Starting phenix.real_space_refine on Fri May 16 15:39:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3b_29691/05_2025/8g3b_29691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3b_29691/05_2025/8g3b_29691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3b_29691/05_2025/8g3b_29691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3b_29691/05_2025/8g3b_29691.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3b_29691/05_2025/8g3b_29691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3b_29691/05_2025/8g3b_29691.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 1 5.49 5 S 62 5.16 5 C 9348 2.51 5 N 2373 2.21 5 O 2611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14395 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'6OU': 1, 'OLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.37, per 1000 atoms: 0.58 Number of scatterers: 14395 At special positions: 0 Unit cell: (109, 115.104, 198.816, 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 62 16.00 P 1 15.00 O 2611 8.00 N 2373 7.00 C 9348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 61.3% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.714A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 41 removed outlier: 3.994A pdb=" N VAL A 22 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.726A pdb=" N ASN A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 46 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.626A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.697A pdb=" N ILE A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 removed outlier: 4.118A pdb=" N GLU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.756A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 176 removed outlier: 4.120A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 removed outlier: 4.111A pdb=" N LEU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 268 removed outlier: 3.930A pdb=" N LEU A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 Processing helix chain 'A' and resid 290 through 316 removed outlier: 3.840A pdb=" N SER A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.582A pdb=" N VAL A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 3.866A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.671A pdb=" N GLN A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.566A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 4.152A pdb=" N ALA A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 556 removed outlier: 3.817A pdb=" N VAL A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 removed outlier: 3.826A pdb=" N TYR A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 602 removed outlier: 3.888A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 3.814A pdb=" N VAL A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 removed outlier: 6.054A pdb=" N PHE A 606 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 644 removed outlier: 3.975A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU A 633 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 635 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.623A pdb=" N ASN B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 4.060A pdb=" N ILE B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 113 " --> pdb=" O LEU B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 113' Processing helix chain 'B' and resid 117 through 131 removed outlier: 3.923A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.821A pdb=" N ARG B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 101 through 108 removed outlier: 3.644A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.569A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.636A pdb=" N GLN C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 193 Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 233 through 246 removed outlier: 4.216A pdb=" N LEU C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 9 through 30 removed outlier: 3.746A pdb=" N ILE D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 72 removed outlier: 3.899A pdb=" N LYS D 59 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 79 removed outlier: 3.643A pdb=" N ALA D 78 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE D 79 " --> pdb=" O VAL D 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 75 through 79' Processing helix chain 'D' and resid 84 through 138 Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 142 through 169 Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 183 through 194 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 217 through 235 Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 290 through 300 Processing helix chain 'D' and resid 324 through 327 Processing helix chain 'D' and resid 328 through 334 removed outlier: 3.667A pdb=" N VAL D 334 " --> pdb=" O HIS D 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 11 through 26 Processing helix chain 'E' and resid 35 through 61 removed outlier: 3.753A pdb=" N PHE E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 removed outlier: 3.824A pdb=" N LYS E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 138 removed outlier: 3.612A pdb=" N ALA E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET E 89 " --> pdb=" O PRO E 85 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 143 through 169 Processing helix chain 'E' and resid 171 through 176 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 218 through 235 Processing helix chain 'E' and resid 264 through 271 Proline residue: E 269 - end of helix Processing helix chain 'E' and resid 281 through 286 Processing helix chain 'E' and resid 290 through 300 Processing helix chain 'E' and resid 324 through 327 Processing helix chain 'E' and resid 328 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.620A pdb=" N LEU A 511 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.724A pdb=" N LYS A 354 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.716A pdb=" N LYS A 425 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 363 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N VAL A 458 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA A 386 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 402 through 404 removed outlier: 7.441A pdb=" N ALA A 403 " --> pdb=" O LYS A 438 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 30 removed outlier: 5.739A pdb=" N ILE B 26 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 8 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 6 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 30 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 4 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 63 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 9 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N HIS B 61 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 90 removed outlier: 6.804A pdb=" N ILE B 90 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 212 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 213 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 39 removed outlier: 6.692A pdb=" N SER C 37 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AB1, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.039A pdb=" N GLY C 88 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 167 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 179 through 182 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 209 removed outlier: 3.716A pdb=" N SER D 245 " --> pdb=" O GLN D 208 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D 316 " --> pdb=" O ASP D 258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 178 through 182 removed outlier: 3.820A pdb=" N SER E 216 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 204 through 209 removed outlier: 3.512A pdb=" N ASP E 258 " --> pdb=" O THR E 316 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS E 305 " --> pdb=" O THR E 321 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2370 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: 4.40 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2340 1.32 - 1.44: 3760 1.44 - 1.57: 8439 1.57 - 1.69: 10 1.69 - 1.82: 114 Bond restraints: 14663 Sorted by residual: bond pdb=" C10 OLA E 401 " pdb=" C9 OLA E 401 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C10 OLA A 701 " pdb=" C9 OLA A 701 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C16 6OU E 402 " pdb=" O18 6OU E 402 " ideal model delta sigma weight residual 1.327 1.461 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C31 6OU E 402 " pdb=" O30 6OU E 402 " ideal model delta sigma weight residual 1.331 1.418 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C14 6OU E 402 " pdb=" C15 6OU E 402 " ideal model delta sigma weight residual 1.521 1.606 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 14658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 19695 5.06 - 10.12: 29 10.12 - 15.18: 0 15.18 - 20.25: 2 20.25 - 25.31: 1 Bond angle restraints: 19727 Sorted by residual: angle pdb=" C40 6OU E 402 " pdb=" C41 6OU E 402 " pdb=" C42 6OU E 402 " ideal model delta sigma weight residual 127.56 152.87 -25.31 3.00e+00 1.11e-01 7.12e+01 angle pdb=" O22 6OU E 402 " pdb=" P23 6OU E 402 " pdb=" O26 6OU E 402 " ideal model delta sigma weight residual 93.95 109.91 -15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" C39 6OU E 402 " pdb=" C40 6OU E 402 " pdb=" C41 6OU E 402 " ideal model delta sigma weight residual 127.60 112.39 15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N PHE A 124 " pdb=" CA PHE A 124 " pdb=" C PHE A 124 " ideal model delta sigma weight residual 112.54 107.02 5.52 1.22e+00 6.72e-01 2.05e+01 angle pdb=" CA VAL E 42 " pdb=" C VAL E 42 " pdb=" O VAL E 42 " ideal model delta sigma weight residual 120.95 116.72 4.23 1.04e+00 9.25e-01 1.66e+01 ... (remaining 19722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.49: 8560 32.49 - 64.97: 269 64.97 - 97.46: 24 97.46 - 129.95: 0 129.95 - 162.43: 4 Dihedral angle restraints: 8857 sinusoidal: 3645 harmonic: 5212 Sorted by residual: dihedral pdb=" C19 6OU E 402 " pdb=" C20 6OU E 402 " pdb=" C21 6OU E 402 " pdb=" O22 6OU E 402 " ideal model delta sinusoidal sigma weight residual -59.00 103.43 -162.43 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA TRP E 70 " pdb=" C TRP E 70 " pdb=" N GLU E 71 " pdb=" CA GLU E 71 " ideal model delta harmonic sigma weight residual 180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C12 6OU E 402 " pdb=" C13 6OU E 402 " pdb=" C14 6OU E 402 " pdb=" C15 6OU E 402 " ideal model delta sinusoidal sigma weight residual 186.47 34.86 151.61 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 8854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1879 0.055 - 0.110: 314 0.110 - 0.164: 48 0.164 - 0.219: 3 0.219 - 0.274: 1 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C20 6OU E 402 " pdb=" C19 6OU E 402 " pdb=" C21 6OU E 402 " pdb=" O30 6OU E 402 " both_signs ideal model delta sigma weight residual False 2.35 2.62 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA GLU A 557 " pdb=" N GLU A 557 " pdb=" C GLU A 557 " pdb=" CB GLU A 557 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CA ILE A 563 " pdb=" N ILE A 563 " pdb=" C ILE A 563 " pdb=" CB ILE A 563 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 2242 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " -0.143 2.00e-02 2.50e+03 1.12e-01 1.26e+02 pdb=" C11 OLA E 401 " 0.068 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " -0.068 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 701 " 0.116 2.00e-02 2.50e+03 9.08e-02 8.25e+01 pdb=" C11 OLA A 701 " -0.055 2.00e-02 2.50e+03 pdb=" C8 OLA A 701 " 0.055 2.00e-02 2.50e+03 pdb=" C9 OLA A 701 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 128 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO E 129 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " 0.033 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2881 2.78 - 3.31: 13431 3.31 - 3.84: 22351 3.84 - 4.37: 23814 4.37 - 4.90: 43326 Nonbonded interactions: 105803 Sorted by model distance: nonbonded pdb=" O THR B 101 " pdb=" ND2 ASN B 105 " model vdw 2.251 3.120 nonbonded pdb=" O GLY C 45 " pdb=" OG1 THR C 48 " model vdw 2.269 3.040 nonbonded pdb=" N ILE B 3 " pdb=" O ILE B 30 " model vdw 2.278 3.120 nonbonded pdb=" OE2 GLU B 5 " pdb=" ND2 ASN B 7 " model vdw 2.290 3.120 nonbonded pdb=" NH1 ARG C 212 " pdb=" OE1 GLN C 224 " model vdw 2.293 3.120 ... (remaining 105798 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 32.210 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 14663 Z= 0.226 Angle : 0.660 25.308 19727 Z= 0.337 Chirality : 0.042 0.274 2245 Planarity : 0.004 0.112 2466 Dihedral : 15.662 162.433 5483 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.49 % 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: 0.87 (0.21), residues: 1779 helix: 2.05 (0.17), residues: 1000 sheet: -0.28 (0.40), residues: 211 loop : -1.85 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 613 HIS 0.003 0.001 HIS D 165 PHE 0.023 0.001 PHE C 35 TYR 0.013 0.001 TYR A 314 ARG 0.006 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.16089 ( 817) hydrogen bonds : angle 5.08245 ( 2370) covalent geometry : bond 0.00431 (14663) covalent geometry : angle 0.65970 (19727) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 159 time to evaluate : 1.546 Fit side-chains REVERT: E 23 MET cc_start: 0.7637 (mmm) cc_final: 0.7280 (tpt) outliers start: 4 outliers final: 1 residues processed: 161 average time/residue: 0.2534 time to fit residues: 61.0688 Evaluate side-chains 129 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 160 optimal weight: 9.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN C 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.231203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.179895 restraints weight = 19474.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.177986 restraints weight = 34014.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174562 restraints weight = 28748.554| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14663 Z= 0.181 Angle : 0.563 10.329 19727 Z= 0.300 Chirality : 0.042 0.172 2245 Planarity : 0.004 0.057 2466 Dihedral : 9.485 157.881 1976 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.83 % Allowed : 6.01 % Favored : 93.15 % 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: 0.96 (0.21), residues: 1779 helix: 2.10 (0.17), residues: 1001 sheet: -0.29 (0.39), residues: 211 loop : -1.75 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.005 0.001 HIS A 147 PHE 0.022 0.001 PHE A 529 TYR 0.020 0.002 TYR A 314 ARG 0.004 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.06623 ( 817) hydrogen bonds : angle 4.33147 ( 2370) covalent geometry : bond 0.00427 (14663) covalent geometry : angle 0.56262 (19727) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.565 Fit side-chains REVERT: A 376 MET cc_start: 0.2689 (pmm) cc_final: 0.1827 (pmm) outliers start: 13 outliers final: 13 residues processed: 135 average time/residue: 0.2438 time to fit residues: 49.9456 Evaluate side-chains 135 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 145 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 133 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN C 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.235101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.186346 restraints weight = 19455.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.183287 restraints weight = 34069.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.177072 restraints weight = 29647.609| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14663 Z= 0.107 Angle : 0.473 9.807 19727 Z= 0.249 Chirality : 0.039 0.163 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.961 155.387 1976 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.77 % Allowed : 9.09 % Favored : 90.15 % 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: 1.29 (0.21), residues: 1779 helix: 2.38 (0.17), residues: 1002 sheet: -0.27 (0.39), residues: 217 loop : -1.61 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 54 HIS 0.003 0.000 HIS B 160 PHE 0.013 0.001 PHE B 235 TYR 0.011 0.001 TYR E 57 ARG 0.005 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.04970 ( 817) hydrogen bonds : angle 3.89707 ( 2370) covalent geometry : bond 0.00214 (14663) covalent geometry : angle 0.47308 (19727) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.402 Fit side-chains REVERT: B 134 TYR cc_start: 0.8258 (t80) cc_final: 0.7952 (t80) outliers start: 12 outliers final: 8 residues processed: 145 average time/residue: 0.2653 time to fit residues: 57.9138 Evaluate side-chains 135 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 118 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 161 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 60 optimal weight: 0.0970 chunk 85 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 585 ASN B 51 ASN D 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.228896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.173340 restraints weight = 19172.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170367 restraints weight = 32689.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.166749 restraints weight = 28149.751| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14663 Z= 0.218 Angle : 0.588 10.016 19727 Z= 0.310 Chirality : 0.043 0.149 2245 Planarity : 0.004 0.056 2466 Dihedral : 9.050 155.854 1974 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.47 % Allowed : 11.13 % Favored : 87.40 % 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: 0.99 (0.21), residues: 1779 helix: 2.12 (0.17), residues: 997 sheet: -0.43 (0.39), residues: 220 loop : -1.66 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 54 HIS 0.006 0.001 HIS A 147 PHE 0.041 0.002 PHE B 235 TYR 0.026 0.002 TYR A 314 ARG 0.003 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.07258 ( 817) hydrogen bonds : angle 4.17265 ( 2370) covalent geometry : bond 0.00530 (14663) covalent geometry : angle 0.58757 (19727) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.706 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 144 average time/residue: 0.2517 time to fit residues: 55.0754 Evaluate side-chains 131 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 33 optimal weight: 9.9990 chunk 26 optimal weight: 0.1980 chunk 41 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 chunk 39 optimal weight: 0.4980 chunk 125 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN B 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.231335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.180597 restraints weight = 19389.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.177563 restraints weight = 34993.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.172376 restraints weight = 31500.361| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14663 Z= 0.136 Angle : 0.507 10.332 19727 Z= 0.268 Chirality : 0.041 0.166 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.765 154.933 1974 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.60 % Allowed : 12.92 % Favored : 85.48 % 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: 1.18 (0.21), residues: 1779 helix: 2.29 (0.17), residues: 999 sheet: -0.33 (0.39), residues: 216 loop : -1.63 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 54 HIS 0.003 0.000 HIS A 147 PHE 0.017 0.001 PHE A 529 TYR 0.015 0.001 TYR A 314 ARG 0.003 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.05773 ( 817) hydrogen bonds : angle 3.92707 ( 2370) covalent geometry : bond 0.00308 (14663) covalent geometry : angle 0.50667 (19727) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 1.599 Fit side-chains REVERT: C 94 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.6270 (p90) REVERT: E 46 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7430 (tp) outliers start: 25 outliers final: 15 residues processed: 147 average time/residue: 0.2472 time to fit residues: 55.3332 Evaluate side-chains 136 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 124 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 156 optimal weight: 10.0000 chunk 65 optimal weight: 0.0980 chunk 130 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 150 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN B 160 HIS E 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.231932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181943 restraints weight = 19578.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.179329 restraints weight = 35322.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.173796 restraints weight = 29926.676| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14663 Z= 0.127 Angle : 0.496 10.193 19727 Z= 0.262 Chirality : 0.040 0.153 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.556 158.675 1974 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.98 % Allowed : 13.50 % Favored : 84.52 % 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: 1.27 (0.21), residues: 1779 helix: 2.39 (0.17), residues: 998 sheet: -0.37 (0.39), residues: 220 loop : -1.61 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 54 HIS 0.003 0.000 HIS B 160 PHE 0.019 0.001 PHE B 236 TYR 0.013 0.001 TYR A 314 ARG 0.004 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.05508 ( 817) hydrogen bonds : angle 3.82955 ( 2370) covalent geometry : bond 0.00282 (14663) covalent geometry : angle 0.49578 (19727) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: C 94 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.6365 (p90) REVERT: E 46 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7419 (tp) outliers start: 31 outliers final: 19 residues processed: 142 average time/residue: 0.2488 time to fit residues: 53.7035 Evaluate side-chains 142 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 96 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 135 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 118 optimal weight: 0.0000 chunk 172 optimal weight: 9.9990 chunk 8 optimal weight: 0.0970 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN C 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.234587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.186638 restraints weight = 19456.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.183339 restraints weight = 29443.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.176844 restraints weight = 27083.996| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14663 Z= 0.108 Angle : 0.488 10.865 19727 Z= 0.254 Chirality : 0.040 0.159 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.284 159.634 1974 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.17 % Rotamer: Outliers : 1.28 % Allowed : 14.91 % Favored : 83.81 % 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: 1.43 (0.21), residues: 1779 helix: 2.48 (0.17), residues: 1000 sheet: -0.20 (0.39), residues: 217 loop : -1.51 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 54 HIS 0.003 0.000 HIS C 65 PHE 0.026 0.001 PHE B 235 TYR 0.012 0.001 TYR D 57 ARG 0.004 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 817) hydrogen bonds : angle 3.68585 ( 2370) covalent geometry : bond 0.00216 (14663) covalent geometry : angle 0.48767 (19727) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: B 134 TYR cc_start: 0.8272 (t80) cc_final: 0.8041 (t80) REVERT: C 94 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.6322 (p90) REVERT: C 110 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8489 (mp) REVERT: E 46 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7588 (tp) outliers start: 20 outliers final: 14 residues processed: 150 average time/residue: 0.2480 time to fit residues: 56.6805 Evaluate side-chains 140 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 166 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 139 optimal weight: 50.0000 chunk 149 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN B 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.232262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.183783 restraints weight = 19303.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.180383 restraints weight = 34173.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167392 restraints weight = 33042.625| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14663 Z= 0.139 Angle : 0.518 13.175 19727 Z= 0.268 Chirality : 0.040 0.151 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.287 162.820 1974 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Rotamer: Outliers : 1.79 % Allowed : 14.84 % Favored : 83.37 % 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: 1.37 (0.21), residues: 1779 helix: 2.44 (0.17), residues: 1001 sheet: -0.33 (0.39), residues: 219 loop : -1.52 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 54 HIS 0.004 0.000 HIS B 160 PHE 0.020 0.001 PHE A 529 TYR 0.016 0.001 TYR A 314 ARG 0.005 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.05433 ( 817) hydrogen bonds : angle 3.75611 ( 2370) covalent geometry : bond 0.00319 (14663) covalent geometry : angle 0.51820 (19727) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: B 134 TYR cc_start: 0.8246 (t80) cc_final: 0.7970 (t80) REVERT: B 221 MET cc_start: 0.8073 (mmm) cc_final: 0.7743 (tpp) REVERT: C 94 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.6465 (p90) REVERT: C 110 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8421 (mp) REVERT: E 46 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7476 (tp) outliers start: 28 outliers final: 19 residues processed: 141 average time/residue: 0.2449 time to fit residues: 52.1780 Evaluate side-chains 139 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 113 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 chunk 53 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN B 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.231390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.178929 restraints weight = 19434.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.176475 restraints weight = 35257.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174005 restraints weight = 31234.620| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14663 Z= 0.129 Angle : 0.511 14.049 19727 Z= 0.265 Chirality : 0.040 0.148 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.261 167.848 1974 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.00 % Favored : 94.88 % Rotamer: Outliers : 1.73 % Allowed : 14.97 % Favored : 83.30 % 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: 1.35 (0.21), residues: 1779 helix: 2.42 (0.17), residues: 1003 sheet: -0.27 (0.39), residues: 217 loop : -1.56 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 54 HIS 0.004 0.000 HIS B 160 PHE 0.021 0.001 PHE B 236 TYR 0.014 0.001 TYR A 314 ARG 0.005 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.05324 ( 817) hydrogen bonds : angle 3.73082 ( 2370) covalent geometry : bond 0.00289 (14663) covalent geometry : angle 0.51078 (19727) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: B 134 TYR cc_start: 0.8349 (t80) cc_final: 0.8016 (t80) REVERT: B 221 MET cc_start: 0.7998 (mmm) cc_final: 0.7757 (tpp) REVERT: C 28 ILE cc_start: 0.7499 (mp) cc_final: 0.7204 (mp) REVERT: C 94 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.6490 (p90) REVERT: C 110 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8428 (mp) REVERT: E 46 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7608 (tp) outliers start: 27 outliers final: 22 residues processed: 139 average time/residue: 0.2541 time to fit residues: 53.8461 Evaluate side-chains 145 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 109 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.230944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.182331 restraints weight = 19212.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.177410 restraints weight = 33305.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.172456 restraints weight = 36006.586| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14663 Z= 0.155 Angle : 0.536 14.534 19727 Z= 0.278 Chirality : 0.041 0.140 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.344 175.415 1974 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 1.73 % Allowed : 15.16 % Favored : 83.11 % 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 (0.21), residues: 1779 helix: 2.32 (0.17), residues: 1009 sheet: -0.31 (0.39), residues: 217 loop : -1.59 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 54 HIS 0.004 0.001 HIS B 160 PHE 0.022 0.001 PHE B 236 TYR 0.019 0.001 TYR A 314 ARG 0.006 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.05880 ( 817) hydrogen bonds : angle 3.80878 ( 2370) covalent geometry : bond 0.00362 (14663) covalent geometry : angle 0.53620 (19727) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: A 584 TYR cc_start: 0.8025 (m-10) cc_final: 0.7824 (m-80) REVERT: B 134 TYR cc_start: 0.8349 (t80) cc_final: 0.8052 (t80) REVERT: B 221 MET cc_start: 0.8040 (mmm) cc_final: 0.7763 (tpp) REVERT: C 28 ILE cc_start: 0.7540 (mp) cc_final: 0.7249 (mp) REVERT: C 94 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.6522 (p90) REVERT: C 110 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8421 (mp) REVERT: E 46 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7711 (tp) outliers start: 27 outliers final: 23 residues processed: 135 average time/residue: 0.2483 time to fit residues: 51.1982 Evaluate side-chains 142 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 36 optimal weight: 0.0370 chunk 125 optimal weight: 0.0270 chunk 74 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 103 optimal weight: 0.2980 chunk 136 optimal weight: 40.0000 chunk 157 optimal weight: 9.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.234824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.186227 restraints weight = 19378.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.181211 restraints weight = 39933.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.176982 restraints weight = 36311.068| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14663 Z= 0.108 Angle : 0.492 14.013 19727 Z= 0.255 Chirality : 0.039 0.172 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.062 176.475 1974 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 1.41 % Allowed : 15.55 % Favored : 83.05 % 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: 1.44 (0.21), residues: 1779 helix: 2.50 (0.17), residues: 1004 sheet: -0.21 (0.41), residues: 204 loop : -1.53 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 220 HIS 0.002 0.000 HIS B 160 PHE 0.026 0.001 PHE B 236 TYR 0.013 0.001 TYR D 57 ARG 0.005 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 817) hydrogen bonds : angle 3.62872 ( 2370) covalent geometry : bond 0.00217 (14663) covalent geometry : angle 0.49216 (19727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4082.02 seconds wall clock time: 72 minutes 35.45 seconds (4355.45 seconds total)