Starting phenix.real_space_refine on Sun May 11 19:08:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ket_37167/05_2025/8ket_37167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ket_37167/05_2025/8ket_37167.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/8ket_37167/05_2025/8ket_37167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ket_37167/05_2025/8ket_37167.map" model { file = "/net/cci-nas-00/data/ceres_data/8ket_37167/05_2025/8ket_37167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ket_37167/05_2025/8ket_37167.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= 0.000 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 5200 2.51 5 N 1531 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8399 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1323 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 7, 'TRANS': 258} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 918 Unresolved non-hydrogen angles: 1184 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 8, 'TYR:plan': 13, 'ASN:plan1': 3, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 27, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 487 Chain: "B" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1436 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 7, 'TRANS': 259} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 805 Unresolved non-hydrogen angles: 1034 Unresolved non-hydrogen dihedrals: 697 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 3, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 25, 'GLU:plan': 9, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 427 Chain: "F" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1801 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 21, 'TRANS': 234} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 175 Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "C" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 3682 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 9, 'TRANS': 527} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 578 Unresolved non-hydrogen angles: 734 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 5, 'TYR:plan': 14, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 366 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 2, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.61, per 1000 atoms: 0.67 Number of scatterers: 8399 At special positions: 0 Unit cell: (98.44, 105.93, 148.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1643 8.00 N 1531 7.00 C 5200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 79 " - pdb=" SG CYS F 261 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 199 " - pdb=" SG CYS F 232 " distance=2.03 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 539 " distance=2.02 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 ALPHA1-4 " NAG D 2 " - " MAN D 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 6 " BETA1-3 " NAG D 1 " - " NAG D 2 " " MAN D 4 " - " BMA D 5 " BETA1-4 " MAN D 3 " - " BMA D 7 " NAG-ASN " NAG C 801 " - " ASN C 217 " " NAG C 802 " - " ASN C 272 " " NAG C 803 " - " ASN C 431 " " NAG C 804 " - " ASN C 608 " " NAG D 1 " - " ASN H 350 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2496 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 5 sheets defined 72.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 1 through 26 removed outlier: 4.209A pdb=" N LEU A 25 " --> pdb=" O HIS A 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 39 through 66 Processing helix chain 'A' and resid 72 through 96 removed outlier: 3.672A pdb=" N THR A 86 " --> pdb=" O TRP A 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 130 removed outlier: 4.007A pdb=" N VAL A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 166 Processing helix chain 'A' and resid 169 through 200 removed outlier: 4.230A pdb=" N VAL A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 237 removed outlier: 4.403A pdb=" N ALA A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 266 removed outlier: 3.564A pdb=" N TYR A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 removed outlier: 3.512A pdb=" N MET B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 25 " --> pdb=" O HIS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 39 through 66 removed outlier: 3.712A pdb=" N VAL B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 56 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 95 removed outlier: 3.671A pdb=" N TYR B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 93 " --> pdb=" O CYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 130 removed outlier: 3.550A pdb=" N ALA B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 166 Processing helix chain 'B' and resid 169 through 201 removed outlier: 4.294A pdb=" N VAL B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 236 removed outlier: 4.444A pdb=" N VAL B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 267 Processing helix chain 'F' and resid 99 through 111 removed outlier: 3.913A pdb=" N LEU F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 104 " --> pdb=" O PRO F 100 " (cutoff:3.500A) Proline residue: F 106 - end of helix removed outlier: 3.799A pdb=" N SER F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 169 removed outlier: 3.604A pdb=" N LEU F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 removed outlier: 4.401A pdb=" N SER F 245 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 286 removed outlier: 3.636A pdb=" N VAL F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 197 removed outlier: 3.620A pdb=" N ILE C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 216 removed outlier: 3.701A pdb=" N TYR C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.810A pdb=" N ARG C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 253 removed outlier: 3.587A pdb=" N GLU C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 268 removed outlier: 3.810A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.638A pdb=" N VAL C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 304 removed outlier: 3.582A pdb=" N TRP C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 329 removed outlier: 3.653A pdb=" N HIS C 317 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 321 " --> pdb=" O HIS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 348 Processing helix chain 'C' and resid 362 through 370 Processing helix chain 'C' and resid 372 through 385 Processing helix chain 'C' and resid 393 through 408 removed outlier: 3.656A pdb=" N ALA C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 423 Processing helix chain 'C' and resid 430 through 445 removed outlier: 3.828A pdb=" N ALA C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 460 Processing helix chain 'C' and resid 466 through 481 removed outlier: 3.740A pdb=" N LYS C 476 " --> pdb=" O LYS C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 495 removed outlier: 3.516A pdb=" N LEU C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET C 492 " --> pdb=" O GLN C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.768A pdb=" N GLN C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 532 removed outlier: 3.524A pdb=" N SER C 531 " --> pdb=" O GLN C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 551 removed outlier: 3.796A pdb=" N ALA C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN C 548 " --> pdb=" O GLU C 544 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 549 " --> pdb=" O LEU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 Processing helix chain 'C' and resid 571 through 585 removed outlier: 3.536A pdb=" N VAL C 575 " --> pdb=" O TYR C 571 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 3.912A pdb=" N ALA C 594 " --> pdb=" O GLN C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 623 removed outlier: 3.813A pdb=" N HIS C 617 " --> pdb=" O ARG C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 640 removed outlier: 3.549A pdb=" N HIS C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 660 removed outlier: 3.538A pdb=" N SER C 658 " --> pdb=" O TYR C 654 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN C 660 " --> pdb=" O LEU C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 677 removed outlier: 3.582A pdb=" N MET C 667 " --> pdb=" O SER C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 698 removed outlier: 3.863A pdb=" N ALA C 694 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 723 removed outlier: 3.594A pdb=" N ALA C 708 " --> pdb=" O PRO C 704 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 43 through 46 removed outlier: 6.149A pdb=" N ARG F 44 " --> pdb=" O ILE F 259 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N CYS F 261 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN F 46 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N SER F 263 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ASP F 258 " --> pdb=" O PRO F 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE F 260 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASN F 65 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 10.543A pdb=" N LEU F 83 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N GLU F 63 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 122 through 125 removed outlier: 6.057A pdb=" N ILE F 131 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 149 " --> pdb=" O GLN F 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 178 through 181 Processing sheet with id=AA4, first strand: chain 'F' and resid 189 through 193 removed outlier: 7.310A pdb=" N SER F 208 " --> pdb=" O TYR F 234 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N VAL F 236 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR F 210 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE F 238 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET F 212 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR F 240 " --> pdb=" O MET F 212 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE F 214 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLU F 233 " --> pdb=" O GLU F 228 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU F 228 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU F 235 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL F 226 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL F 237 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 198 through 199 removed outlier: 3.732A pdb=" N ARG F 205 " --> pdb=" O CYS F 199 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2091 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: 2.47 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2333 1.34 - 1.46: 1558 1.46 - 1.58: 4583 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 8512 Sorted by residual: bond pdb=" CA ARG C 689 " pdb=" C ARG C 689 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.27e-02 6.20e+03 1.13e+01 bond pdb=" C6 MAN D 4 " pdb=" O6 MAN D 4 " ideal model delta sigma weight residual 1.407 1.466 -0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" CB CYS C 539 " pdb=" SG CYS C 539 " ideal model delta sigma weight residual 1.808 1.723 0.085 3.30e-02 9.18e+02 6.68e+00 bond pdb=" CA LYS C 688 " pdb=" C LYS C 688 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.29e-02 6.01e+03 5.31e+00 bond pdb=" C1 NAG C 803 " pdb=" O5 NAG C 803 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 ... (remaining 8507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 11280 1.85 - 3.69: 339 3.69 - 5.54: 50 5.54 - 7.39: 11 7.39 - 9.24: 5 Bond angle restraints: 11685 Sorted by residual: angle pdb=" CA TYR B 23 " pdb=" CB TYR B 23 " pdb=" CG TYR B 23 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CB LYS F 74 " pdb=" CG LYS F 74 " pdb=" CD LYS F 74 " ideal model delta sigma weight residual 111.30 119.37 -8.07 2.30e+00 1.89e-01 1.23e+01 angle pdb=" C GLN F 203 " pdb=" N ASN F 204 " pdb=" CA ASN F 204 " ideal model delta sigma weight residual 122.46 127.17 -4.71 1.41e+00 5.03e-01 1.12e+01 angle pdb=" CB GLN C 240 " pdb=" CG GLN C 240 " pdb=" CD GLN C 240 " ideal model delta sigma weight residual 112.60 117.87 -5.27 1.70e+00 3.46e-01 9.61e+00 angle pdb=" N GLU C 432 " pdb=" CA GLU C 432 " pdb=" C GLU C 432 " ideal model delta sigma weight residual 111.07 114.18 -3.11 1.07e+00 8.73e-01 8.43e+00 ... (remaining 11680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 4783 25.69 - 51.38: 274 51.38 - 77.07: 39 77.07 - 102.76: 31 102.76 - 128.45: 21 Dihedral angle restraints: 5148 sinusoidal: 1284 harmonic: 3864 Sorted by residual: dihedral pdb=" CA CYS C 539 " pdb=" C CYS C 539 " pdb=" N HIS C 540 " pdb=" CA HIS C 540 " ideal model delta harmonic sigma weight residual -180.00 -153.89 -26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA CYS C 311 " pdb=" C CYS C 311 " pdb=" N GLU C 312 " pdb=" CA GLU C 312 " ideal model delta harmonic sigma weight residual 180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA SER F 38 " pdb=" C SER F 38 " pdb=" N ASP F 39 " pdb=" CA ASP F 39 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 5145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 1446 0.257 - 0.515: 0 0.515 - 0.772: 1 0.772 - 1.029: 0 1.029 - 1.286: 1 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C1 MAN D 3 " pdb=" O4 NAG D 2 " pdb=" C2 MAN D 3 " pdb=" O5 MAN D 3 " both_signs ideal model delta sigma weight residual False 2.40 1.87 0.53 2.00e-02 2.50e+03 7.01e+02 chirality pdb=" C1 MAN D 6 " pdb=" O6 MAN D 4 " pdb=" C2 MAN D 6 " pdb=" O5 MAN D 6 " both_signs ideal model delta sigma weight residual False 2.40 2.65 -0.25 2.00e-02 2.50e+03 1.53e+02 chirality pdb=" C1 BMA D 7 " pdb=" O4 MAN D 3 " pdb=" C2 BMA D 7 " pdb=" O5 BMA D 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.23e+01 ... (remaining 1445 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.342 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG D 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.103 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.297 2.00e-02 2.50e+03 2.50e-01 7.80e+02 pdb=" C7 NAG D 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.427 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 608 " 0.032 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" CG ASN C 608 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C 608 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 608 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG C 804 " 0.034 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1822 2.77 - 3.30: 7904 3.30 - 3.84: 13859 3.84 - 4.37: 14220 4.37 - 4.90: 25501 Nonbonded interactions: 63306 Sorted by model distance: nonbonded pdb=" O SER C 273 " pdb=" OG SER C 273 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP C 635 " pdb=" OH TYR C 654 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP C 598 " pdb=" OH TYR C 636 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR F 122 " pdb=" O TYR F 134 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR F 61 " pdb=" O ASP F 258 " model vdw 2.300 3.040 ... (remaining 63301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (name N or name CA or name C or name O or name CB )) selection = (chain 'B' and ((resid 1 through 57 and (name N or name CA or name C or name O o \ r name CB )) or resid 58 through 266)) } 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 22.500 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 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 : 0.004 0.085 8527 Z= 0.209 Angle : 0.793 11.972 11726 Z= 0.414 Chirality : 0.057 1.286 1448 Planarity : 0.011 0.297 1568 Dihedral : 21.356 128.454 2640 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 1.70 % Allowed : 26.75 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.90 (0.20), residues: 1317 helix: -0.99 (0.14), residues: 923 sheet: -0.61 (0.60), residues: 81 loop : -1.69 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 555 HIS 0.007 0.001 HIS C 540 PHE 0.009 0.001 PHE F 260 TYR 0.035 0.002 TYR F 123 ARG 0.014 0.001 ARG F 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00909 ( 5) link_NAG-ASN : angle 5.70466 ( 15) link_ALPHA1-4 : bond 0.00807 ( 1) link_ALPHA1-4 : angle 7.55633 ( 3) link_ALPHA1-6 : bond 0.02556 ( 2) link_ALPHA1-6 : angle 5.14733 ( 6) link_BETA1-4 : bond 0.00615 ( 1) link_BETA1-4 : angle 1.99040 ( 3) hydrogen bonds : bond 0.23284 ( 703) hydrogen bonds : angle 7.49306 ( 2091) SS BOND : bond 0.00621 ( 4) SS BOND : angle 4.34475 ( 8) link_BETA1-3 : bond 0.00268 ( 2) link_BETA1-3 : angle 1.63279 ( 6) covalent geometry : bond 0.00415 ( 8512) covalent geometry : angle 0.73905 (11685) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 285 ARG cc_start: 0.6799 (ttp-110) cc_final: 0.6574 (ttm-80) outliers start: 8 outliers final: 6 residues processed: 138 average time/residue: 0.1866 time to fit residues: 36.1578 Evaluate side-chains 137 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 269 PHE Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 541 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 30.0000 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 40.0000 chunk 61 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 130 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.268777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.241188 restraints weight = 9466.567| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 1.14 r_work: 0.4283 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 8527 Z= 0.328 Angle : 0.760 10.395 11726 Z= 0.377 Chirality : 0.048 0.376 1448 Planarity : 0.006 0.069 1568 Dihedral : 15.795 115.532 1624 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 5.73 % Allowed : 24.20 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.22), residues: 1317 helix: 0.70 (0.16), residues: 933 sheet: -0.92 (0.56), residues: 79 loop : -1.79 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 302 HIS 0.011 0.002 HIS C 518 PHE 0.019 0.002 PHE C 668 TYR 0.020 0.002 TYR B 30 ARG 0.005 0.001 ARG F 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00971 ( 5) link_NAG-ASN : angle 4.69980 ( 15) link_ALPHA1-4 : bond 0.00724 ( 1) link_ALPHA1-4 : angle 1.98757 ( 3) link_ALPHA1-6 : bond 0.01383 ( 2) link_ALPHA1-6 : angle 2.29536 ( 6) link_BETA1-4 : bond 0.00417 ( 1) link_BETA1-4 : angle 4.36026 ( 3) hydrogen bonds : bond 0.04668 ( 703) hydrogen bonds : angle 4.15479 ( 2091) SS BOND : bond 0.00333 ( 4) SS BOND : angle 2.99656 ( 8) link_BETA1-3 : bond 0.00806 ( 2) link_BETA1-3 : angle 1.86531 ( 6) covalent geometry : bond 0.00770 ( 8512) covalent geometry : angle 0.73112 (11685) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: F 258 ASP cc_start: 0.8012 (p0) cc_final: 0.7734 (p0) REVERT: C 223 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: C 578 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: C 587 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8090 (tm-30) outliers start: 27 outliers final: 20 residues processed: 151 average time/residue: 0.1983 time to fit residues: 41.7005 Evaluate side-chains 146 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 105 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 104 optimal weight: 0.1980 chunk 116 optimal weight: 0.7980 chunk 48 optimal weight: 50.0000 chunk 12 optimal weight: 40.0000 chunk 18 optimal weight: 40.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.275315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.246977 restraints weight = 9578.336| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 1.55 r_work: 0.4242 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8527 Z= 0.121 Angle : 0.599 9.385 11726 Z= 0.285 Chirality : 0.042 0.315 1448 Planarity : 0.004 0.053 1568 Dihedral : 13.100 117.915 1622 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 4.67 % Allowed : 25.90 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.23), residues: 1317 helix: 1.69 (0.16), residues: 938 sheet: -1.22 (0.57), residues: 79 loop : -1.64 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 121 HIS 0.003 0.001 HIS C 674 PHE 0.008 0.001 PHE F 43 TYR 0.013 0.001 TYR F 120 ARG 0.003 0.000 ARG F 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00735 ( 5) link_NAG-ASN : angle 3.79459 ( 15) link_ALPHA1-4 : bond 0.01300 ( 1) link_ALPHA1-4 : angle 2.76826 ( 3) link_ALPHA1-6 : bond 0.01004 ( 2) link_ALPHA1-6 : angle 2.35191 ( 6) link_BETA1-4 : bond 0.01279 ( 1) link_BETA1-4 : angle 2.98496 ( 3) hydrogen bonds : bond 0.03217 ( 703) hydrogen bonds : angle 3.32077 ( 2091) SS BOND : bond 0.00356 ( 4) SS BOND : angle 2.39649 ( 8) link_BETA1-3 : bond 0.00944 ( 2) link_BETA1-3 : angle 1.77152 ( 6) covalent geometry : bond 0.00253 ( 8512) covalent geometry : angle 0.57359 (11685) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 258 ASP cc_start: 0.8020 (p0) cc_final: 0.7711 (p0) REVERT: C 209 TYR cc_start: 0.5759 (m-80) cc_final: 0.5539 (m-80) REVERT: C 235 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8396 (mp) outliers start: 22 outliers final: 12 residues processed: 155 average time/residue: 0.1815 time to fit residues: 39.6582 Evaluate side-chains 141 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 683 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 68 optimal weight: 0.0030 chunk 18 optimal weight: 40.0000 chunk 100 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.274294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.246797 restraints weight = 9454.005| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 1.10 r_work: 0.4283 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8527 Z= 0.131 Angle : 0.600 9.286 11726 Z= 0.282 Chirality : 0.042 0.319 1448 Planarity : 0.004 0.048 1568 Dihedral : 11.093 118.558 1617 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 4.46 % Allowed : 24.84 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.70 (0.23), residues: 1317 helix: 2.15 (0.17), residues: 938 sheet: -1.39 (0.56), residues: 79 loop : -1.53 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 302 HIS 0.007 0.001 HIS F 130 PHE 0.017 0.001 PHE C 706 TYR 0.016 0.001 TYR C 234 ARG 0.004 0.000 ARG F 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 5) link_NAG-ASN : angle 3.68558 ( 15) link_ALPHA1-4 : bond 0.01014 ( 1) link_ALPHA1-4 : angle 2.66106 ( 3) link_ALPHA1-6 : bond 0.01246 ( 2) link_ALPHA1-6 : angle 2.37054 ( 6) link_BETA1-4 : bond 0.01033 ( 1) link_BETA1-4 : angle 4.25962 ( 3) hydrogen bonds : bond 0.02863 ( 703) hydrogen bonds : angle 3.13034 ( 2091) SS BOND : bond 0.00435 ( 4) SS BOND : angle 2.29491 ( 8) link_BETA1-3 : bond 0.00818 ( 2) link_BETA1-3 : angle 1.59837 ( 6) covalent geometry : bond 0.00293 ( 8512) covalent geometry : angle 0.57366 (11685) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 234 TYR cc_start: 0.7647 (m-80) cc_final: 0.7258 (m-80) REVERT: F 258 ASP cc_start: 0.7994 (p0) cc_final: 0.7660 (p0) REVERT: C 235 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8370 (mp) REVERT: C 587 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8047 (tm-30) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 0.1825 time to fit residues: 39.6038 Evaluate side-chains 144 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 539 CYS Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 110 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 42 optimal weight: 0.4980 chunk 24 optimal weight: 40.0000 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 6 optimal weight: 50.0000 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.273435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.249186 restraints weight = 9400.586| |-----------------------------------------------------------------------------| r_work (start): 0.4726 rms_B_bonded: 1.25 r_work: 0.4331 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4016 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8527 Z= 0.160 Angle : 0.595 10.171 11726 Z= 0.284 Chirality : 0.042 0.296 1448 Planarity : 0.004 0.045 1568 Dihedral : 9.940 119.213 1615 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer: Outliers : 5.52 % Allowed : 25.05 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.92 (0.24), residues: 1317 helix: 2.33 (0.17), residues: 937 sheet: -1.51 (0.57), residues: 80 loop : -1.43 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 121 HIS 0.008 0.001 HIS F 130 PHE 0.014 0.001 PHE C 668 TYR 0.015 0.001 TYR F 120 ARG 0.002 0.000 ARG F 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 5) link_NAG-ASN : angle 3.19716 ( 15) link_ALPHA1-4 : bond 0.00834 ( 1) link_ALPHA1-4 : angle 3.03915 ( 3) link_ALPHA1-6 : bond 0.01601 ( 2) link_ALPHA1-6 : angle 2.76678 ( 6) link_BETA1-4 : bond 0.00899 ( 1) link_BETA1-4 : angle 4.30401 ( 3) hydrogen bonds : bond 0.02856 ( 703) hydrogen bonds : angle 3.11466 ( 2091) SS BOND : bond 0.00544 ( 4) SS BOND : angle 2.22970 ( 8) link_BETA1-3 : bond 0.00944 ( 2) link_BETA1-3 : angle 1.44923 ( 6) covalent geometry : bond 0.00366 ( 8512) covalent geometry : angle 0.57118 (11685) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 234 TYR cc_start: 0.7959 (m-80) cc_final: 0.7316 (m-80) REVERT: F 258 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7738 (p0) REVERT: C 235 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8540 (mp) REVERT: C 587 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8163 (tm-30) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 0.1848 time to fit residues: 37.7256 Evaluate side-chains 146 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 539 CYS Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7182 > 50: distance: 48 - 53: 23.426 distance: 53 - 54: 36.592 distance: 54 - 55: 67.866 distance: 55 - 56: 40.244 distance: 55 - 57: 61.245 distance: 57 - 58: 39.735 distance: 58 - 59: 36.929 distance: 58 - 61: 34.645 distance: 59 - 60: 37.024 distance: 59 - 66: 45.838 distance: 61 - 62: 34.100 distance: 62 - 63: 31.061 distance: 63 - 64: 41.020 distance: 63 - 65: 31.111 distance: 66 - 67: 46.755 distance: 67 - 68: 39.026 distance: 67 - 70: 55.604 distance: 68 - 69: 58.163 distance: 68 - 74: 39.780 distance: 70 - 71: 41.316 distance: 71 - 72: 29.420 distance: 71 - 73: 45.184 distance: 73 - 193: 26.872 distance: 74 - 75: 37.047 distance: 75 - 76: 67.535 distance: 75 - 78: 39.984 distance: 76 - 77: 38.865 distance: 76 - 83: 50.629 distance: 78 - 79: 23.548 distance: 79 - 80: 28.713 distance: 80 - 81: 16.278 distance: 80 - 82: 18.879 distance: 83 - 84: 64.092 distance: 84 - 85: 55.975 distance: 84 - 87: 70.153 distance: 85 - 86: 57.490 distance: 85 - 90: 40.370 distance: 86 - 120: 44.860 distance: 87 - 88: 56.514 distance: 87 - 89: 55.543 distance: 91 - 92: 41.124 distance: 91 - 94: 53.319 distance: 92 - 93: 40.357 distance: 92 - 102: 59.707 distance: 93 - 125: 17.619 distance: 94 - 95: 38.792 distance: 95 - 96: 33.544 distance: 95 - 97: 16.096 distance: 96 - 98: 50.496 distance: 97 - 99: 51.510 distance: 98 - 100: 29.527 distance: 99 - 100: 15.848 distance: 100 - 101: 22.690 distance: 102 - 103: 45.652 distance: 102 - 108: 58.877 distance: 103 - 104: 58.128 distance: 103 - 106: 57.155 distance: 104 - 105: 45.414 distance: 104 - 109: 43.026 distance: 105 - 133: 27.924 distance: 106 - 107: 57.724 distance: 107 - 108: 68.674 distance: 110 - 111: 58.004 distance: 110 - 113: 47.482 distance: 111 - 112: 38.990 distance: 111 - 120: 23.416 distance: 113 - 114: 48.519 distance: 114 - 115: 18.462 distance: 115 - 116: 40.842 distance: 116 - 117: 60.845 distance: 117 - 118: 57.467 distance: 117 - 119: 56.922 distance: 120 - 121: 42.990 distance: 121 - 122: 40.879 distance: 121 - 124: 37.565 distance: 122 - 123: 51.367 distance: 122 - 125: 45.453 distance: 123 - 150: 34.364 distance: 125 - 126: 36.202 distance: 126 - 127: 36.486 distance: 126 - 129: 39.810 distance: 127 - 128: 16.336 distance: 127 - 133: 29.283 distance: 128 - 160: 34.970 distance: 129 - 130: 42.426 distance: 130 - 131: 41.303 distance: 130 - 132: 27.675