Starting phenix.real_space_refine on Wed Feb 12 01:02:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r12_14228/02_2025/7r12_14228.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r12_14228/02_2025/7r12_14228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r12_14228/02_2025/7r12_14228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r12_14228/02_2025/7r12_14228.map" model { file = "/net/cci-nas-00/data/ceres_data/7r12_14228/02_2025/7r12_14228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r12_14228/02_2025/7r12_14228.cif" } resolution = 3.3 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= 0.002 sd= 0.089 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 39 5.16 5 C 4383 2.51 5 N 1130 2.21 5 O 1305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6858 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1972 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 1 Chain: "D" 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: "A" 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 Time building chain proxies: 5.04, per 1000 atoms: 0.73 Number of scatterers: 6858 At special positions: 0 Unit cell: (75.46, 98.098, 139.062, 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 39 16.00 O 1305 8.00 N 1130 7.00 C 4383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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 NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 331 " " NAG D 902 " - " ASN D 53 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 103 " " NAG D 905 " - " ASN D 546 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 911.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 52.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.441A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 4.067A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.642A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.763A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 155 removed outlier: 3.523A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.556A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.594A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.059A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.704A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.036A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.700A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.618A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.970A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.547A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.602A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.543A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.533A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.964A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 4.081A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.622A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.617A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.216A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.696A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.862A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.525A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.752A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.199A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.287A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.643A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 301 hydrogen bonds defined for protein. 846 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: 1.76 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2194 1.34 - 1.46: 1719 1.46 - 1.58: 3068 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 7041 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" C1 NAG D 902 " pdb=" O5 NAG D 902 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG D 904 " pdb=" O5 NAG D 904 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 7036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 9391 1.72 - 3.44: 152 3.44 - 5.15: 20 5.15 - 6.87: 2 6.87 - 8.59: 1 Bond angle restraints: 9566 Sorted by residual: angle pdb=" C ASN D 90 " pdb=" N LEU D 91 " pdb=" CA LEU D 91 " ideal model delta sigma weight residual 121.54 126.61 -5.07 1.91e+00 2.74e-01 7.05e+00 angle pdb=" C LEU D 423 " pdb=" N LEU D 424 " pdb=" CA LEU D 424 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 7.00e+00 angle pdb=" CA LEU A 546 " pdb=" CB LEU A 546 " pdb=" CG LEU A 546 " ideal model delta sigma weight residual 116.30 124.89 -8.59 3.50e+00 8.16e-02 6.02e+00 angle pdb=" N ILE D 421 " pdb=" CA ILE D 421 " pdb=" C ILE D 421 " ideal model delta sigma weight residual 110.42 112.54 -2.12 9.60e-01 1.09e+00 4.87e+00 angle pdb=" N ASP D 427 " pdb=" CA ASP D 427 " pdb=" C ASP D 427 " ideal model delta sigma weight residual 110.88 108.11 2.77 1.28e+00 6.10e-01 4.68e+00 ... (remaining 9561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3824 17.55 - 35.10: 336 35.10 - 52.65: 66 52.65 - 70.20: 12 70.20 - 87.75: 4 Dihedral angle restraints: 4242 sinusoidal: 1787 harmonic: 2455 Sorted by residual: dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual -86.00 -119.56 33.56 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 123.28 -30.28 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CA CYS D 344 " pdb=" C CYS D 344 " pdb=" N HIS D 345 " pdb=" CA HIS D 345 " ideal model delta harmonic sigma weight residual 180.00 163.88 16.12 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 604 0.030 - 0.060: 300 0.060 - 0.089: 67 0.089 - 0.119: 55 0.119 - 0.149: 6 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" C1 NAG D 904 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D 904 " pdb=" O5 NAG D 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL A 433 " pdb=" N VAL A 433 " pdb=" C VAL A 433 " pdb=" CB VAL A 433 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1029 not shown) Planarity restraints: 1235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO D 146 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 234 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO D 235 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 578 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 579 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 579 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 579 " 0.017 5.00e-02 4.00e+02 ... (remaining 1232 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 133 2.71 - 3.26: 6429 3.26 - 3.80: 10119 3.80 - 4.35: 13356 4.35 - 4.90: 23311 Nonbonded interactions: 53348 Sorted by model distance: nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 901 " model vdw 2.211 2.230 nonbonded pdb=" O ARG A 408 " pdb=" NE2 GLN A 414 " model vdw 2.257 3.120 nonbonded pdb=" O ASP A 442 " pdb=" ND2 ASN A 448 " model vdw 2.308 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.325 3.040 ... (remaining 53343 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=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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.860 Find NCS groups from input model: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.003 0.044 7041 Z= 0.223 Angle : 0.549 8.591 9566 Z= 0.283 Chirality : 0.041 0.149 1032 Planarity : 0.004 0.050 1229 Dihedral : 13.554 87.747 2640 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.39 (0.29), residues: 831 helix: 1.22 (0.28), residues: 374 sheet: 0.95 (0.60), residues: 70 loop : -0.81 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS D 401 PHE 0.011 0.001 PHE D 308 TYR 0.021 0.001 TYR D 199 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.684 Fit side-chains REVERT: D 160 GLU cc_start: 0.6626 (tt0) cc_final: 0.6374 (tt0) REVERT: D 470 LYS cc_start: 0.7909 (mttt) cc_final: 0.7490 (mmtm) REVERT: A 420 ASP cc_start: 0.8332 (m-30) cc_final: 0.7965 (m-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1850 time to fit residues: 23.3707 Evaluate side-chains 79 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.152598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.125524 restraints weight = 7099.054| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.29 r_work: 0.3131 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7041 Z= 0.259 Angle : 0.546 6.694 9566 Z= 0.278 Chirality : 0.042 0.151 1032 Planarity : 0.004 0.049 1229 Dihedral : 6.055 58.997 1032 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.35 % Allowed : 4.60 % Favored : 94.05 % 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: 0.50 (0.29), residues: 831 helix: 1.27 (0.28), residues: 383 sheet: 0.93 (0.60), residues: 70 loop : -0.75 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 566 HIS 0.003 0.001 HIS D 540 PHE 0.016 0.002 PHE D 327 TYR 0.020 0.002 TYR D 183 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.837 Fit side-chains REVERT: D 160 GLU cc_start: 0.7213 (tt0) cc_final: 0.6786 (tt0) REVERT: D 470 LYS cc_start: 0.8102 (mttt) cc_final: 0.7476 (mmtm) REVERT: A 405 ASP cc_start: 0.8235 (m-30) cc_final: 0.7993 (m-30) REVERT: A 420 ASP cc_start: 0.8809 (m-30) cc_final: 0.8271 (m-30) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.1768 time to fit residues: 21.6112 Evaluate side-chains 82 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 71 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.153876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.127258 restraints weight = 7201.787| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.21 r_work: 0.2957 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7041 Z= 0.193 Angle : 0.492 6.045 9566 Z= 0.251 Chirality : 0.041 0.152 1032 Planarity : 0.004 0.048 1229 Dihedral : 5.131 54.488 1032 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.49 % Allowed : 6.77 % Favored : 91.75 % 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: 0.70 (0.29), residues: 831 helix: 1.42 (0.28), residues: 381 sheet: 1.03 (0.60), residues: 70 loop : -0.62 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 566 HIS 0.003 0.001 HIS D 540 PHE 0.012 0.001 PHE D 327 TYR 0.018 0.001 TYR D 183 ARG 0.001 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.757 Fit side-chains REVERT: D 160 GLU cc_start: 0.7165 (tt0) cc_final: 0.6763 (tt0) REVERT: D 175 GLN cc_start: 0.7264 (mt0) cc_final: 0.6884 (mt0) REVERT: D 470 LYS cc_start: 0.8062 (mttt) cc_final: 0.7409 (mmtm) REVERT: A 420 ASP cc_start: 0.8741 (m-30) cc_final: 0.8254 (m-30) outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 0.1639 time to fit residues: 20.5450 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.150823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.119214 restraints weight = 7299.300| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.65 r_work: 0.3093 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7041 Z= 0.315 Angle : 0.576 7.990 9566 Z= 0.294 Chirality : 0.044 0.281 1032 Planarity : 0.004 0.049 1229 Dihedral : 4.994 57.155 1032 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.89 % Allowed : 7.31 % Favored : 90.80 % 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: 0.48 (0.29), residues: 831 helix: 1.23 (0.28), residues: 384 sheet: 0.89 (0.60), residues: 71 loop : -0.74 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 566 HIS 0.004 0.001 HIS D 540 PHE 0.018 0.002 PHE D 327 TYR 0.016 0.002 TYR D 183 ARG 0.002 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.804 Fit side-chains REVERT: D 160 GLU cc_start: 0.7227 (tt0) cc_final: 0.6820 (tt0) REVERT: A 405 ASP cc_start: 0.8302 (m-30) cc_final: 0.8010 (m-30) REVERT: A 420 ASP cc_start: 0.8831 (m-30) cc_final: 0.8306 (m-30) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.1738 time to fit residues: 21.7149 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 59.5063 > 50: distance: 103 - 135: 14.882 distance: 109 - 118: 14.010 distance: 110 - 141: 24.872 distance: 118 - 119: 14.612 distance: 119 - 120: 13.485 distance: 119 - 122: 8.027 distance: 120 - 121: 18.120 distance: 120 - 128: 7.708 distance: 122 - 123: 10.002 distance: 123 - 124: 42.164 distance: 123 - 125: 22.354 distance: 124 - 126: 37.153 distance: 125 - 127: 37.518 distance: 126 - 127: 13.407 distance: 128 - 129: 6.287 distance: 129 - 130: 3.164 distance: 129 - 132: 31.604 distance: 130 - 131: 13.628 distance: 130 - 135: 10.218 distance: 132 - 133: 16.106 distance: 132 - 134: 34.997 distance: 135 - 136: 25.421 distance: 136 - 137: 8.632 distance: 136 - 139: 15.110 distance: 137 - 138: 20.959 distance: 137 - 141: 23.135 distance: 139 - 140: 20.439 distance: 141 - 142: 7.502 distance: 142 - 143: 21.154 distance: 142 - 145: 3.531 distance: 143 - 144: 32.306 distance: 143 - 149: 15.192 distance: 145 - 146: 35.598 distance: 146 - 147: 28.312 distance: 146 - 148: 13.996 distance: 149 - 150: 16.738 distance: 150 - 151: 19.618 distance: 150 - 153: 26.214 distance: 151 - 152: 38.190 distance: 151 - 157: 23.865 distance: 153 - 154: 18.324 distance: 154 - 155: 46.467 distance: 154 - 156: 12.012 distance: 157 - 158: 29.965 distance: 158 - 159: 22.787 distance: 158 - 161: 26.110 distance: 159 - 160: 9.878 distance: 159 - 169: 12.753 distance: 161 - 162: 9.799 distance: 162 - 163: 15.854 distance: 162 - 164: 27.200 distance: 163 - 165: 33.911 distance: 164 - 166: 23.398 distance: 165 - 167: 25.185 distance: 166 - 167: 15.209 distance: 167 - 168: 27.782 distance: 169 - 170: 15.913 distance: 170 - 171: 6.572 distance: 170 - 173: 10.959 distance: 171 - 172: 7.265 distance: 171 - 175: 22.617 distance: 173 - 174: 39.311 distance: 175 - 176: 18.248 distance: 176 - 177: 15.042 distance: 176 - 179: 13.067 distance: 177 - 186: 13.051 distance: 179 - 180: 13.801 distance: 180 - 181: 6.009 distance: 180 - 182: 24.747 distance: 181 - 183: 26.250 distance: 182 - 184: 13.613 distance: 183 - 185: 20.065 distance: 184 - 185: 28.156 distance: 186 - 187: 27.245 distance: 187 - 188: 17.441 distance: 187 - 190: 18.809 distance: 188 - 189: 43.361 distance: 188 - 194: 46.198 distance: 190 - 191: 8.646 distance: 190 - 192: 39.585 distance: 191 - 193: 54.738 distance: 194 - 195: 43.188 distance: 195 - 196: 40.431 distance: 195 - 198: 36.571 distance: 196 - 197: 5.892 distance: 196 - 205: 24.683 distance: 198 - 199: 3.220 distance: 199 - 200: 18.191 distance: 200 - 201: 8.927 distance: 202 - 203: 22.672 distance: 202 - 204: 6.767