Starting phenix.real_space_refine on Tue May 13 22:02:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x52_38059/05_2025/8x52_38059.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x52_38059/05_2025/8x52_38059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x52_38059/05_2025/8x52_38059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x52_38059/05_2025/8x52_38059.map" model { file = "/net/cci-nas-00/data/ceres_data/8x52_38059/05_2025/8x52_38059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x52_38059/05_2025/8x52_38059.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.064 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 P 2 5.49 5 S 43 5.16 5 C 7142 2.51 5 N 1727 2.21 5 O 1993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10907 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 145 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "A" Number of atoms: 5233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5233 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2424 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'CLR': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 7.19, per 1000 atoms: 0.66 Number of scatterers: 10907 At special positions: 0 Unit cell: (109.79, 95.5173, 131.748, 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) S 43 16.00 P 2 15.00 O 1993 8.00 N 1727 7.00 C 7142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS A 242 " distance=1.47 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA G 3 " - " BMA G 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 55 " " NAG H 1 " - " ASN A 435 " " NAG I 1 " - " ASN A 573 " " NAG J 1 " - " ASN A 530 " " NAG K 1 " - " ASN A 562 " Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.3 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 58.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'E' and resid 30 through 37 removed outlier: 3.614A pdb=" N LEU E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 42 removed outlier: 3.536A pdb=" N ILE E 41 " --> pdb=" O GLY E 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 79 through 87 removed outlier: 4.052A pdb=" N GLN A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.948A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.597A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.888A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.513A pdb=" N SER A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.767A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.072A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.555A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.699A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.724A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.751A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.775A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 78 through 103 removed outlier: 3.898A pdb=" N VAL B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 156 Processing helix chain 'B' and resid 158 through 175 removed outlier: 4.032A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.919A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.969A pdb=" N PHE B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 429 removed outlier: 3.977A pdb=" N THR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 450 removed outlier: 4.187A pdb=" N PHE B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.626A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.903A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 103 removed outlier: 3.739A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 3.534A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.768A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.872A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.661A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.790A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.591A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 81 removed outlier: 4.129A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing sheet with id=AA1, first strand: chain 'B' and resid 288 through 289 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.765A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 94 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY A 120 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA4, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.550A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 275 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL A 363 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 365 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA A 279 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.509A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.551A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1668 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: 3.44 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 71 1.23 - 1.37: 3543 1.37 - 1.52: 4934 1.52 - 1.67: 2566 1.67 - 1.81: 66 Bond restraints: 11180 Sorted by residual: bond pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 1.467 1.685 -0.218 1.17e-02 7.31e+03 3.48e+02 bond pdb=" C GLY B 384 " pdb=" O GLY B 384 " ideal model delta sigma weight residual 1.236 1.090 0.146 1.08e-02 8.57e+03 1.82e+02 bond pdb=" C LEU B 435 " pdb=" N PRO B 436 " ideal model delta sigma weight residual 1.335 1.501 -0.166 1.38e-02 5.25e+03 1.45e+02 bond pdb=" C PRO B 433 " pdb=" O PRO B 433 " ideal model delta sigma weight residual 1.233 1.080 0.153 1.39e-02 5.18e+03 1.22e+02 bond pdb=" C LEU B 435 " pdb=" O LEU B 435 " ideal model delta sigma weight residual 1.244 1.150 0.094 9.10e-03 1.21e+04 1.07e+02 ... (remaining 11175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 15170 5.73 - 11.46: 62 11.46 - 17.18: 10 17.18 - 22.91: 0 22.91 - 28.64: 1 Bond angle restraints: 15243 Sorted by residual: angle pdb=" N GLY C 233 " pdb=" CA GLY C 233 " pdb=" C GLY C 233 " ideal model delta sigma weight residual 115.43 144.07 -28.64 1.41e+00 5.03e-01 4.13e+02 angle pdb=" C LEU B 432 " pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 119.93 137.02 -17.09 1.07e+00 8.73e-01 2.55e+02 angle pdb=" CA LEU B 435 " pdb=" C LEU B 435 " pdb=" N PRO B 436 " ideal model delta sigma weight residual 120.58 130.94 -10.36 7.40e-01 1.83e+00 1.96e+02 angle pdb=" C LEU B 435 " pdb=" N PRO B 436 " pdb=" CA PRO B 436 " ideal model delta sigma weight residual 119.24 131.85 -12.61 1.04e+00 9.25e-01 1.47e+02 angle pdb=" O LEU B 432 " pdb=" C LEU B 432 " pdb=" N PRO B 433 " ideal model delta sigma weight residual 121.72 111.32 10.40 9.80e-01 1.04e+00 1.13e+02 ... (remaining 15238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 6630 23.49 - 46.98: 207 46.98 - 70.46: 43 70.46 - 93.95: 21 93.95 - 117.44: 18 Dihedral angle restraints: 6919 sinusoidal: 3033 harmonic: 3886 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -164.69 78.69 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" C PHE B 386 " pdb=" N PHE B 386 " pdb=" CA PHE B 386 " pdb=" CB PHE B 386 " ideal model delta harmonic sigma weight residual -122.60 -104.19 -18.41 0 2.50e+00 1.60e-01 5.42e+01 dihedral pdb=" CB CYS E 28 " pdb=" SG CYS E 28 " pdb=" SG CYS A 242 " pdb=" CB CYS A 242 " ideal model delta sinusoidal sigma weight residual 93.00 30.42 62.58 1 1.00e+01 1.00e-02 5.18e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1782 0.146 - 0.292: 36 0.292 - 0.438: 10 0.438 - 0.584: 1 0.584 - 0.730: 1 Chirality restraints: 1830 Sorted by residual: chirality pdb=" CA PRO B 433 " pdb=" N PRO B 433 " pdb=" C PRO B 433 " pdb=" CB PRO B 433 " both_signs ideal model delta sigma weight residual False 2.72 3.45 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 1827 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 573 " 0.117 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN A 573 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " -0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " -0.013 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 114 " 0.021 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ILE B 114 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE B 114 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR B 115 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 284 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C PRO B 284 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO B 284 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 285 " 0.022 2.00e-02 2.50e+03 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 3 2.26 - 2.92: 4391 2.92 - 3.58: 15318 3.58 - 4.24: 25252 4.24 - 4.90: 42436 Nonbonded interactions: 87400 Sorted by model distance: nonbonded pdb=" OD1 ASN A 573 " pdb=" C1 NAG I 1 " model vdw 1.598 2.776 nonbonded pdb=" OH TYR B 389 " pdb=" O ALA B 434 " model vdw 2.168 3.040 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.263 3.040 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.297 3.040 ... (remaining 87395 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 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.320 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 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 : 0.017 1.465 11206 Z= 0.918 Angle : 1.455 66.549 15316 Z= 0.771 Chirality : 0.066 0.730 1830 Planarity : 0.007 0.071 1845 Dihedral : 14.341 117.440 4400 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.69 % Favored : 95.16 % Rotamer: Outliers : 0.88 % Allowed : 2.98 % Favored : 96.14 % Cbeta Deviations : 0.56 % 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: -3.49 (0.18), residues: 1322 helix: -1.90 (0.15), residues: 722 sheet: -1.54 (0.47), residues: 114 loop : -2.97 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP C 227 HIS 0.024 0.003 HIS C 197 PHE 0.040 0.003 PHE B 386 TYR 0.035 0.003 TYR A 565 ARG 0.009 0.001 ARG A 626 Details of bonding type rmsd link_NAG-ASN : bond 0.42302 ( 12) link_NAG-ASN : angle 15.17502 ( 36) link_BETA1-4 : bond 0.00225 ( 7) link_BETA1-4 : angle 2.21319 ( 21) hydrogen bonds : bond 0.19489 ( 579) hydrogen bonds : angle 7.11599 ( 1668) link_BETA1-6 : bond 0.00494 ( 1) link_BETA1-6 : angle 1.46481 ( 3) SS BOND : bond 0.25216 ( 5) SS BOND : angle 21.23594 ( 10) link_BETA1-3 : bond 0.00009 ( 1) link_BETA1-3 : angle 1.61013 ( 3) covalent geometry : bond 0.00897 (11180) covalent geometry : angle 1.13135 (15243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 267 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.6147 (m110) cc_final: 0.5830 (m110) REVERT: A 37 GLU cc_start: 0.6912 (pt0) cc_final: 0.6573 (pt0) REVERT: A 58 HIS cc_start: 0.6969 (m90) cc_final: 0.6035 (m90) REVERT: A 78 LYS cc_start: 0.6766 (ptpt) cc_final: 0.6278 (pttm) REVERT: A 81 ASP cc_start: 0.5412 (m-30) cc_final: 0.4677 (m-30) REVERT: A 143 ASP cc_start: 0.6268 (t0) cc_final: 0.6011 (t70) REVERT: A 201 LEU cc_start: 0.7606 (mt) cc_final: 0.7318 (mm) REVERT: A 224 VAL cc_start: 0.7972 (m) cc_final: 0.7630 (t) REVERT: A 237 GLN cc_start: 0.6411 (mm-40) cc_final: 0.5699 (tm-30) REVERT: A 357 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7748 (pm20) REVERT: A 374 LEU cc_start: 0.7211 (mt) cc_final: 0.6950 (mp) REVERT: A 391 ARG cc_start: 0.6665 (ttp-110) cc_final: 0.6204 (ttm110) REVERT: A 392 ASN cc_start: 0.7428 (m-40) cc_final: 0.7098 (m-40) REVERT: A 474 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6715 (mp0) REVERT: A 478 ASN cc_start: 0.7820 (m-40) cc_final: 0.7455 (m-40) REVERT: A 500 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7190 (tt0) REVERT: A 509 ASP cc_start: 0.7397 (m-30) cc_final: 0.6425 (p0) REVERT: A 540 GLN cc_start: 0.7852 (tt0) cc_final: 0.7600 (tp40) REVERT: A 543 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6667 (mtm110) REVERT: A 565 TYR cc_start: 0.7732 (m-80) cc_final: 0.7311 (m-80) REVERT: A 666 LYS cc_start: 0.5949 (tptt) cc_final: 0.5542 (ttpt) REVERT: B 80 LYS cc_start: 0.6672 (tptt) cc_final: 0.6377 (tptt) REVERT: B 130 LEU cc_start: 0.7391 (tp) cc_final: 0.7126 (mm) REVERT: B 155 LYS cc_start: 0.7243 (tptt) cc_final: 0.7018 (tttm) REVERT: B 163 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7410 (m-70) REVERT: B 187 LYS cc_start: 0.6847 (mttp) cc_final: 0.6624 (mtmp) REVERT: B 380 LYS cc_start: 0.7257 (mttm) cc_final: 0.6939 (mptt) REVERT: C 52 VAL cc_start: 0.7687 (t) cc_final: 0.7318 (m) REVERT: C 56 LEU cc_start: 0.8019 (mt) cc_final: 0.7763 (mt) REVERT: C 119 TYR cc_start: 0.7007 (t80) cc_final: 0.6754 (t80) REVERT: C 140 ASP cc_start: 0.7438 (m-30) cc_final: 0.7043 (m-30) REVERT: C 146 VAL cc_start: 0.7406 (p) cc_final: 0.7086 (m) REVERT: D 59 ARG cc_start: 0.5719 (ttm170) cc_final: 0.5189 (tmt170) REVERT: D 84 ARG cc_start: 0.6642 (mtt90) cc_final: 0.6361 (mtm180) REVERT: D 91 TYR cc_start: 0.6352 (m-80) cc_final: 0.6149 (m-10) outliers start: 10 outliers final: 7 residues processed: 271 average time/residue: 0.9775 time to fit residues: 290.0305 Evaluate side-chains 168 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 194 GLN A 355 GLN A 358 ASN A 385 GLN A 393 GLN A 454 GLN A 531 ASN B 214 HIS B 405 ASN B 454 GLN B 463 HIS C 58 HIS C 68 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.152707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122921 restraints weight = 14419.891| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.29 r_work: 0.3379 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11206 Z= 0.160 Angle : 0.689 9.485 15316 Z= 0.335 Chirality : 0.045 0.403 1830 Planarity : 0.005 0.050 1845 Dihedral : 12.453 104.884 2084 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.24 % Allowed : 10.96 % Favored : 85.80 % 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: -1.25 (0.22), residues: 1322 helix: 0.20 (0.19), residues: 721 sheet: -1.11 (0.49), residues: 109 loop : -2.30 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 209 HIS 0.011 0.001 HIS C 197 PHE 0.037 0.002 PHE A 302 TYR 0.028 0.002 TYR A 645 ARG 0.008 0.001 ARG A 520 Details of bonding type rmsd link_NAG-ASN : bond 0.00841 ( 12) link_NAG-ASN : angle 3.27999 ( 36) link_BETA1-4 : bond 0.00473 ( 7) link_BETA1-4 : angle 2.00596 ( 21) hydrogen bonds : bond 0.04811 ( 579) hydrogen bonds : angle 4.58582 ( 1668) link_BETA1-6 : bond 0.01369 ( 1) link_BETA1-6 : angle 3.21455 ( 3) SS BOND : bond 0.00536 ( 5) SS BOND : angle 1.61783 ( 10) link_BETA1-3 : bond 0.00717 ( 1) link_BETA1-3 : angle 2.19590 ( 3) covalent geometry : bond 0.00359 (11180) covalent geometry : angle 0.66483 (15243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.6945 (tp) REVERT: A 58 HIS cc_start: 0.8100 (m90) cc_final: 0.7677 (m90) REVERT: A 81 ASP cc_start: 0.6338 (m-30) cc_final: 0.6040 (m-30) REVERT: A 237 GLN cc_start: 0.6966 (mm-40) cc_final: 0.6525 (tm-30) REVERT: A 391 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.7294 (ttm110) REVERT: A 392 ASN cc_start: 0.8118 (m-40) cc_final: 0.7773 (m-40) REVERT: A 509 ASP cc_start: 0.7434 (m-30) cc_final: 0.6637 (p0) REVERT: A 543 ARG cc_start: 0.7869 (mtm180) cc_final: 0.7585 (mtm110) REVERT: A 617 LEU cc_start: 0.8132 (mp) cc_final: 0.7795 (mm) REVERT: B 80 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7407 (tptt) REVERT: B 128 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7212 (ttp-170) REVERT: B 130 LEU cc_start: 0.8061 (tp) cc_final: 0.7860 (mm) REVERT: B 154 TYR cc_start: 0.8428 (t80) cc_final: 0.8139 (t80) REVERT: B 163 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7587 (m-70) REVERT: B 165 TRP cc_start: 0.8405 (t60) cc_final: 0.8110 (t60) REVERT: B 169 SER cc_start: 0.8604 (t) cc_final: 0.8090 (p) REVERT: B 184 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6870 (mm-30) REVERT: B 380 LYS cc_start: 0.7234 (mttm) cc_final: 0.6847 (mptt) REVERT: B 463 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8428 (m90) REVERT: C 140 ASP cc_start: 0.8277 (m-30) cc_final: 0.7898 (m-30) REVERT: D 59 ARG cc_start: 0.6627 (ttm170) cc_final: 0.6064 (tmt170) outliers start: 37 outliers final: 17 residues processed: 202 average time/residue: 0.9220 time to fit residues: 205.3458 Evaluate side-chains 157 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 113 optimal weight: 0.0270 chunk 94 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 47 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN A 531 ASN A 596 ASN B 463 HIS C 58 HIS D 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115042 restraints weight = 14645.872| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.29 r_work: 0.3278 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11206 Z= 0.149 Angle : 0.656 9.904 15316 Z= 0.312 Chirality : 0.045 0.385 1830 Planarity : 0.004 0.042 1845 Dihedral : 10.543 111.833 2078 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.65 % Favored : 97.28 % Rotamer: Outliers : 4.47 % Allowed : 13.41 % Favored : 82.12 % 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: -0.47 (0.23), residues: 1322 helix: 0.84 (0.19), residues: 732 sheet: -1.01 (0.47), residues: 116 loop : -1.97 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 209 HIS 0.023 0.002 HIS B 463 PHE 0.036 0.002 PHE A 302 TYR 0.016 0.001 TYR A 569 ARG 0.006 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 12) link_NAG-ASN : angle 3.27632 ( 36) link_BETA1-4 : bond 0.00427 ( 7) link_BETA1-4 : angle 2.03943 ( 21) hydrogen bonds : bond 0.04143 ( 579) hydrogen bonds : angle 4.22197 ( 1668) link_BETA1-6 : bond 0.01697 ( 1) link_BETA1-6 : angle 2.93274 ( 3) SS BOND : bond 0.00413 ( 5) SS BOND : angle 0.85727 ( 10) link_BETA1-3 : bond 0.00761 ( 1) link_BETA1-3 : angle 2.09227 ( 3) covalent geometry : bond 0.00349 (11180) covalent geometry : angle 0.63110 (15243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.6893 (tp) REVERT: A 58 HIS cc_start: 0.8676 (m90) cc_final: 0.8380 (m90) REVERT: A 391 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7470 (ttm110) REVERT: A 392 ASN cc_start: 0.8114 (m-40) cc_final: 0.7772 (m-40) REVERT: A 543 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7559 (mtm110) REVERT: A 617 LEU cc_start: 0.8236 (mp) cc_final: 0.7951 (mm) REVERT: A 624 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8574 (m) REVERT: A 693 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6825 (pttt) REVERT: B 128 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7143 (ttp-170) REVERT: B 130 LEU cc_start: 0.8079 (tp) cc_final: 0.7831 (mm) REVERT: B 154 TYR cc_start: 0.8329 (t80) cc_final: 0.8106 (t80) REVERT: B 163 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7586 (m-70) REVERT: B 169 SER cc_start: 0.8860 (t) cc_final: 0.8374 (p) REVERT: B 177 PHE cc_start: 0.8405 (m-80) cc_final: 0.8168 (m-80) REVERT: B 184 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7471 (mm-30) REVERT: B 380 LYS cc_start: 0.7704 (mttm) cc_final: 0.7240 (mptt) REVERT: C 31 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7802 (mtt180) REVERT: C 62 ARG cc_start: 0.6568 (mmt90) cc_final: 0.5756 (ttp80) REVERT: C 186 ARG cc_start: 0.8127 (ptp-170) cc_final: 0.7711 (ptp-170) REVERT: C 206 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8054 (mt) REVERT: D 59 ARG cc_start: 0.6961 (ttm170) cc_final: 0.6306 (tmt170) REVERT: D 84 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6933 (mtm180) outliers start: 51 outliers final: 20 residues processed: 174 average time/residue: 0.9508 time to fit residues: 182.3569 Evaluate side-chains 151 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 693 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105469 restraints weight = 14442.298| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.26 r_work: 0.3138 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11206 Z= 0.166 Angle : 0.651 11.447 15316 Z= 0.312 Chirality : 0.044 0.307 1830 Planarity : 0.004 0.038 1845 Dihedral : 9.477 107.468 2074 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 5.26 % Allowed : 15.16 % Favored : 79.58 % 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: -0.08 (0.23), residues: 1322 helix: 1.18 (0.20), residues: 732 sheet: -0.91 (0.47), residues: 118 loop : -1.80 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 209 HIS 0.007 0.002 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.027 0.002 TYR A 499 ARG 0.008 0.001 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 12) link_NAG-ASN : angle 2.74798 ( 36) link_BETA1-4 : bond 0.00442 ( 7) link_BETA1-4 : angle 1.94524 ( 21) hydrogen bonds : bond 0.03848 ( 579) hydrogen bonds : angle 4.09737 ( 1668) link_BETA1-6 : bond 0.01385 ( 1) link_BETA1-6 : angle 3.15594 ( 3) SS BOND : bond 0.00412 ( 5) SS BOND : angle 0.96659 ( 10) link_BETA1-3 : bond 0.00852 ( 1) link_BETA1-3 : angle 1.77006 ( 3) covalent geometry : bond 0.00386 (11180) covalent geometry : angle 0.63213 (15243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8413 (mp) REVERT: A 231 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8008 (mmp) REVERT: A 249 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7742 (p0) REVERT: A 391 ARG cc_start: 0.7661 (ttp-110) cc_final: 0.7392 (ttp-110) REVERT: A 392 ASN cc_start: 0.8091 (m-40) cc_final: 0.7766 (m-40) REVERT: A 543 ARG cc_start: 0.7865 (mtm180) cc_final: 0.7510 (mtm110) REVERT: A 582 THR cc_start: 0.7139 (OUTLIER) cc_final: 0.6646 (m) REVERT: A 617 LEU cc_start: 0.8365 (mp) cc_final: 0.8147 (mm) REVERT: A 624 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8763 (m) REVERT: A 655 ASP cc_start: 0.6336 (t0) cc_final: 0.5898 (t70) REVERT: B 80 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7444 (tppt) REVERT: B 128 ARG cc_start: 0.7650 (mtp180) cc_final: 0.7015 (ttp-170) REVERT: B 130 LEU cc_start: 0.8035 (tp) cc_final: 0.7800 (mm) REVERT: B 163 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7542 (m-70) REVERT: B 177 PHE cc_start: 0.8394 (m-80) cc_final: 0.8177 (m-80) REVERT: B 184 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7551 (mm-30) REVERT: B 253 ILE cc_start: 0.8179 (tt) cc_final: 0.7929 (tt) REVERT: C 62 ARG cc_start: 0.6649 (mmt90) cc_final: 0.6022 (ttp80) REVERT: C 186 ARG cc_start: 0.8133 (ptp-170) cc_final: 0.7831 (ptp-170) REVERT: C 206 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8101 (mt) REVERT: C 236 LEU cc_start: 0.8048 (mm) cc_final: 0.7735 (tp) REVERT: D 59 ARG cc_start: 0.7500 (ttm170) cc_final: 0.6665 (tmt170) REVERT: D 84 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7172 (mtm180) outliers start: 60 outliers final: 18 residues processed: 193 average time/residue: 0.9712 time to fit residues: 206.6020 Evaluate side-chains 154 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 72 optimal weight: 0.0570 chunk 26 optimal weight: 0.7980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 393 GLN A 585 GLN A 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104094 restraints weight = 14428.010| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.26 r_work: 0.3126 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11206 Z= 0.153 Angle : 0.641 11.346 15316 Z= 0.304 Chirality : 0.043 0.295 1830 Planarity : 0.004 0.038 1845 Dihedral : 9.098 94.211 2074 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.50 % Rotamer: Outliers : 4.21 % Allowed : 17.44 % Favored : 78.35 % 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: 0.19 (0.24), residues: 1322 helix: 1.42 (0.20), residues: 728 sheet: -0.89 (0.48), residues: 118 loop : -1.69 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.021 0.001 TYR A 499 ARG 0.007 0.001 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 12) link_NAG-ASN : angle 2.78774 ( 36) link_BETA1-4 : bond 0.00294 ( 7) link_BETA1-4 : angle 1.83424 ( 21) hydrogen bonds : bond 0.03638 ( 579) hydrogen bonds : angle 4.02355 ( 1668) link_BETA1-6 : bond 0.01706 ( 1) link_BETA1-6 : angle 3.39589 ( 3) SS BOND : bond 0.00409 ( 5) SS BOND : angle 2.31847 ( 10) link_BETA1-3 : bond 0.00518 ( 1) link_BETA1-3 : angle 1.60922 ( 3) covalent geometry : bond 0.00358 (11180) covalent geometry : angle 0.61905 (15243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8452 (pt0) cc_final: 0.8212 (pt0) REVERT: A 118 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8475 (mp) REVERT: A 249 ASP cc_start: 0.8160 (t0) cc_final: 0.7697 (p0) REVERT: A 253 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8397 (t0) REVERT: A 364 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: A 391 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7312 (ttm110) REVERT: A 392 ASN cc_start: 0.8037 (m-40) cc_final: 0.7587 (m-40) REVERT: A 482 ASP cc_start: 0.7741 (m-30) cc_final: 0.7319 (m-30) REVERT: A 540 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7969 (tp40) REVERT: A 543 ARG cc_start: 0.7792 (mtm180) cc_final: 0.7460 (mtm110) REVERT: A 617 LEU cc_start: 0.8403 (mp) cc_final: 0.8199 (mm) REVERT: A 624 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8772 (m) REVERT: A 655 ASP cc_start: 0.6439 (t0) cc_final: 0.5950 (t70) REVERT: B 128 ARG cc_start: 0.7603 (mtp180) cc_final: 0.6963 (ttp-170) REVERT: B 130 LEU cc_start: 0.8063 (tp) cc_final: 0.7820 (mm) REVERT: B 177 PHE cc_start: 0.8321 (m-80) cc_final: 0.8117 (m-80) REVERT: B 184 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7685 (mm-30) REVERT: B 253 ILE cc_start: 0.8216 (tt) cc_final: 0.7975 (tt) REVERT: B 457 MET cc_start: 0.9190 (tpp) cc_final: 0.8944 (mmt) REVERT: C 62 ARG cc_start: 0.6644 (mmt90) cc_final: 0.5974 (ttp80) REVERT: C 206 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8104 (mt) REVERT: C 236 LEU cc_start: 0.8041 (mm) cc_final: 0.7746 (tp) REVERT: D 59 ARG cc_start: 0.7552 (ttm170) cc_final: 0.6701 (tmt170) REVERT: D 65 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6820 (tm) REVERT: D 84 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7134 (mtm180) outliers start: 48 outliers final: 18 residues processed: 169 average time/residue: 0.9248 time to fit residues: 172.6034 Evaluate side-chains 153 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 118 optimal weight: 0.0000 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104659 restraints weight = 14484.271| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.25 r_work: 0.3139 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11206 Z= 0.125 Angle : 0.601 10.870 15316 Z= 0.286 Chirality : 0.042 0.282 1830 Planarity : 0.004 0.038 1845 Dihedral : 8.427 72.706 2072 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.20 % Rotamer: Outliers : 3.77 % Allowed : 18.32 % Favored : 77.91 % 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: 0.36 (0.24), residues: 1322 helix: 1.59 (0.20), residues: 729 sheet: -0.87 (0.47), residues: 123 loop : -1.64 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.019 0.001 TYR A 499 ARG 0.009 0.001 ARG C 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 12) link_NAG-ASN : angle 2.43073 ( 36) link_BETA1-4 : bond 0.00428 ( 7) link_BETA1-4 : angle 1.61069 ( 21) hydrogen bonds : bond 0.03325 ( 579) hydrogen bonds : angle 3.91283 ( 1668) link_BETA1-6 : bond 0.01465 ( 1) link_BETA1-6 : angle 3.44231 ( 3) SS BOND : bond 0.00388 ( 5) SS BOND : angle 1.27537 ( 10) link_BETA1-3 : bond 0.00656 ( 1) link_BETA1-3 : angle 1.43650 ( 3) covalent geometry : bond 0.00289 (11180) covalent geometry : angle 0.58482 (15243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8171 (tp) REVERT: A 37 GLU cc_start: 0.8524 (pt0) cc_final: 0.8286 (pt0) REVERT: A 237 GLN cc_start: 0.7214 (tp40) cc_final: 0.6709 (mm110) REVERT: A 249 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7773 (p0) REVERT: A 253 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8320 (t0) REVERT: A 259 MET cc_start: 0.9338 (tpt) cc_final: 0.9037 (tpp) REVERT: A 364 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: A 391 ARG cc_start: 0.7703 (ttp-110) cc_final: 0.7312 (ttm110) REVERT: A 392 ASN cc_start: 0.8093 (m-40) cc_final: 0.7674 (m-40) REVERT: A 482 ASP cc_start: 0.7799 (m-30) cc_final: 0.7456 (m-30) REVERT: A 540 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7949 (tp40) REVERT: A 543 ARG cc_start: 0.7799 (mtm180) cc_final: 0.7464 (mtm110) REVERT: A 587 GLN cc_start: 0.7998 (mm110) cc_final: 0.7712 (mp10) REVERT: A 624 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8685 (m) REVERT: A 655 ASP cc_start: 0.6409 (t0) cc_final: 0.5940 (t70) REVERT: A 677 PHE cc_start: 0.8312 (m-80) cc_final: 0.7970 (m-10) REVERT: B 130 LEU cc_start: 0.8049 (tp) cc_final: 0.7809 (mm) REVERT: B 147 THR cc_start: 0.6949 (m) cc_final: 0.6635 (m) REVERT: B 165 TRP cc_start: 0.8555 (t60) cc_final: 0.8068 (t60) REVERT: B 184 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 236 VAL cc_start: 0.7806 (t) cc_final: 0.7502 (p) REVERT: B 253 ILE cc_start: 0.8192 (tt) cc_final: 0.7947 (tt) REVERT: B 256 TYR cc_start: 0.7501 (t80) cc_final: 0.7286 (t80) REVERT: B 457 MET cc_start: 0.9164 (tpp) cc_final: 0.8959 (mmt) REVERT: C 55 ILE cc_start: 0.7505 (mt) cc_final: 0.7210 (mt) REVERT: C 62 ARG cc_start: 0.6678 (mmt90) cc_final: 0.6127 (ttp80) REVERT: D 59 ARG cc_start: 0.7571 (ttm170) cc_final: 0.6739 (mmt180) REVERT: D 84 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7160 (mtm180) outliers start: 43 outliers final: 17 residues processed: 172 average time/residue: 0.8972 time to fit residues: 170.5082 Evaluate side-chains 152 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 121 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 393 GLN A 585 GLN A 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100963 restraints weight = 14751.873| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.29 r_work: 0.3071 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 11206 Z= 0.170 Angle : 0.637 10.999 15316 Z= 0.303 Chirality : 0.044 0.277 1830 Planarity : 0.004 0.039 1845 Dihedral : 8.044 71.757 2071 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 4.03 % Allowed : 19.02 % Favored : 76.95 % 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: 0.36 (0.24), residues: 1322 helix: 1.56 (0.20), residues: 729 sheet: -0.88 (0.46), residues: 121 loop : -1.59 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 244 HIS 0.006 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.018 0.002 TYR A 499 ARG 0.005 0.001 ARG C 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 12) link_NAG-ASN : angle 2.51138 ( 36) link_BETA1-4 : bond 0.00315 ( 7) link_BETA1-4 : angle 1.73533 ( 21) hydrogen bonds : bond 0.03609 ( 579) hydrogen bonds : angle 3.98503 ( 1668) link_BETA1-6 : bond 0.01014 ( 1) link_BETA1-6 : angle 3.16581 ( 3) SS BOND : bond 0.00436 ( 5) SS BOND : angle 1.40499 ( 10) link_BETA1-3 : bond 0.00606 ( 1) link_BETA1-3 : angle 1.59495 ( 3) covalent geometry : bond 0.00408 (11180) covalent geometry : angle 0.62010 (15243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8172 (tp) REVERT: A 37 GLU cc_start: 0.8512 (pt0) cc_final: 0.8255 (pt0) REVERT: A 118 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8388 (mp) REVERT: A 249 ASP cc_start: 0.8108 (t0) cc_final: 0.7739 (p0) REVERT: A 253 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8440 (t0) REVERT: A 364 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: A 391 ARG cc_start: 0.7662 (ttp-110) cc_final: 0.7234 (ttm110) REVERT: A 392 ASN cc_start: 0.8051 (m-40) cc_final: 0.7674 (m-40) REVERT: A 482 ASP cc_start: 0.7870 (m-30) cc_final: 0.7573 (m-30) REVERT: A 543 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7527 (mtm-85) REVERT: A 587 GLN cc_start: 0.8088 (mm110) cc_final: 0.7801 (mp10) REVERT: A 624 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8785 (m) REVERT: A 655 ASP cc_start: 0.6731 (t0) cc_final: 0.6196 (t70) REVERT: A 677 PHE cc_start: 0.8308 (m-80) cc_final: 0.7938 (m-10) REVERT: B 130 LEU cc_start: 0.8042 (tp) cc_final: 0.7818 (mm) REVERT: B 147 THR cc_start: 0.7006 (m) cc_final: 0.6662 (m) REVERT: B 165 TRP cc_start: 0.8583 (t60) cc_final: 0.8100 (t60) REVERT: B 184 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 253 ILE cc_start: 0.8334 (tt) cc_final: 0.8103 (tt) REVERT: B 457 MET cc_start: 0.9177 (tpp) cc_final: 0.8939 (mmt) REVERT: C 31 ARG cc_start: 0.8208 (mtt180) cc_final: 0.8007 (mtt180) REVERT: C 62 ARG cc_start: 0.6723 (mmt90) cc_final: 0.6093 (ttp80) REVERT: D 59 ARG cc_start: 0.7627 (ttm170) cc_final: 0.6815 (mmt180) REVERT: D 84 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7325 (mtm180) outliers start: 46 outliers final: 24 residues processed: 173 average time/residue: 0.9833 time to fit residues: 186.5408 Evaluate side-chains 158 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 585 GLN A 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.102395 restraints weight = 14416.553| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.29 r_work: 0.3095 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11206 Z= 0.134 Angle : 0.603 10.761 15316 Z= 0.285 Chirality : 0.042 0.271 1830 Planarity : 0.004 0.039 1845 Dihedral : 7.716 63.616 2071 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 3.33 % Allowed : 19.72 % Favored : 76.95 % 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: 0.49 (0.24), residues: 1322 helix: 1.68 (0.20), residues: 728 sheet: -0.92 (0.46), residues: 123 loop : -1.54 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 244 HIS 0.005 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.023 0.001 TYR B 115 ARG 0.009 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 2.34293 ( 36) link_BETA1-4 : bond 0.00309 ( 7) link_BETA1-4 : angle 1.58166 ( 21) hydrogen bonds : bond 0.03350 ( 579) hydrogen bonds : angle 3.91985 ( 1668) link_BETA1-6 : bond 0.00995 ( 1) link_BETA1-6 : angle 3.01488 ( 3) SS BOND : bond 0.00313 ( 5) SS BOND : angle 1.09287 ( 10) link_BETA1-3 : bond 0.00636 ( 1) link_BETA1-3 : angle 1.43888 ( 3) covalent geometry : bond 0.00313 (11180) covalent geometry : angle 0.58862 (15243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8248 (tp) REVERT: A 37 GLU cc_start: 0.8514 (pt0) cc_final: 0.8248 (pt0) REVERT: A 237 GLN cc_start: 0.7270 (tp40) cc_final: 0.6816 (mm110) REVERT: A 249 ASP cc_start: 0.8096 (t0) cc_final: 0.7780 (p0) REVERT: A 253 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8388 (t0) REVERT: A 259 MET cc_start: 0.9374 (tpt) cc_final: 0.9096 (tpp) REVERT: A 364 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: A 391 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.7350 (ttm110) REVERT: A 392 ASN cc_start: 0.7992 (m-40) cc_final: 0.7630 (m-40) REVERT: A 482 ASP cc_start: 0.7838 (m-30) cc_final: 0.7590 (m-30) REVERT: A 543 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7548 (mtm-85) REVERT: A 582 THR cc_start: 0.8098 (m) cc_final: 0.7882 (p) REVERT: A 587 GLN cc_start: 0.8125 (mm110) cc_final: 0.7848 (mp10) REVERT: A 624 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8712 (m) REVERT: A 655 ASP cc_start: 0.6480 (t0) cc_final: 0.5957 (t70) REVERT: A 677 PHE cc_start: 0.8328 (m-80) cc_final: 0.7938 (m-10) REVERT: B 147 THR cc_start: 0.7014 (m) cc_final: 0.6616 (m) REVERT: B 165 TRP cc_start: 0.8576 (t60) cc_final: 0.8090 (t60) REVERT: B 184 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 253 ILE cc_start: 0.8322 (tt) cc_final: 0.8082 (tt) REVERT: C 55 ILE cc_start: 0.7535 (mt) cc_final: 0.7256 (mt) REVERT: C 62 ARG cc_start: 0.6709 (mmt90) cc_final: 0.6157 (ttp80) REVERT: D 59 ARG cc_start: 0.7609 (ttm170) cc_final: 0.6757 (mmt180) REVERT: D 65 LEU cc_start: 0.7236 (tm) cc_final: 0.6979 (tp) REVERT: D 84 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7416 (mtm180) outliers start: 38 outliers final: 21 residues processed: 165 average time/residue: 0.9659 time to fit residues: 175.0151 Evaluate side-chains 158 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 89 optimal weight: 5.9990 chunk 7 optimal weight: 0.0060 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 0.0060 chunk 94 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 overall best weight: 0.5412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 393 GLN A 585 GLN A 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102915 restraints weight = 14588.917| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.26 r_work: 0.3113 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11206 Z= 0.128 Angle : 0.606 10.630 15316 Z= 0.288 Chirality : 0.042 0.272 1830 Planarity : 0.004 0.040 1845 Dihedral : 7.463 61.402 2071 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 3.16 % Allowed : 20.42 % Favored : 76.42 % 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: 0.53 (0.24), residues: 1322 helix: 1.73 (0.20), residues: 729 sheet: -0.94 (0.45), residues: 123 loop : -1.53 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 58 HIS 0.005 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.022 0.001 TYR B 115 ARG 0.010 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 12) link_NAG-ASN : angle 2.22174 ( 36) link_BETA1-4 : bond 0.00295 ( 7) link_BETA1-4 : angle 1.54841 ( 21) hydrogen bonds : bond 0.03299 ( 579) hydrogen bonds : angle 3.88958 ( 1668) link_BETA1-6 : bond 0.00958 ( 1) link_BETA1-6 : angle 2.76408 ( 3) SS BOND : bond 0.00348 ( 5) SS BOND : angle 1.13850 ( 10) link_BETA1-3 : bond 0.00677 ( 1) link_BETA1-3 : angle 1.45041 ( 3) covalent geometry : bond 0.00299 (11180) covalent geometry : angle 0.59269 (15243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 37 GLU cc_start: 0.8501 (pt0) cc_final: 0.8227 (pt0) REVERT: A 118 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8494 (mp) REVERT: A 237 GLN cc_start: 0.7222 (tp40) cc_final: 0.6737 (mm110) REVERT: A 249 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7758 (p0) REVERT: A 253 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8355 (t0) REVERT: A 364 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: A 391 ARG cc_start: 0.7643 (ttp-110) cc_final: 0.7335 (ttm110) REVERT: A 392 ASN cc_start: 0.7966 (m-40) cc_final: 0.7604 (m-40) REVERT: A 543 ARG cc_start: 0.7839 (mtm180) cc_final: 0.7596 (mtm-85) REVERT: A 582 THR cc_start: 0.8061 (m) cc_final: 0.7817 (p) REVERT: A 587 GLN cc_start: 0.8155 (mm110) cc_final: 0.7871 (mp10) REVERT: A 624 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8719 (m) REVERT: A 655 ASP cc_start: 0.6562 (t0) cc_final: 0.6046 (t70) REVERT: A 677 PHE cc_start: 0.8328 (m-80) cc_final: 0.8006 (m-10) REVERT: B 147 THR cc_start: 0.6970 (m) cc_final: 0.6663 (m) REVERT: B 165 TRP cc_start: 0.8562 (t60) cc_final: 0.7994 (t60) REVERT: B 184 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 253 ILE cc_start: 0.8313 (tt) cc_final: 0.8082 (tt) REVERT: C 55 ILE cc_start: 0.7530 (mt) cc_final: 0.7245 (mt) REVERT: C 62 ARG cc_start: 0.6776 (mmt90) cc_final: 0.6272 (ttp80) REVERT: D 59 ARG cc_start: 0.7602 (ttm170) cc_final: 0.6749 (mmt180) REVERT: D 65 LEU cc_start: 0.7257 (tm) cc_final: 0.7009 (tp) REVERT: D 84 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7424 (mtm180) outliers start: 36 outliers final: 22 residues processed: 159 average time/residue: 1.0195 time to fit residues: 177.8586 Evaluate side-chains 160 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 69.2472 > 50: distance: 31 - 120: 23.571 distance: 107 - 112: 20.243 distance: 112 - 113: 12.936 distance: 113 - 114: 43.577 distance: 113 - 116: 30.750 distance: 114 - 115: 12.267 distance: 114 - 120: 45.184 distance: 116 - 117: 37.417 distance: 117 - 118: 19.093 distance: 117 - 119: 21.791 distance: 120 - 121: 33.932 distance: 121 - 122: 25.319 distance: 121 - 124: 29.700 distance: 122 - 123: 27.975 distance: 122 - 131: 38.960 distance: 124 - 125: 24.611 distance: 125 - 126: 16.146 distance: 126 - 127: 23.404 distance: 127 - 128: 7.692 distance: 128 - 129: 8.677 distance: 128 - 130: 15.624 distance: 131 - 132: 23.958 distance: 132 - 133: 20.895 distance: 132 - 135: 21.389 distance: 133 - 134: 16.480 distance: 133 - 142: 39.016 distance: 135 - 136: 34.921 distance: 136 - 137: 20.971 distance: 137 - 138: 21.042 distance: 138 - 139: 13.074 distance: 139 - 140: 7.983 distance: 139 - 141: 8.480 distance: 142 - 143: 8.379 distance: 142 - 148: 6.964 distance: 143 - 144: 43.719 distance: 143 - 146: 31.508 distance: 144 - 145: 3.853 distance: 144 - 149: 19.706 distance: 146 - 147: 16.420 distance: 147 - 148: 32.380 distance: 149 - 150: 30.514 distance: 150 - 151: 27.780 distance: 150 - 153: 30.727 distance: 151 - 152: 17.733 distance: 151 - 157: 6.285 distance: 153 - 154: 12.438 distance: 154 - 155: 7.677 distance: 154 - 156: 32.615 distance: 157 - 158: 26.529 distance: 158 - 159: 37.597 distance: 159 - 160: 17.881 distance: 159 - 166: 25.097 distance: 161 - 162: 34.814 distance: 162 - 163: 9.233 distance: 163 - 164: 16.526 distance: 163 - 165: 18.180 distance: 166 - 167: 12.499 distance: 167 - 168: 33.790 distance: 167 - 170: 34.575 distance: 168 - 169: 41.118 distance: 168 - 172: 55.565 distance: 170 - 171: 42.244 distance: 172 - 173: 24.217 distance: 173 - 174: 22.244 distance: 173 - 176: 32.180 distance: 174 - 175: 33.448 distance: 174 - 181: 28.571 distance: 176 - 177: 24.000 distance: 177 - 178: 18.850 distance: 178 - 179: 15.350 distance: 178 - 180: 36.002 distance: 181 - 182: 17.790 distance: 181 - 187: 40.143 distance: 182 - 183: 15.573 distance: 182 - 185: 26.302 distance: 183 - 184: 45.460 distance: 183 - 188: 52.420 distance: 185 - 186: 19.748 distance: 186 - 187: 4.523 distance: 188 - 189: 25.518 distance: 189 - 190: 24.240 distance: 189 - 192: 40.091 distance: 190 - 191: 49.089 distance: 190 - 196: 28.976 distance: 192 - 193: 12.390 distance: 193 - 194: 17.752 distance: 193 - 195: 17.351