Starting phenix.real_space_refine on Tue Jan 14 11:13:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hg0_34730/01_2025/8hg0_34730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hg0_34730/01_2025/8hg0_34730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hg0_34730/01_2025/8hg0_34730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hg0_34730/01_2025/8hg0_34730.map" model { file = "/net/cci-nas-00/data/ceres_data/8hg0_34730/01_2025/8hg0_34730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hg0_34730/01_2025/8hg0_34730.cif" } resolution = 3.51 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= -0.003 sd= 0.017 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 38 5.16 5 C 4132 2.51 5 N 1064 2.21 5 O 1235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6470 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4884 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 Time building chain proxies: 5.57, per 1000 atoms: 0.86 Number of scatterers: 6470 At special positions: 0 Unit cell: (77.35, 90.95, 119.85, 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 38 16.00 O 1235 8.00 N 1064 7.00 C 4132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.04 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 NAG-ASN " NAG A 701 " - " ASN A 299 " " NAG A 702 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 945.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 374 " 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 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: 35 helices and 6 sheets defined 55.2% alpha, 6.5% 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 21 through 54 removed outlier: 3.625A pdb=" N THR A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP A 39 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 82 removed outlier: 3.524A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.560A pdb=" N LEU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.825A pdb=" N ARG A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.526A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.550A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.649A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.253A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 252 removed outlier: 4.256A pdb=" N GLU A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.596A pdb=" N TYR A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.671A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 299 through 302 removed outlier: 4.144A pdb=" N TRP A 302 " --> pdb=" O ASN A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.786A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.835A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 329' Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.580A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.685A 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 399 through 414 removed outlier: 3.629A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.610A pdb=" N LEU A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.851A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.244A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.533A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 532 removed outlier: 4.336A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.625A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.917A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 600 Proline residue: A 590 - end of helix removed outlier: 3.811A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.210A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.511A pdb=" N LEU A 142 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.694A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.450A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.606A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.818A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 264 hydrogen bonds defined for protein. 759 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: 1.82 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2068 1.35 - 1.46: 1734 1.46 - 1.58: 2786 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6648 Sorted by residual: bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" CA LEU B 518 " pdb=" CB LEU B 518 " ideal model delta sigma weight residual 1.535 1.519 0.016 1.32e-02 5.74e+03 1.49e+00 bond pdb=" CG LYS B 417 " pdb=" CD LYS B 417 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" C LYS A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.334 1.352 -0.018 1.51e-02 4.39e+03 1.40e+00 ... (remaining 6643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 8851 1.87 - 3.75: 140 3.75 - 5.62: 23 5.62 - 7.49: 3 7.49 - 9.37: 3 Bond angle restraints: 9020 Sorted by residual: angle pdb=" CB LYS B 417 " pdb=" CG LYS B 417 " pdb=" CD LYS B 417 " ideal model delta sigma weight residual 111.30 120.67 -9.37 2.30e+00 1.89e-01 1.66e+01 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 112.83 108.82 4.01 9.90e-01 1.02e+00 1.64e+01 angle pdb=" N SER A 104 " pdb=" CA SER A 104 " pdb=" C SER A 104 " ideal model delta sigma weight residual 112.13 108.27 3.86 1.37e+00 5.33e-01 7.94e+00 angle pdb=" N SER B 375 " pdb=" CA SER B 375 " pdb=" C SER B 375 " ideal model delta sigma weight residual 114.56 111.11 3.45 1.27e+00 6.20e-01 7.36e+00 angle pdb=" CB MET A 455 " pdb=" CG MET A 455 " pdb=" SD MET A 455 " ideal model delta sigma weight residual 112.70 120.76 -8.06 3.00e+00 1.11e-01 7.21e+00 ... (remaining 9015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.96: 3494 20.96 - 41.92: 399 41.92 - 62.88: 71 62.88 - 83.84: 4 83.84 - 104.80: 9 Dihedral angle restraints: 3977 sinusoidal: 1650 harmonic: 2327 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -143.61 57.61 1 1.00e+01 1.00e-02 4.46e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -128.35 42.35 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" O4 NAG A 701 " ideal model delta sinusoidal sigma weight residual 175.11 70.31 104.80 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 3974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 681 0.036 - 0.072: 191 0.072 - 0.107: 63 0.107 - 0.143: 9 0.143 - 0.179: 1 Chirality restraints: 945 Sorted by residual: chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA ILE A 468 " pdb=" N ILE A 468 " pdb=" C ILE A 468 " pdb=" CB ILE A 468 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 942 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A 258 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO A 146 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 235 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.027 5.00e-02 4.00e+02 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 96 2.66 - 3.22: 6013 3.22 - 3.78: 9451 3.78 - 4.34: 13113 4.34 - 4.90: 21292 Nonbonded interactions: 49965 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 703 " model vdw 2.098 2.230 nonbonded pdb=" O THR A 123 " pdb=" OG1 THR A 126 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP B 467 " pdb=" OG SER B 469 " model vdw 2.270 3.040 nonbonded pdb=" O THR A 119 " pdb=" OG1 THR A 123 " model vdw 2.300 3.040 nonbonded pdb=" O THR A 126 " pdb=" OG1 THR A 130 " model vdw 2.302 3.040 ... (remaining 49960 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 group one per residue 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: 8.900 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.910 Find NCS groups from input model: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 0.054 6648 Z= 0.200 Angle : 0.612 9.367 9020 Z= 0.346 Chirality : 0.038 0.179 945 Planarity : 0.005 0.062 1160 Dihedral : 17.579 104.802 2467 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.78 % Favored : 98.09 % Rotamer: Outliers : 1.15 % Allowed : 26.19 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.06 (0.30), residues: 786 helix: 0.27 (0.28), residues: 334 sheet: 1.49 (0.84), residues: 49 loop : -0.24 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 610 HIS 0.003 0.001 HIS A 241 PHE 0.019 0.001 PHE A 428 TYR 0.015 0.001 TYR A 429 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 498 CYS cc_start: 0.7594 (t) cc_final: 0.7364 (p) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.2090 time to fit residues: 17.0825 Evaluate side-chains 50 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 52 ASN A 97 GLN A 103 GLN A 118 ASN A 122 ASN A 194 ASN A 239 GLN A 374 HIS A 493 HIS A 522 GLN A 599 ASN B 409 GLN B 498 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.030772 restraints weight = 38341.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031895 restraints weight = 21655.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032664 restraints weight = 14908.780| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6648 Z= 0.189 Angle : 0.577 7.843 9020 Z= 0.298 Chirality : 0.041 0.188 945 Planarity : 0.005 0.059 1160 Dihedral : 7.258 60.524 938 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 3.45 % Allowed : 23.02 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.58 (0.31), residues: 786 helix: 0.91 (0.27), residues: 376 sheet: 1.20 (0.80), residues: 49 loop : -0.19 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 610 HIS 0.005 0.000 HIS A 241 PHE 0.010 0.001 PHE A 438 TYR 0.018 0.001 TYR A 429 ARG 0.007 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.9399 (mmm) cc_final: 0.9191 (mmm) REVERT: A 233 ILE cc_start: 0.9871 (OUTLIER) cc_final: 0.9661 (mm) REVERT: A 249 MET cc_start: 0.9352 (mmm) cc_final: 0.9063 (mmm) REVERT: A 297 MET cc_start: 0.9233 (mtt) cc_final: 0.9021 (ttm) REVERT: A 347 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.8935 (p) REVERT: A 366 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8713 (mtp) REVERT: A 401 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8651 (t-90) REVERT: A 429 TYR cc_start: 0.8584 (t80) cc_final: 0.8315 (t80) REVERT: A 462 MET cc_start: 0.9553 (mmm) cc_final: 0.8969 (tpp) REVERT: A 498 CYS cc_start: 0.8556 (t) cc_final: 0.6965 (p) REVERT: B 406 GLU cc_start: 0.9020 (tp30) cc_final: 0.8739 (tp30) outliers start: 24 outliers final: 5 residues processed: 66 average time/residue: 0.2016 time to fit residues: 17.8719 Evaluate side-chains 51 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 367 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.030974 restraints weight = 37499.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.032067 restraints weight = 21377.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.032806 restraints weight = 14799.171| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6648 Z= 0.162 Angle : 0.521 7.913 9020 Z= 0.266 Chirality : 0.040 0.184 945 Planarity : 0.004 0.060 1160 Dihedral : 4.633 27.978 933 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 2.73 % Allowed : 21.87 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.75 (0.31), residues: 786 helix: 1.22 (0.28), residues: 372 sheet: 1.25 (0.79), residues: 49 loop : -0.30 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.004 0.000 HIS A 241 PHE 0.008 0.001 PHE A 369 TYR 0.011 0.001 TYR A 429 ARG 0.004 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7838 (p) REVERT: A 80 MET cc_start: 0.9516 (mtp) cc_final: 0.9259 (ttt) REVERT: A 124 MET cc_start: 0.9394 (mmm) cc_final: 0.9151 (mmm) REVERT: A 366 MET cc_start: 0.8872 (tpp) cc_final: 0.8645 (mtt) REVERT: A 367 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8850 (p0) REVERT: A 429 TYR cc_start: 0.8639 (t80) cc_final: 0.8320 (t80) REVERT: A 462 MET cc_start: 0.9594 (mmm) cc_final: 0.8928 (tpp) REVERT: B 406 GLU cc_start: 0.9122 (tp30) cc_final: 0.8485 (tp30) REVERT: B 417 LYS cc_start: 0.9021 (tppt) cc_final: 0.8792 (tppt) outliers start: 19 outliers final: 8 residues processed: 60 average time/residue: 0.2091 time to fit residues: 17.2813 Evaluate side-chains 53 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 0.0030 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 chunk 43 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.040808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.031217 restraints weight = 37759.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.032311 restraints weight = 21513.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.033047 restraints weight = 14826.959| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6648 Z= 0.135 Angle : 0.496 8.197 9020 Z= 0.252 Chirality : 0.039 0.182 945 Planarity : 0.004 0.059 1160 Dihedral : 4.032 18.138 932 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.07 % Rotamer: Outliers : 2.01 % Allowed : 23.31 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.87 (0.31), residues: 786 helix: 1.42 (0.28), residues: 365 sheet: 1.14 (0.77), residues: 49 loop : -0.31 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.004 0.000 HIS A 241 PHE 0.008 0.001 PHE A 369 TYR 0.007 0.001 TYR A 429 ARG 0.004 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7665 (p) REVERT: A 80 MET cc_start: 0.9507 (mtp) cc_final: 0.9306 (ttt) REVERT: A 124 MET cc_start: 0.9408 (mmm) cc_final: 0.9155 (mmm) REVERT: A 249 MET cc_start: 0.9263 (mmm) cc_final: 0.9056 (mmp) REVERT: A 347 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8799 (p) REVERT: A 429 TYR cc_start: 0.8669 (t80) cc_final: 0.8354 (t80) REVERT: A 462 MET cc_start: 0.9618 (mmm) cc_final: 0.8997 (tpp) REVERT: B 406 GLU cc_start: 0.9131 (tp30) cc_final: 0.8916 (tp30) outliers start: 14 outliers final: 8 residues processed: 55 average time/residue: 0.2129 time to fit residues: 15.9580 Evaluate side-chains 52 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 367 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS A 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.040486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.030763 restraints weight = 38698.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.031837 restraints weight = 21869.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.032571 restraints weight = 15163.479| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6648 Z= 0.162 Angle : 0.498 8.496 9020 Z= 0.252 Chirality : 0.039 0.181 945 Planarity : 0.004 0.059 1160 Dihedral : 3.912 16.754 931 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 3.17 % Allowed : 22.88 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.99 (0.31), residues: 786 helix: 1.54 (0.28), residues: 365 sheet: 1.03 (0.75), residues: 49 loop : -0.23 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 369 TYR 0.007 0.001 TYR A 381 ARG 0.005 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.9402 (mmm) cc_final: 0.9151 (mmm) REVERT: A 347 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8797 (p) REVERT: A 429 TYR cc_start: 0.8703 (t80) cc_final: 0.8382 (t80) REVERT: A 462 MET cc_start: 0.9621 (mmm) cc_final: 0.9006 (tpp) REVERT: B 406 GLU cc_start: 0.9152 (tp30) cc_final: 0.8946 (tp30) outliers start: 22 outliers final: 11 residues processed: 62 average time/residue: 0.1972 time to fit residues: 16.8275 Evaluate side-chains 53 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.040213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.030499 restraints weight = 38888.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.031562 restraints weight = 22497.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.032297 restraints weight = 15473.670| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6648 Z= 0.167 Angle : 0.508 8.932 9020 Z= 0.254 Chirality : 0.039 0.181 945 Planarity : 0.004 0.059 1160 Dihedral : 3.841 17.950 931 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 3.17 % Allowed : 24.17 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.06 (0.31), residues: 786 helix: 1.61 (0.28), residues: 367 sheet: 0.89 (0.75), residues: 49 loop : -0.20 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 523 TYR 0.009 0.001 TYR A 51 ARG 0.006 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7540 (p) REVERT: A 124 MET cc_start: 0.9394 (mmm) cc_final: 0.9118 (mmm) REVERT: A 249 MET cc_start: 0.9295 (mmm) cc_final: 0.9059 (mmm) REVERT: A 347 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8737 (p) REVERT: A 462 MET cc_start: 0.9634 (mmm) cc_final: 0.9092 (mmm) REVERT: A 474 MET cc_start: 0.9276 (mmt) cc_final: 0.8658 (mpp) outliers start: 22 outliers final: 11 residues processed: 59 average time/residue: 0.2007 time to fit residues: 16.2786 Evaluate side-chains 53 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 58 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.040568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.030959 restraints weight = 38691.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.032031 restraints weight = 21975.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.032771 restraints weight = 15154.469| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6648 Z= 0.143 Angle : 0.514 9.272 9020 Z= 0.255 Chirality : 0.039 0.183 945 Planarity : 0.004 0.059 1160 Dihedral : 3.697 16.273 931 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.16 % Favored : 97.71 % Rotamer: Outliers : 2.16 % Allowed : 24.46 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.07 (0.31), residues: 786 helix: 1.61 (0.28), residues: 367 sheet: 0.99 (0.73), residues: 49 loop : -0.19 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.003 0.000 HIS A 241 PHE 0.008 0.001 PHE A 438 TYR 0.008 0.001 TYR A 51 ARG 0.006 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7450 (p) REVERT: A 124 MET cc_start: 0.9378 (mmm) cc_final: 0.9096 (mmm) REVERT: A 162 LEU cc_start: 0.9750 (tp) cc_final: 0.9486 (pp) REVERT: A 347 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8768 (p) REVERT: A 462 MET cc_start: 0.9634 (mmm) cc_final: 0.9111 (mmm) REVERT: A 474 MET cc_start: 0.9227 (mmt) cc_final: 0.8842 (mpp) REVERT: B 406 GLU cc_start: 0.9025 (tp30) cc_final: 0.8785 (tp30) outliers start: 15 outliers final: 11 residues processed: 55 average time/residue: 0.1920 time to fit residues: 14.4738 Evaluate side-chains 53 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 54.8068 > 50: distance: 3 - 25: 3.331 distance: 7 - 33: 3.594 distance: 16 - 39: 7.177 distance: 23 - 48: 3.863 distance: 26 - 29: 3.218 distance: 29 - 30: 3.933 distance: 30 - 32: 4.575 distance: 33 - 34: 4.185 distance: 34 - 35: 3.819 distance: 35 - 36: 5.715 distance: 35 - 39: 7.213 distance: 37 - 38: 8.932 distance: 38 - 119: 8.955 distance: 40 - 41: 5.035 distance: 40 - 43: 4.113 distance: 41 - 42: 15.779 distance: 41 - 48: 9.184 distance: 43 - 44: 10.475 distance: 44 - 45: 13.192 distance: 45 - 46: 9.080 distance: 48 - 49: 5.986 distance: 49 - 50: 8.340 distance: 50 - 51: 9.913 distance: 52 - 53: 5.193 distance: 52 - 54: 4.683 distance: 55 - 56: 3.910 distance: 56 - 57: 5.659 distance: 56 - 59: 9.423 distance: 57 - 58: 11.066 distance: 57 - 60: 5.014 distance: 60 - 61: 4.572 distance: 61 - 64: 5.837 distance: 62 - 63: 5.637 distance: 62 - 68: 3.147 distance: 64 - 65: 4.586 distance: 65 - 67: 5.434 distance: 69 - 70: 7.711 distance: 69 - 72: 9.532 distance: 70 - 71: 5.521 distance: 70 - 78: 10.372 distance: 72 - 73: 9.969 distance: 73 - 74: 9.677 distance: 73 - 75: 6.682 distance: 74 - 76: 6.667 distance: 75 - 77: 9.862 distance: 76 - 77: 6.157 distance: 78 - 79: 4.927 distance: 79 - 80: 7.299 distance: 79 - 82: 8.686 distance: 80 - 81: 30.615 distance: 80 - 87: 24.668 distance: 82 - 83: 8.544 distance: 83 - 84: 4.627 distance: 84 - 85: 6.487 distance: 84 - 86: 4.065 distance: 87 - 88: 7.828 distance: 88 - 89: 12.424 distance: 89 - 90: 14.246 distance: 89 - 91: 9.888 distance: 91 - 92: 14.081 distance: 92 - 93: 14.129 distance: 92 - 95: 5.776 distance: 93 - 94: 15.038 distance: 93 - 96: 14.815