Starting phenix.real_space_refine on Wed May 14 08:48:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8we1_37470/05_2025/8we1_37470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8we1_37470/05_2025/8we1_37470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8we1_37470/05_2025/8we1_37470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8we1_37470/05_2025/8we1_37470.map" model { file = "/net/cci-nas-00/data/ceres_data/8we1_37470/05_2025/8we1_37470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8we1_37470/05_2025/8we1_37470.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6332 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4194 2.51 5 N 1077 2.21 5 O 1250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6559 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4872 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4987 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1550 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" 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: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 34 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 34 " occ=0.50 Time building chain proxies: 6.67, per 1000 atoms: 1.02 Number of scatterers: 6559 At special positions: 0 Unit cell: (74.8, 87.55, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1250 8.00 N 1077 7.00 C 4194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 905 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 374 " 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 53.1% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.510A pdb=" N ASP A 38 " --> pdb=" O AHIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.784A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 4.072A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.831A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.554A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.608A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.837A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.947A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.594A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.935A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.679A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.275A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.532A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.611A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.685A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.773A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.793A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.299A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.101A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.725A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 289 hydrogen bonds defined for protein. 820 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: 1.62 Time building geometry restraints manager: 2.26 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: 2079 1.34 - 1.46: 1687 1.46 - 1.58: 2920 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6744 Sorted by residual: bond pdb=" CE1BHIS A 34 " pdb=" NE2BHIS A 34 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.55e+01 bond pdb=" CE1AHIS A 34 " pdb=" NE2AHIS A 34 " ideal model delta sigma weight residual 1.321 1.358 -0.037 1.00e-02 1.00e+04 1.36e+01 bond pdb=" N GLN A 24 " pdb=" CA GLN A 24 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.89e+00 bond pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.75e+00 bond pdb=" N GLN B 493 " pdb=" CA GLN B 493 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.85e+00 ... (remaining 6739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 9038 2.32 - 4.64: 116 4.64 - 6.97: 16 6.97 - 9.29: 0 9.29 - 11.61: 1 Bond angle restraints: 9171 Sorted by residual: angle pdb=" C TYR A 83 " pdb=" N PRO A 84 " pdb=" CA PRO A 84 " ideal model delta sigma weight residual 119.78 123.81 -4.03 1.03e+00 9.43e-01 1.53e+01 angle pdb=" CB MET A 408 " pdb=" CG MET A 408 " pdb=" SD MET A 408 " ideal model delta sigma weight residual 112.70 124.31 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA AHIS A 34 " pdb=" C AHIS A 34 " pdb=" O AHIS A 34 " ideal model delta sigma weight residual 119.97 116.07 3.90 1.15e+00 7.56e-01 1.15e+01 angle pdb=" CA GLU A 150 " pdb=" CB GLU A 150 " pdb=" CG GLU A 150 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C ASN B 487 " pdb=" CA ASN B 487 " pdb=" CB ASN B 487 " ideal model delta sigma weight residual 111.51 116.17 -4.66 1.58e+00 4.01e-01 8.69e+00 ... (remaining 9166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 3590 21.39 - 42.78: 399 42.78 - 64.16: 90 64.16 - 85.55: 17 85.55 - 106.94: 7 Dihedral angle restraints: 4103 sinusoidal: 1777 harmonic: 2326 Sorted by residual: dihedral pdb=" CA GLN A 139 " pdb=" C GLN A 139 " pdb=" N GLU A 140 " pdb=" CA GLU A 140 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C4 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual 53.78 -53.16 106.94 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C4 NAG A 901 " pdb=" O4 NAG A 901 " ideal model delta sinusoidal sigma weight residual 175.11 68.48 106.63 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 4100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 843 0.059 - 0.118: 130 0.118 - 0.178: 12 0.178 - 0.237: 1 0.237 - 0.296: 1 Chirality restraints: 987 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ASN B 477 " pdb=" N ASN B 477 " pdb=" C ASN B 477 " pdb=" CB ASN B 477 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 984 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA AHIS A 34 " 0.028 2.00e-02 2.50e+03 5.63e-02 3.17e+01 pdb=" C AHIS A 34 " -0.097 2.00e-02 2.50e+03 pdb=" O AHIS A 34 " 0.036 2.00e-02 2.50e+03 pdb=" N GLU A 35 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 415 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA BHIS A 34 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C BHIS A 34 " 0.036 2.00e-02 2.50e+03 pdb=" O BHIS A 34 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 35 " -0.013 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 52 2.58 - 3.16: 5107 3.16 - 3.74: 10141 3.74 - 4.32: 13701 4.32 - 4.90: 23083 Nonbonded interactions: 52084 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 905 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP A 494 " pdb=" OG1 THR A 496 " model vdw 2.164 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.165 3.040 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.177 3.040 nonbonded pdb=" O ALA A 501 " pdb=" OG SER A 507 " model vdw 2.188 3.040 ... (remaining 52079 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.790 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.005 0.199 6763 Z= 0.230 Angle : 0.619 11.611 9215 Z= 0.326 Chirality : 0.044 0.296 987 Planarity : 0.004 0.059 1177 Dihedral : 18.672 106.937 2590 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.89 % Allowed : 25.36 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.31), residues: 790 helix: 1.60 (0.28), residues: 370 sheet: 0.79 (0.76), residues: 45 loop : -0.79 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 203 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE B 347 TYR 0.025 0.001 TYR A 521 ARG 0.006 0.001 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 7) link_NAG-ASN : angle 2.38613 ( 21) link_BETA1-4 : bond 0.00410 ( 2) link_BETA1-4 : angle 0.84185 ( 6) hydrogen bonds : bond 0.17674 ( 289) hydrogen bonds : angle 5.35209 ( 820) link_BETA1-6 : bond 0.00400 ( 1) link_BETA1-6 : angle 1.55128 ( 3) metal coordination : bond 0.19891 ( 2) SS BOND : bond 0.00246 ( 7) SS BOND : angle 0.48696 ( 14) covalent geometry : bond 0.00366 ( 6744) covalent geometry : angle 0.60881 ( 9171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.704 Fit side-chains REVERT: B 364 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6739 (p0) outliers start: 27 outliers final: 23 residues processed: 186 average time/residue: 1.0116 time to fit residues: 199.0048 Evaluate side-chains 178 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 61 ASN A 81 GLN A 154 ASN A 210 ASN A 374 HIS A 580 ASN A 586 ASN B 439 ASN B 448 ASN B 450 ASN B 487 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.138891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.119208 restraints weight = 18028.631| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.87 r_work: 0.3521 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.556 6763 Z= 0.267 Angle : 0.586 12.454 9215 Z= 0.287 Chirality : 0.044 0.251 987 Planarity : 0.004 0.058 1177 Dihedral : 10.553 76.210 1118 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.19 % Allowed : 22.33 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.30), residues: 790 helix: 1.60 (0.28), residues: 370 sheet: 0.51 (0.74), residues: 45 loop : -0.82 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 PHE 0.008 0.001 PHE B 347 TYR 0.021 0.001 TYR A 521 ARG 0.004 0.001 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 7) link_NAG-ASN : angle 2.73173 ( 21) link_BETA1-4 : bond 0.00302 ( 2) link_BETA1-4 : angle 0.86238 ( 6) hydrogen bonds : bond 0.05073 ( 289) hydrogen bonds : angle 4.24688 ( 820) link_BETA1-6 : bond 0.00388 ( 1) link_BETA1-6 : angle 1.43358 ( 3) metal coordination : bond 0.39308 ( 2) SS BOND : bond 0.00375 ( 7) SS BOND : angle 0.55401 ( 14) covalent geometry : bond 0.00319 ( 6744) covalent geometry : angle 0.57174 ( 9171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.759 Fit side-chains REVERT: A 364 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8151 (t) REVERT: B 364 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7421 (p0) outliers start: 36 outliers final: 27 residues processed: 182 average time/residue: 0.9910 time to fit residues: 190.8744 Evaluate side-chains 179 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 0.0000 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 340 GLN A 580 ASN A 586 ASN B 370 ASN B 448 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.121179 restraints weight = 10992.424| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.21 r_work: 0.3577 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6763 Z= 0.135 Angle : 0.572 11.679 9215 Z= 0.276 Chirality : 0.044 0.313 987 Planarity : 0.004 0.058 1177 Dihedral : 7.427 57.210 1095 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.48 % Allowed : 22.91 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.30), residues: 790 helix: 1.61 (0.27), residues: 370 sheet: 0.30 (0.73), residues: 45 loop : -0.84 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE B 347 TYR 0.018 0.001 TYR A 521 ARG 0.005 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 7) link_NAG-ASN : angle 2.74683 ( 21) link_BETA1-4 : bond 0.00414 ( 2) link_BETA1-4 : angle 0.85183 ( 6) hydrogen bonds : bond 0.04709 ( 289) hydrogen bonds : angle 4.01272 ( 820) link_BETA1-6 : bond 0.00329 ( 1) link_BETA1-6 : angle 1.31426 ( 3) metal coordination : bond 0.00459 ( 2) SS BOND : bond 0.00337 ( 7) SS BOND : angle 0.50669 ( 14) covalent geometry : bond 0.00307 ( 6744) covalent geometry : angle 0.55684 ( 9171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.767 Fit side-chains REVERT: A 364 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8178 (t) REVERT: B 423 TYR cc_start: 0.8027 (t80) cc_final: 0.7820 (t80) REVERT: B 424 LYS cc_start: 0.8046 (tppt) cc_final: 0.7824 (tppt) outliers start: 38 outliers final: 25 residues processed: 170 average time/residue: 1.0263 time to fit residues: 184.1474 Evaluate side-chains 174 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.6148 > 50: distance: 22 - 172: 31.820 distance: 25 - 169: 33.274 distance: 86 - 91: 15.406 distance: 92 - 93: 10.347 distance: 92 - 95: 8.927 distance: 93 - 94: 7.859 distance: 93 - 99: 13.727 distance: 95 - 96: 13.704 distance: 96 - 98: 6.826 distance: 99 - 100: 17.268 distance: 100 - 101: 26.414 distance: 100 - 103: 22.729 distance: 101 - 102: 16.215 distance: 101 - 111: 40.919 distance: 103 - 104: 7.179 distance: 104 - 105: 15.558 distance: 104 - 106: 6.375 distance: 105 - 107: 19.261 distance: 106 - 108: 14.844 distance: 107 - 109: 10.606 distance: 108 - 109: 13.051 distance: 109 - 110: 35.174 distance: 111 - 112: 45.548 distance: 112 - 113: 36.509 distance: 112 - 115: 18.014 distance: 113 - 114: 14.675 distance: 113 - 120: 24.122 distance: 115 - 116: 23.795 distance: 116 - 117: 15.502 distance: 117 - 118: 30.422 distance: 118 - 119: 18.591 distance: 120 - 121: 22.827 distance: 121 - 122: 34.566 distance: 121 - 124: 43.461 distance: 122 - 123: 40.920 distance: 122 - 128: 29.708 distance: 124 - 125: 3.595 distance: 125 - 126: 9.865 distance: 125 - 127: 5.547 distance: 128 - 129: 29.647 distance: 128 - 134: 37.910 distance: 129 - 130: 12.814 distance: 129 - 132: 41.093 distance: 130 - 135: 35.709 distance: 132 - 133: 14.234 distance: 133 - 134: 44.290 distance: 135 - 136: 33.316 distance: 136 - 137: 14.695 distance: 136 - 139: 34.848 distance: 137 - 138: 28.642 distance: 137 - 143: 21.766 distance: 139 - 140: 10.002 distance: 140 - 141: 31.430 distance: 140 - 142: 22.442 distance: 143 - 144: 9.302 distance: 144 - 145: 13.219 distance: 144 - 147: 21.718 distance: 145 - 146: 24.635 distance: 145 - 151: 16.864 distance: 147 - 148: 32.422 distance: 148 - 149: 9.589 distance: 148 - 150: 29.341 distance: 151 - 152: 15.713 distance: 152 - 153: 14.747 distance: 152 - 155: 16.463 distance: 153 - 154: 4.464 distance: 153 - 162: 24.185 distance: 155 - 156: 6.313 distance: 156 - 157: 7.762 distance: 156 - 158: 16.745 distance: 157 - 159: 23.062 distance: 158 - 160: 20.874 distance: 159 - 161: 28.956 distance: 160 - 161: 25.718 distance: 162 - 163: 34.097 distance: 163 - 164: 27.275 distance: 163 - 166: 16.757 distance: 164 - 165: 16.252 distance: 164 - 169: 13.870 distance: 166 - 167: 28.692 distance: 166 - 168: 40.403 distance: 169 - 170: 26.999 distance: 170 - 171: 4.078 distance: 171 - 172: 3.059 distance: 171 - 173: 28.464