Starting phenix.real_space_refine on Fri Jun 13 03:07:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3b_29691/06_2025/8g3b_29691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3b_29691/06_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_29691/06_2025/8g3b_29691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3b_29691/06_2025/8g3b_29691.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3b_29691/06_2025/8g3b_29691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3b_29691/06_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-5710/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: 9.07, per 1000 atoms: 0.63 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: 3.42 Conformation dependent library (CDL) restraints added in 1.7 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: 1.36 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: 4.72 Time building geometry restraints manager: 3.91 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: 3.300 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.480 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.310 ------------------------------------------------------------------------------- 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 : 1.535 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: 0.3477 time to fit residues: 85.2879 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 : 1.636 ------------------------------------------------------------------------------- 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 = 19474.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.177986 restraints weight = 34013.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174564 restraints weight = 28741.701| |-----------------------------------------------------------------------------| 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 : 1.575 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: 0.2473 time to fit residues: 50.7575 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 : 1.433 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 133 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4566 r_free = 0.4566 target = 0.231287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.181147 restraints weight = 19413.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.178109 restraints weight = 37691.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174094 restraints weight = 32836.847| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1138 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= 0.151 Angle : 0.517 9.825 19727 Z= 0.273 Chirality : 0.041 0.163 2245 Planarity : 0.003 0.056 2466 Dihedral : 9.188 156.262 1976 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.15 % Allowed : 9.53 % Favored : 89.32 % 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: 1.09 (0.21), residues: 1779 helix: 2.21 (0.17), residues: 1002 sheet: -0.40 (0.39), residues: 220 loop : -1.67 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 54 HIS 0.004 0.001 HIS A 147 PHE 0.019 0.001 PHE A 529 TYR 0.017 0.001 TYR A 314 ARG 0.005 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.06086 ( 817) hydrogen bonds : angle 4.05907 ( 2370) covalent geometry : bond 0.00350 (14663) covalent geometry : angle 0.51730 (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 143 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.450 Fit side-chains REVERT: C 130 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8394 (tm-30) REVERT: D 54 TRP cc_start: 0.7251 (t-100) cc_final: 0.6513 (t60) outliers start: 18 outliers final: 13 residues processed: 139 average time/residue: 0.2515 time to fit residues: 52.8213 Evaluate side-chains 131 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 585 ASN 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 202 HIS Chi-restraints excluded: chain D residue 29 VAL 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: 7.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 4 optimal weight: 0.0670 chunk 94 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.4722 ------------------------------------------------------------------------------- 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 D 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.230494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.177346 restraints weight = 19302.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.174243 restraints weight = 35828.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170370 restraints weight = 37258.258| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14663 Z= 0.162 Angle : 0.520 10.174 19727 Z= 0.275 Chirality : 0.041 0.161 2245 Planarity : 0.003 0.056 2466 Dihedral : 9.006 155.762 1974 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.73 % Allowed : 11.07 % Favored : 87.20 % 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: 1.10 (0.21), residues: 1779 helix: 2.22 (0.17), residues: 1000 sheet: -0.38 (0.39), residues: 220 loop : -1.65 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 54 HIS 0.004 0.001 HIS A 147 PHE 0.042 0.001 PHE B 235 TYR 0.018 0.001 TYR A 314 ARG 0.003 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.06229 ( 817) hydrogen bonds : angle 4.01899 ( 2370) covalent geometry : bond 0.00379 (14663) covalent geometry : angle 0.51967 (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: 27 poor density : 121 time to evaluate : 1.456 Fit side-chains REVERT: C 130 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8371 (tm-30) REVERT: E 46 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7649 (tp) REVERT: E 98 THR cc_start: 0.8446 (m) cc_final: 0.8201 (p) outliers start: 27 outliers final: 17 residues processed: 141 average time/residue: 0.2472 time to fit residues: 53.4068 Evaluate side-chains 136 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 537 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 585 ASN 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 D residue 29 VAL 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 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: 7.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.0470 chunk 162 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 171 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.233450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.183948 restraints weight = 19476.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.180897 restraints weight = 36088.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.177877 restraints weight = 30198.363| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14663 Z= 0.111 Angle : 0.469 10.438 19727 Z= 0.248 Chirality : 0.039 0.165 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.664 154.393 1974 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.73 % Allowed : 12.16 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1779 helix: 2.43 (0.17), residues: 998 sheet: -0.25 (0.39), residues: 216 loop : -1.58 (0.26), residues: 565 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 0.014 0.001 PHE A 529 TYR 0.010 0.001 TYR A 314 ARG 0.003 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.05133 ( 817) hydrogen bonds : angle 3.79647 ( 2370) covalent geometry : bond 0.00230 (14663) covalent geometry : angle 0.46877 (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 156 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.469 Fit side-chains REVERT: C 94 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.6216 (p90) REVERT: C 130 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8421 (tm-30) REVERT: E 46 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7631 (tp) outliers start: 27 outliers final: 15 residues processed: 146 average time/residue: 0.2495 time to fit residues: 55.0733 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 : 1.558 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain A residue 541 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 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 156 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 98 optimal weight: 0.0870 chunk 150 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN E 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.231901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.182193 restraints weight = 19507.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.178361 restraints weight = 37051.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176324 restraints weight = 30252.439| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14663 Z= 0.138 Angle : 0.500 10.279 19727 Z= 0.263 Chirality : 0.040 0.159 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.554 156.233 1974 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.24 % Allowed : 13.05 % Favored : 84.71 % 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: 1.31 (0.21), residues: 1779 helix: 2.42 (0.17), residues: 998 sheet: -0.38 (0.39), residues: 221 loop : -1.57 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 54 HIS 0.004 0.001 HIS B 160 PHE 0.020 0.001 PHE A 529 TYR 0.016 0.001 TYR A 314 ARG 0.004 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.05696 ( 817) hydrogen bonds : angle 3.82790 ( 2370) covalent geometry : bond 0.00314 (14663) covalent geometry : angle 0.50002 (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 160 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 1.519 Fit side-chains REVERT: A 376 MET cc_start: 0.2051 (pmm) cc_final: 0.1844 (mpp) REVERT: C 94 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.6388 (p90) REVERT: C 110 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8556 (mp) REVERT: E 23 MET cc_start: 0.7837 (tpt) cc_final: 0.7619 (tpt) REVERT: E 46 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7644 (tp) outliers start: 35 outliers final: 17 residues processed: 150 average time/residue: 0.3142 time to fit residues: 72.2744 Evaluate side-chains 141 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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 541 THR 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 94 TYR Chi-restraints excluded: chain C residue 110 LEU 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: 0.6980 chunk 64 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 582 GLN C 65 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.227577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.176545 restraints weight = 19540.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.173170 restraints weight = 35302.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.169590 restraints weight = 31784.021| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14663 Z= 0.192 Angle : 0.571 11.356 19727 Z= 0.300 Chirality : 0.042 0.158 2245 Planarity : 0.004 0.056 2466 Dihedral : 8.718 166.266 1974 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 1.92 % Allowed : 14.14 % Favored : 83.94 % 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: 1.06 (0.21), residues: 1779 helix: 2.18 (0.17), residues: 1003 sheet: -0.40 (0.39), residues: 218 loop : -1.65 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 54 HIS 0.005 0.001 HIS B 160 PHE 0.041 0.002 PHE B 235 TYR 0.024 0.002 TYR A 314 ARG 0.004 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.06702 ( 817) hydrogen bonds : angle 4.01499 ( 2370) covalent geometry : bond 0.00462 (14663) covalent geometry : angle 0.57128 (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 157 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.696 Fit side-chains revert: symmetry clash REVERT: C 94 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.6622 (p90) REVERT: C 110 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 130 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8307 (tm-30) REVERT: E 23 MET cc_start: 0.7924 (tpt) cc_final: 0.7288 (tpt) REVERT: E 46 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7779 (tp) outliers start: 30 outliers final: 16 residues processed: 149 average time/residue: 0.2594 time to fit residues: 58.5375 Evaluate side-chains 138 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 537 THR 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 29 HIS Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain D residue 29 VAL 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: 8.9990 chunk 111 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 149 optimal weight: 0.0970 chunk 96 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 155 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.231262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.179955 restraints weight = 19436.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.176972 restraints weight = 35220.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.175095 restraints weight = 28646.349| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1779 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= 0.118 Angle : 0.498 12.533 19727 Z= 0.261 Chirality : 0.040 0.158 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.482 172.062 1974 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.89 % Favored : 95.05 % Rotamer: Outliers : 1.60 % Allowed : 14.78 % Favored : 83.62 % 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: 2.38 (0.17), residues: 1005 sheet: -0.41 (0.41), residues: 207 loop : -1.63 (0.26), residues: 567 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 0.015 0.001 PHE A 529 TYR 0.013 0.001 TYR D 57 ARG 0.004 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.05272 ( 817) hydrogen bonds : angle 3.77669 ( 2370) covalent geometry : bond 0.00249 (14663) covalent geometry : angle 0.49825 (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 148 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: B 134 TYR cc_start: 0.8341 (t80) cc_final: 0.8083 (t80) REVERT: C 94 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.6503 (p90) REVERT: C 110 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 130 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8287 (tm-30) REVERT: D 140 MET cc_start: 0.0624 (tpt) cc_final: -0.1547 (mmt) REVERT: E 23 MET cc_start: 0.7910 (tpt) cc_final: 0.7646 (tpt) REVERT: E 46 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7655 (tp) outliers start: 25 outliers final: 16 residues processed: 141 average time/residue: 0.2387 time to fit residues: 50.9928 Evaluate side-chains 140 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 94 TYR Chi-restraints excluded: chain C residue 110 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 113 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 170 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.229989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179492 restraints weight = 19510.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.177771 restraints weight = 33709.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.171966 restraints weight = 30430.663| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14663 Z= 0.142 Angle : 0.522 14.000 19727 Z= 0.272 Chirality : 0.040 0.156 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.468 179.361 1974 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 1.66 % Allowed : 14.84 % Favored : 83.49 % 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: 1.24 (0.21), residues: 1779 helix: 2.34 (0.17), residues: 1006 sheet: -0.40 (0.39), residues: 219 loop : -1.61 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 54 HIS 0.004 0.000 HIS B 160 PHE 0.022 0.001 PHE B 236 TYR 0.016 0.001 TYR A 314 ARG 0.005 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.05727 ( 817) hydrogen bonds : angle 3.80972 ( 2370) covalent geometry : bond 0.00326 (14663) covalent geometry : angle 0.52231 (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 146 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: C 94 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.6523 (p90) REVERT: C 110 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8396 (mp) REVERT: E 46 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7559 (tp) outliers start: 26 outliers final: 20 residues processed: 140 average time/residue: 0.2466 time to fit residues: 52.8447 Evaluate side-chains 140 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 170 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 537 THR 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 107 LEU 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 110 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain D residue 29 VAL 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: 3.9990 chunk 105 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 109 optimal weight: 0.2980 chunk 79 optimal weight: 0.0470 chunk 118 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.234630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.183608 restraints weight = 19360.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.179574 restraints weight = 37710.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.178776 restraints weight = 35026.119| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14663 Z= 0.108 Angle : 0.492 14.086 19727 Z= 0.255 Chirality : 0.039 0.166 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.058 171.624 1974 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 1.15 % Allowed : 15.16 % Favored : 83.69 % 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: 1.42 (0.21), residues: 1779 helix: 2.49 (0.17), residues: 1007 sheet: -0.23 (0.41), residues: 204 loop : -1.57 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 220 HIS 0.003 0.000 HIS A 147 PHE 0.025 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 0.04565 ( 817) hydrogen bonds : angle 3.64599 ( 2370) covalent geometry : bond 0.00222 (14663) covalent geometry : angle 0.49153 (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 141 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 TYR cc_start: 0.8289 (t80) cc_final: 0.8069 (t80) REVERT: C 28 ILE cc_start: 0.7307 (mp) cc_final: 0.7019 (mp) REVERT: C 94 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.6435 (p90) REVERT: C 110 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8339 (mp) REVERT: C 130 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8292 (tm-30) REVERT: E 46 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7475 (tp) outliers start: 18 outliers final: 14 residues processed: 137 average time/residue: 0.2466 time to fit residues: 51.7433 Evaluate side-chains 141 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 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 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 216 ILE 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: 5.9990 chunk 125 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 136 optimal weight: 40.0000 chunk 157 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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** B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.228335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177610 restraints weight = 19462.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.173303 restraints weight = 34352.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.168407 restraints weight = 32895.502| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14663 Z= 0.225 Angle : 0.599 13.676 19727 Z= 0.314 Chirality : 0.043 0.150 2245 Planarity : 0.004 0.056 2466 Dihedral : 8.397 167.895 1974 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.10 % Rotamer: Outliers : 1.41 % Allowed : 15.23 % 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: 1.04 (0.21), residues: 1779 helix: 2.15 (0.17), residues: 1004 sheet: -0.35 (0.39), residues: 217 loop : -1.67 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 54 HIS 0.006 0.001 HIS B 160 PHE 0.024 0.002 PHE A 529 TYR 0.027 0.002 TYR A 314 ARG 0.006 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.07032 ( 817) hydrogen bonds : angle 4.02972 ( 2370) covalent geometry : bond 0.00554 (14663) covalent geometry : angle 0.59914 (19727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4171.70 seconds wall clock time: 74 minutes 7.63 seconds (4447.63 seconds total)