Starting phenix.real_space_refine on Mon Jun 9 22:23:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x52_38059/06_2025/8x52_38059.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x52_38059/06_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_38059/06_2025/8x52_38059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x52_38059/06_2025/8x52_38059.map" model { file = "/net/cci-nas-00/data/ceres_data/8x52_38059/06_2025/8x52_38059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x52_38059/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.55, per 1000 atoms: 0.69 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: 3.10 Conformation dependent library (CDL) restraints added in 1.5 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: 1.14 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: 3.45 Time building geometry restraints manager: 3.63 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: 2.140 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.000 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.240 ------------------------------------------------------------------------------- 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 : 1.124 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: 1.0288 time to fit residues: 304.3731 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 : 1.303 ------------------------------------------------------------------------------- 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 = 0.152712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122930 restraints weight = 14420.600| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.29 r_work: 0.3380 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2448 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 9.487 15316 Z= 0.335 Chirality : 0.045 0.403 1830 Planarity : 0.005 0.050 1845 Dihedral : 12.454 104.881 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 0.00842 ( 12) link_NAG-ASN : angle 3.28044 ( 36) link_BETA1-4 : bond 0.00475 ( 7) link_BETA1-4 : angle 2.00546 ( 21) hydrogen bonds : bond 0.04811 ( 579) hydrogen bonds : angle 4.58589 ( 1668) link_BETA1-6 : bond 0.01362 ( 1) link_BETA1-6 : angle 3.21446 ( 3) SS BOND : bond 0.00536 ( 5) SS BOND : angle 1.61904 ( 10) link_BETA1-3 : bond 0.00716 ( 1) link_BETA1-3 : angle 2.19579 ( 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 : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.6944 (tp) REVERT: A 58 HIS cc_start: 0.8099 (m90) cc_final: 0.7676 (m90) REVERT: A 81 ASP cc_start: 0.6336 (m-30) cc_final: 0.6037 (m-30) REVERT: A 237 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6531 (tm-30) REVERT: A 391 ARG cc_start: 0.7596 (ttp-110) cc_final: 0.7302 (ttm110) REVERT: A 392 ASN cc_start: 0.8127 (m-40) cc_final: 0.7783 (m-40) REVERT: A 509 ASP cc_start: 0.7431 (m-30) cc_final: 0.6639 (p0) REVERT: A 543 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7589 (mtm110) REVERT: A 617 LEU cc_start: 0.8131 (mp) cc_final: 0.7794 (mm) REVERT: B 80 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7414 (tptt) REVERT: B 128 ARG cc_start: 0.7704 (mtp180) cc_final: 0.7229 (ttp-170) REVERT: B 154 TYR cc_start: 0.8432 (t80) cc_final: 0.8145 (t80) REVERT: B 163 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7562 (m-70) REVERT: B 165 TRP cc_start: 0.8406 (t60) cc_final: 0.8110 (t60) REVERT: B 169 SER cc_start: 0.8605 (t) cc_final: 0.8091 (p) REVERT: B 184 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6867 (mm-30) REVERT: B 380 LYS cc_start: 0.7238 (mttm) cc_final: 0.6852 (mptt) REVERT: B 463 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8428 (m90) REVERT: C 140 ASP cc_start: 0.8279 (m-30) cc_final: 0.7900 (m-30) REVERT: D 59 ARG cc_start: 0.6626 (ttm170) cc_final: 0.6070 (tmt170) outliers start: 37 outliers final: 17 residues processed: 202 average time/residue: 0.9825 time to fit residues: 219.3364 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 : 1.174 ------------------------------------------------------------------------------- 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: 0.8980 chunk 94 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 A 478 ASN A 531 ASN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS C 58 HIS D 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.141348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110112 restraints weight = 14630.981| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.27 r_work: 0.3210 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11206 Z= 0.178 Angle : 0.688 10.077 15316 Z= 0.328 Chirality : 0.046 0.382 1830 Planarity : 0.004 0.042 1845 Dihedral : 10.478 112.350 2078 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.73 % Allowed : 13.06 % Favored : 82.21 % 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: -0.56 (0.23), residues: 1322 helix: 0.74 (0.19), residues: 734 sheet: -0.93 (0.47), residues: 117 loop : -1.99 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 209 HIS 0.034 0.002 HIS B 463 PHE 0.038 0.002 PHE A 302 TYR 0.016 0.002 TYR A 569 ARG 0.006 0.001 ARG A 434 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 12) link_NAG-ASN : angle 3.11647 ( 36) link_BETA1-4 : bond 0.00517 ( 7) link_BETA1-4 : angle 2.11445 ( 21) hydrogen bonds : bond 0.04305 ( 579) hydrogen bonds : angle 4.26500 ( 1668) link_BETA1-6 : bond 0.01833 ( 1) link_BETA1-6 : angle 2.96514 ( 3) SS BOND : bond 0.00461 ( 5) SS BOND : angle 0.91739 ( 10) link_BETA1-3 : bond 0.00637 ( 1) link_BETA1-3 : angle 1.44351 ( 3) covalent geometry : bond 0.00421 (11180) covalent geometry : angle 0.66583 (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 193 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 139 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.6841 (tp) REVERT: A 231 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8093 (mmp) REVERT: A 391 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.7401 (ttm110) REVERT: A 392 ASN cc_start: 0.8051 (m-40) cc_final: 0.7688 (m-40) REVERT: A 543 ARG cc_start: 0.7923 (mtm180) cc_final: 0.7646 (mtm-85) REVERT: A 617 LEU cc_start: 0.8301 (mp) cc_final: 0.8041 (mm) REVERT: A 624 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8674 (m) REVERT: A 655 ASP cc_start: 0.5962 (t0) cc_final: 0.5716 (t70) REVERT: B 128 ARG cc_start: 0.7544 (mtp180) cc_final: 0.6927 (ttp-170) REVERT: B 154 TYR cc_start: 0.8308 (t80) cc_final: 0.8075 (t80) REVERT: B 163 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7597 (m-70) REVERT: B 177 PHE cc_start: 0.8439 (m-80) cc_final: 0.8209 (m-80) REVERT: B 380 LYS cc_start: 0.7799 (mttm) cc_final: 0.7325 (mptt) REVERT: C 31 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7813 (mtt180) REVERT: C 62 ARG cc_start: 0.6553 (mmt90) cc_final: 0.5825 (ttp80) REVERT: C 186 ARG cc_start: 0.8099 (ptp-170) cc_final: 0.7681 (ptp-170) REVERT: C 206 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8132 (mt) REVERT: D 59 ARG cc_start: 0.7099 (ttm170) cc_final: 0.6444 (tmt170) REVERT: D 84 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6958 (mtm180) outliers start: 54 outliers final: 22 residues processed: 180 average time/residue: 0.9045 time to fit residues: 180.4020 Evaluate side-chains 150 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 231 MET 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 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 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 72 THR 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: 0.7980 chunk 117 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 0.0030 chunk 126 optimal weight: 0.0040 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109633 restraints weight = 14480.847| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.28 r_work: 0.3197 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11206 Z= 0.124 Angle : 0.598 10.719 15316 Z= 0.285 Chirality : 0.042 0.314 1830 Planarity : 0.004 0.037 1845 Dihedral : 9.374 108.208 2074 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.65 % Favored : 97.28 % Rotamer: Outliers : 4.65 % Allowed : 15.78 % 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: 0.02 (0.23), residues: 1322 helix: 1.31 (0.20), residues: 729 sheet: -1.02 (0.47), residues: 121 loop : -1.80 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 209 HIS 0.005 0.001 HIS C 197 PHE 0.032 0.001 PHE A 302 TYR 0.023 0.001 TYR A 499 ARG 0.008 0.001 ARG C 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 12) link_NAG-ASN : angle 2.60936 ( 36) link_BETA1-4 : bond 0.00459 ( 7) link_BETA1-4 : angle 1.78669 ( 21) hydrogen bonds : bond 0.03542 ( 579) hydrogen bonds : angle 4.03354 ( 1668) link_BETA1-6 : bond 0.01343 ( 1) link_BETA1-6 : angle 3.13414 ( 3) SS BOND : bond 0.00315 ( 5) SS BOND : angle 0.67738 ( 10) link_BETA1-3 : bond 0.00841 ( 1) link_BETA1-3 : angle 1.61640 ( 3) covalent geometry : bond 0.00278 (11180) covalent geometry : angle 0.57982 (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 187 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8078 (mmp) REVERT: A 249 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7626 (OUTLIER) REVERT: A 391 ARG cc_start: 0.7587 (ttp-110) cc_final: 0.7266 (ttm110) REVERT: A 392 ASN cc_start: 0.8017 (m-40) cc_final: 0.7663 (m-40) REVERT: A 543 ARG cc_start: 0.7853 (mtm180) cc_final: 0.7474 (mtm110) REVERT: A 585 GLN cc_start: 0.7673 (mt0) cc_final: 0.7230 (mt0) REVERT: A 617 LEU cc_start: 0.8326 (mp) cc_final: 0.8098 (mm) REVERT: A 624 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8550 (m) REVERT: B 80 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7526 (tppt) REVERT: B 128 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7009 (ttp-170) REVERT: B 130 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7294 (mm) REVERT: B 163 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7506 (m-70) REVERT: B 253 ILE cc_start: 0.8076 (tt) cc_final: 0.7814 (tt) REVERT: B 380 LYS cc_start: 0.7927 (mttm) cc_final: 0.7388 (mptt) REVERT: C 55 ILE cc_start: 0.7392 (mt) cc_final: 0.7095 (mt) REVERT: C 62 ARG cc_start: 0.6555 (mmt90) cc_final: 0.5974 (ttp80) REVERT: C 184 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7935 (mtp180) REVERT: C 186 ARG cc_start: 0.8174 (ptp-170) cc_final: 0.7794 (ptp-170) REVERT: C 206 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8070 (mt) REVERT: C 236 LEU cc_start: 0.8031 (mm) cc_final: 0.7830 (tp) REVERT: D 59 ARG cc_start: 0.7358 (ttm170) cc_final: 0.6554 (tmt170) REVERT: D 65 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6699 (tm) REVERT: D 84 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7101 (mtm180) outliers start: 53 outliers final: 14 residues processed: 173 average time/residue: 1.0229 time to fit residues: 194.7898 Evaluate side-chains 145 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 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 466 SER 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 130 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 58 TRP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.135975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104012 restraints weight = 14442.768| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.26 r_work: 0.3122 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11206 Z= 0.170 Angle : 0.647 11.437 15316 Z= 0.308 Chirality : 0.044 0.300 1830 Planarity : 0.004 0.039 1845 Dihedral : 9.130 95.699 2074 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 5.08 % Allowed : 16.83 % Favored : 78.09 % 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: 0.20 (0.24), residues: 1322 helix: 1.44 (0.20), residues: 728 sheet: -0.82 (0.48), residues: 118 loop : -1.70 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 209 HIS 0.007 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.021 0.002 TYR A 499 ARG 0.004 0.001 ARG A 434 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 12) link_NAG-ASN : angle 2.92181 ( 36) link_BETA1-4 : bond 0.00328 ( 7) link_BETA1-4 : angle 1.89673 ( 21) hydrogen bonds : bond 0.03770 ( 579) hydrogen bonds : angle 4.04113 ( 1668) link_BETA1-6 : bond 0.01670 ( 1) link_BETA1-6 : angle 3.36468 ( 3) SS BOND : bond 0.00483 ( 5) SS BOND : angle 2.00535 ( 10) link_BETA1-3 : bond 0.00738 ( 1) link_BETA1-3 : angle 1.65099 ( 3) covalent geometry : bond 0.00404 (11180) covalent geometry : angle 0.62503 (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 191 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8030 (tp) REVERT: A 118 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 184 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 231 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8284 (mmm) REVERT: A 253 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8496 (t0) REVERT: A 364 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: A 391 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7367 (ttp-110) REVERT: A 392 ASN cc_start: 0.8006 (m-40) cc_final: 0.7561 (m-40) REVERT: A 482 ASP cc_start: 0.7761 (m-30) cc_final: 0.7341 (m-30) REVERT: A 540 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7957 (tp40) REVERT: A 543 ARG cc_start: 0.7774 (mtm180) cc_final: 0.7413 (mtm110) REVERT: A 582 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7171 (m) REVERT: A 617 LEU cc_start: 0.8349 (mp) cc_final: 0.8137 (mm) REVERT: A 624 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8729 (m) REVERT: A 655 ASP cc_start: 0.6512 (t0) cc_final: 0.6034 (t70) REVERT: B 80 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7443 (tppt) REVERT: B 130 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7384 (mm) REVERT: B 163 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7531 (m-70) REVERT: B 165 TRP cc_start: 0.8516 (t60) cc_final: 0.8029 (t60) REVERT: B 184 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 253 ILE cc_start: 0.8190 (tt) cc_final: 0.7945 (tt) REVERT: C 62 ARG cc_start: 0.6595 (mmt90) cc_final: 0.5946 (ttp80) REVERT: C 186 ARG cc_start: 0.8216 (ptp-170) cc_final: 0.7982 (ptp-170) REVERT: C 206 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8090 (mt) REVERT: C 236 LEU cc_start: 0.8149 (mm) cc_final: 0.7844 (tp) REVERT: D 59 ARG cc_start: 0.7530 (ttm170) cc_final: 0.6669 (tmt170) REVERT: D 84 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7164 (mtm180) outliers start: 58 outliers final: 20 residues processed: 175 average time/residue: 0.9307 time to fit residues: 179.7176 Evaluate side-chains 154 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 231 MET 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 466 SER Chi-restraints excluded: chain A residue 540 GLN 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 113 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 163 HIS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 102 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 118 optimal weight: 0.0270 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.7242 ------------------------------------------------------------------------------- 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 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103546 restraints weight = 14525.045| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.26 r_work: 0.3118 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11206 Z= 0.145 Angle : 0.618 10.485 15316 Z= 0.294 Chirality : 0.043 0.276 1830 Planarity : 0.004 0.038 1845 Dihedral : 8.514 72.312 2074 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.65 % Favored : 97.28 % Rotamer: Outliers : 3.86 % Allowed : 18.14 % Favored : 78.00 % 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: 0.35 (0.24), residues: 1322 helix: 1.55 (0.20), residues: 733 sheet: -0.90 (0.47), residues: 118 loop : -1.62 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.006 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.020 0.001 TYR A 499 ARG 0.010 0.001 ARG C 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 12) link_NAG-ASN : angle 2.45929 ( 36) link_BETA1-4 : bond 0.00351 ( 7) link_BETA1-4 : angle 1.67435 ( 21) hydrogen bonds : bond 0.03501 ( 579) hydrogen bonds : angle 3.95867 ( 1668) link_BETA1-6 : bond 0.01524 ( 1) link_BETA1-6 : angle 3.29704 ( 3) SS BOND : bond 0.00262 ( 5) SS BOND : angle 1.72334 ( 10) link_BETA1-3 : bond 0.00598 ( 1) link_BETA1-3 : angle 1.49005 ( 3) covalent geometry : bond 0.00341 (11180) covalent geometry : angle 0.60083 (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 176 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8185 (tp) REVERT: A 118 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8414 (mp) REVERT: A 184 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7839 (mt-10) REVERT: A 237 GLN cc_start: 0.7191 (tp40) cc_final: 0.6683 (mm110) REVERT: A 249 ASP cc_start: 0.8058 (t0) cc_final: 0.7820 (p0) REVERT: A 253 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8396 (t0) REVERT: A 364 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: A 391 ARG cc_start: 0.7703 (ttp-110) cc_final: 0.7301 (ttm110) REVERT: A 392 ASN cc_start: 0.8083 (m-40) cc_final: 0.7664 (m-40) REVERT: A 482 ASP cc_start: 0.7866 (m-30) cc_final: 0.7568 (m-30) REVERT: A 543 ARG cc_start: 0.7791 (mtm180) cc_final: 0.7443 (mtm110) REVERT: A 582 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7831 (p) REVERT: A 587 GLN cc_start: 0.7978 (mm110) cc_final: 0.7464 (mp10) REVERT: A 624 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8709 (m) REVERT: A 655 ASP cc_start: 0.6441 (t0) cc_final: 0.5972 (t70) REVERT: A 677 PHE cc_start: 0.8306 (m-80) cc_final: 0.7960 (m-10) REVERT: B 130 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7391 (mm) REVERT: B 165 TRP cc_start: 0.8530 (t60) cc_final: 0.7972 (t60) REVERT: B 253 ILE cc_start: 0.8220 (tt) cc_final: 0.7968 (tt) REVERT: C 62 ARG cc_start: 0.6638 (mmt90) cc_final: 0.6031 (ttp80) REVERT: C 186 ARG cc_start: 0.8146 (ptp-170) cc_final: 0.7835 (ptp-170) REVERT: C 206 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8042 (mt) REVERT: C 236 LEU cc_start: 0.8140 (mm) cc_final: 0.7857 (tp) REVERT: D 59 ARG cc_start: 0.7588 (ttm170) cc_final: 0.6734 (mmt180) REVERT: D 84 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7277 (mtm180) outliers start: 44 outliers final: 16 residues processed: 164 average time/residue: 0.9807 time to fit residues: 178.0131 Evaluate side-chains 145 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 582 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 134 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 121 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 126 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101654 restraints weight = 14691.521| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.30 r_work: 0.3091 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11206 Z= 0.158 Angle : 0.628 10.693 15316 Z= 0.298 Chirality : 0.043 0.278 1830 Planarity : 0.004 0.039 1845 Dihedral : 8.043 71.645 2071 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 3.33 % Allowed : 19.37 % Favored : 77.30 % 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: 0.33 (0.24), residues: 1322 helix: 1.55 (0.19), residues: 735 sheet: -0.93 (0.45), residues: 121 loop : -1.67 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 244 HIS 0.006 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.018 0.001 TYR A 499 ARG 0.004 0.001 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 12) link_NAG-ASN : angle 2.45646 ( 36) link_BETA1-4 : bond 0.00314 ( 7) link_BETA1-4 : angle 1.69915 ( 21) hydrogen bonds : bond 0.03591 ( 579) hydrogen bonds : angle 3.97169 ( 1668) link_BETA1-6 : bond 0.01040 ( 1) link_BETA1-6 : angle 3.25040 ( 3) SS BOND : bond 0.00383 ( 5) SS BOND : angle 1.37897 ( 10) link_BETA1-3 : bond 0.00667 ( 1) link_BETA1-3 : angle 1.50595 ( 3) covalent geometry : bond 0.00374 (11180) covalent geometry : angle 0.61138 (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 174 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 118 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 237 GLN cc_start: 0.7148 (tp40) cc_final: 0.6658 (mm110) REVERT: A 249 ASP cc_start: 0.8073 (t0) cc_final: 0.7782 (p0) REVERT: A 253 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8430 (t0) REVERT: A 364 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: A 391 ARG cc_start: 0.7666 (ttp-110) cc_final: 0.7234 (ttm110) REVERT: A 392 ASN cc_start: 0.8046 (m-40) cc_final: 0.7647 (m-40) REVERT: A 436 ILE cc_start: 0.8848 (pt) cc_final: 0.8642 (mt) REVERT: A 482 ASP cc_start: 0.7817 (m-30) cc_final: 0.7567 (m-30) REVERT: A 540 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8150 (tp40) REVERT: A 543 ARG cc_start: 0.7769 (mtm180) cc_final: 0.7523 (mtm-85) REVERT: A 587 GLN cc_start: 0.8036 (mm110) cc_final: 0.7657 (mp10) REVERT: A 624 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8726 (m) REVERT: A 655 ASP cc_start: 0.6686 (t0) cc_final: 0.6143 (t70) REVERT: A 677 PHE cc_start: 0.8303 (m-80) cc_final: 0.7948 (m-10) REVERT: B 130 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7331 (mm) REVERT: B 165 TRP cc_start: 0.8553 (t60) cc_final: 0.8165 (t60) REVERT: B 253 ILE cc_start: 0.8303 (tt) cc_final: 0.8072 (tt) REVERT: B 457 MET cc_start: 0.9177 (tpp) cc_final: 0.8961 (mmt) REVERT: C 62 ARG cc_start: 0.6673 (mmt90) cc_final: 0.6165 (ttp80) REVERT: C 186 ARG cc_start: 0.8138 (ptp-170) cc_final: 0.7937 (ptp-170) REVERT: C 206 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7901 (mt) REVERT: C 236 LEU cc_start: 0.8123 (mm) cc_final: 0.7846 (tp) REVERT: D 59 ARG cc_start: 0.7621 (ttm170) cc_final: 0.6788 (mmt180) REVERT: D 84 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7320 (mtm180) outliers start: 38 outliers final: 20 residues processed: 164 average time/residue: 1.0088 time to fit residues: 181.6960 Evaluate side-chains 158 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 420 LEU 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 200 THR Chi-restraints excluded: chain C residue 206 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100558 restraints weight = 14321.542| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.30 r_work: 0.3086 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11206 Z= 0.164 Angle : 0.622 10.513 15316 Z= 0.298 Chirality : 0.043 0.273 1830 Planarity : 0.004 0.040 1845 Dihedral : 7.762 71.183 2071 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 3.68 % Allowed : 19.11 % Favored : 77.21 % 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: 0.35 (0.24), residues: 1322 helix: 1.55 (0.19), residues: 736 sheet: -0.92 (0.45), residues: 121 loop : -1.63 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 244 HIS 0.006 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.018 0.001 TYR A 499 ARG 0.006 0.001 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 12) link_NAG-ASN : angle 2.40550 ( 36) link_BETA1-4 : bond 0.00282 ( 7) link_BETA1-4 : angle 1.67540 ( 21) hydrogen bonds : bond 0.03565 ( 579) hydrogen bonds : angle 3.99828 ( 1668) link_BETA1-6 : bond 0.01016 ( 1) link_BETA1-6 : angle 2.91607 ( 3) SS BOND : bond 0.00406 ( 5) SS BOND : angle 1.21106 ( 10) link_BETA1-3 : bond 0.00553 ( 1) link_BETA1-3 : angle 1.54634 ( 3) covalent geometry : bond 0.00389 (11180) covalent geometry : angle 0.60673 (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: 42 poor density : 132 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8358 (tp) REVERT: A 37 GLU cc_start: 0.8534 (pt0) cc_final: 0.8245 (pt0) REVERT: A 237 GLN cc_start: 0.7255 (tp40) cc_final: 0.6770 (mm110) REVERT: A 253 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8394 (t0) REVERT: A 364 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: A 391 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.7306 (ttm110) REVERT: A 392 ASN cc_start: 0.8052 (m-40) cc_final: 0.7692 (m-40) REVERT: A 436 ILE cc_start: 0.8941 (pt) cc_final: 0.8735 (mt) REVERT: A 543 ARG cc_start: 0.7919 (mtm180) cc_final: 0.7691 (mtm-85) REVERT: A 587 GLN cc_start: 0.8238 (mm110) cc_final: 0.7852 (mp10) REVERT: A 624 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8881 (m) REVERT: A 655 ASP cc_start: 0.6618 (t0) cc_final: 0.6225 (t70) REVERT: A 677 PHE cc_start: 0.8382 (m-80) cc_final: 0.8071 (m-10) REVERT: B 130 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7484 (mm) REVERT: B 147 THR cc_start: 0.7098 (m) cc_final: 0.6748 (m) REVERT: B 165 TRP cc_start: 0.8588 (t60) cc_final: 0.8183 (t60) REVERT: B 253 ILE cc_start: 0.8496 (tt) cc_final: 0.8265 (tt) REVERT: C 31 ARG cc_start: 0.8402 (mtt180) cc_final: 0.8202 (mtt180) REVERT: C 62 ARG cc_start: 0.6863 (mmt90) cc_final: 0.6401 (ttp80) REVERT: C 206 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8034 (mt) REVERT: C 236 LEU cc_start: 0.8144 (mm) cc_final: 0.7459 (tp) REVERT: D 59 ARG cc_start: 0.7700 (ttm170) cc_final: 0.6897 (mmt180) REVERT: D 65 LEU cc_start: 0.7320 (tm) cc_final: 0.6961 (tt) REVERT: D 84 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7407 (mtm180) outliers start: 42 outliers final: 19 residues processed: 165 average time/residue: 1.1360 time to fit residues: 205.5501 Evaluate side-chains 149 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU 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 624 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 420 LEU 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 206 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP 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: 0.0670 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101882 restraints weight = 14473.327| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.33 r_work: 0.3104 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11206 Z= 0.127 Angle : 0.600 10.441 15316 Z= 0.287 Chirality : 0.043 0.270 1830 Planarity : 0.004 0.040 1845 Dihedral : 7.350 63.621 2069 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 2.37 % Allowed : 20.42 % Favored : 77.21 % 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 (0.24), residues: 1322 helix: 1.68 (0.20), residues: 735 sheet: -0.96 (0.45), residues: 123 loop : -1.61 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.017 0.001 TYR A 499 ARG 0.009 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 12) link_NAG-ASN : angle 2.20534 ( 36) link_BETA1-4 : bond 0.00280 ( 7) link_BETA1-4 : angle 1.52698 ( 21) hydrogen bonds : bond 0.03340 ( 579) hydrogen bonds : angle 3.94869 ( 1668) link_BETA1-6 : bond 0.00945 ( 1) link_BETA1-6 : angle 2.58656 ( 3) SS BOND : bond 0.00415 ( 5) SS BOND : angle 1.18402 ( 10) link_BETA1-3 : bond 0.00637 ( 1) link_BETA1-3 : angle 1.42980 ( 3) covalent geometry : bond 0.00292 (11180) covalent geometry : angle 0.58653 (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 159 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8360 (tp) REVERT: A 37 GLU cc_start: 0.8542 (pt0) cc_final: 0.8252 (pt0) REVERT: A 118 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8572 (mp) REVERT: A 237 GLN cc_start: 0.7237 (tp40) cc_final: 0.6741 (mm110) REVERT: A 253 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8305 (t0) REVERT: A 364 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: A 391 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7436 (ttm110) REVERT: A 392 ASN cc_start: 0.8072 (m-40) cc_final: 0.7685 (m-40) REVERT: A 436 ILE cc_start: 0.8899 (pt) cc_final: 0.8680 (mt) REVERT: A 543 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7700 (mtm-85) REVERT: A 587 GLN cc_start: 0.8235 (mm110) cc_final: 0.7674 (mp10) REVERT: A 624 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8693 (m) REVERT: A 655 ASP cc_start: 0.6526 (t0) cc_final: 0.6131 (t70) REVERT: A 677 PHE cc_start: 0.8374 (m-80) cc_final: 0.8012 (m-10) REVERT: B 130 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7418 (mm) REVERT: B 147 THR cc_start: 0.7097 (m) cc_final: 0.6691 (m) REVERT: B 165 TRP cc_start: 0.8578 (t60) cc_final: 0.8212 (t60) REVERT: B 253 ILE cc_start: 0.8479 (tt) cc_final: 0.8237 (tt) REVERT: C 62 ARG cc_start: 0.6823 (mmt90) cc_final: 0.6356 (ttp80) REVERT: C 236 LEU cc_start: 0.7887 (mm) cc_final: 0.7547 (tp) REVERT: C 237 ARG cc_start: 0.7310 (mmp80) cc_final: 0.7045 (mmp80) REVERT: D 59 ARG cc_start: 0.7713 (ttm170) cc_final: 0.6886 (mmt180) REVERT: D 65 LEU cc_start: 0.7413 (tm) cc_final: 0.7074 (tt) REVERT: D 84 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7415 (mtm180) outliers start: 27 outliers final: 17 residues processed: 152 average time/residue: 1.0864 time to fit residues: 180.1790 Evaluate side-chains 148 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU 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 310 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 236 VAL 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 193 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2877 > 50: distance: 31 - 120: 37.755 distance: 107 - 112: 24.328 distance: 112 - 113: 29.874 distance: 113 - 114: 66.659 distance: 113 - 116: 41.152 distance: 114 - 115: 57.668 distance: 114 - 120: 55.967 distance: 116 - 117: 54.161 distance: 117 - 118: 39.933 distance: 117 - 119: 43.414 distance: 120 - 121: 57.164 distance: 121 - 122: 38.950 distance: 121 - 124: 69.355 distance: 122 - 123: 55.653 distance: 122 - 131: 55.631 distance: 124 - 125: 21.385 distance: 125 - 126: 29.323 distance: 126 - 127: 46.304 distance: 127 - 128: 33.549 distance: 128 - 129: 37.951 distance: 128 - 130: 38.612 distance: 131 - 132: 63.598 distance: 132 - 133: 30.443 distance: 132 - 135: 58.002 distance: 133 - 134: 22.920 distance: 133 - 142: 58.626 distance: 135 - 136: 53.414 distance: 136 - 137: 43.132 distance: 137 - 138: 47.876 distance: 138 - 139: 31.694 distance: 139 - 140: 21.196 distance: 139 - 141: 20.891 distance: 142 - 143: 9.437 distance: 142 - 148: 46.067 distance: 143 - 144: 55.531 distance: 143 - 146: 44.188 distance: 144 - 145: 39.197 distance: 146 - 147: 51.903 distance: 147 - 148: 56.046 distance: 149 - 150: 67.574 distance: 150 - 151: 68.418 distance: 150 - 153: 56.636 distance: 151 - 152: 55.728 distance: 151 - 157: 55.881 distance: 153 - 154: 68.749 distance: 154 - 155: 58.764 distance: 154 - 156: 31.396 distance: 157 - 158: 41.390 distance: 158 - 159: 46.943 distance: 158 - 161: 51.960 distance: 159 - 160: 60.446 distance: 159 - 166: 31.956 distance: 161 - 162: 65.988 distance: 162 - 163: 46.767 distance: 163 - 164: 48.919 distance: 163 - 165: 26.052 distance: 166 - 167: 52.654 distance: 167 - 168: 64.867 distance: 167 - 170: 55.127 distance: 168 - 169: 39.970 distance: 168 - 172: 60.536 distance: 170 - 171: 39.568 distance: 172 - 173: 23.224 distance: 173 - 174: 42.841 distance: 173 - 176: 40.305 distance: 174 - 175: 37.916 distance: 174 - 181: 69.217 distance: 176 - 177: 52.090 distance: 177 - 178: 69.612 distance: 178 - 179: 62.029 distance: 178 - 180: 69.339 distance: 181 - 187: 40.514 distance: 182 - 183: 32.407 distance: 182 - 185: 39.110 distance: 183 - 184: 64.831 distance: 183 - 188: 30.808 distance: 185 - 186: 35.806 distance: 186 - 187: 54.357 distance: 188 - 189: 8.673 distance: 189 - 190: 47.164 distance: 189 - 192: 65.024 distance: 190 - 191: 5.053 distance: 190 - 196: 33.207 distance: 193 - 194: 15.553 distance: 193 - 195: 4.810