160 - 162: 33.015 distance: 163 - 164: 51.073 distance: 163 - 169: 55.443 distance: 164 - 165: 56.111 distance: 164 - 167: 11.656 distance: 165 - 166: 50.089 distance: 165 - 170: 6.158 distance: 167 - 168: 17.734 distance: 168 - 169: 27.174 distance: 170 - 171: 43.416 distance: 171 - 172: 31.052 distance: 171 - 174: 20.112 distance: 172 - 173: 35.797 distance: 172 - 178: 46.034 distance: 174 - 175: 56.075 distance: 174 - 176: 15.615 distance: 175 - 177: 54.817 distance: 178 - 179: 9.207 distance: 179 - 180: 36.453 distance: 179 - 182: 41.678 distance: 180 - 190: 45.262 distance: 182 - 183: 53.407 distance: 183 - 184: 27.058 distance: 183 - 185: 47.699 distance: 184 - 186: 19.063 distance: 185 - 187: 47.652 distance: 186 - 188: 12.787 distance: 187 - 188: 39.927 distance: 188 - 189: 39.675 distance: 190 - 191: 20.350 distance: 191 - 192: 27.777 distance: 191 - 194: 40.140 distance: 192 - 193: 42.701 distance: 192 - 199: 29.083 distance: 194 - 195: 28.702 distance: 195 - 196: 12.616 distance: 196 - 197: 40.937 distance: 196 - 198: 39.017