Starting phenix.real_space_refine on Fri Jul 3 14:31:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3b_29691/07_2026/8g3b_29691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3b_29691/07_2026/8g3b_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8g3b_29691/07_2026/8g3b_29691.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g3b_29691/07_2026/8g3b_29691.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g3b_29691/07_2026/8g3b_29691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3b_29691/07_2026/8g3b_29691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3b_29691/07_2026/8g3b_29691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3b_29691/07_2026/8g3b_29691.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.06, per 1000 atoms: 0.21 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: 1.21 Conformation dependent library (CDL) restraints added in 606.0 milliseconds 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: 0.23 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: 2.10 Time building geometry restraints manager: 1.50 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 - 30.32: 8496 30.32 - 60.65: 317 60.65 - 90.97: 30 90.97 - 121.29: 0 121.29 - 151.61: 3 Dihedral angle restraints: 8846 sinusoidal: 3634 harmonic: 5212 Sorted by residual: 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 dihedral pdb=" C07 6OU E 402 " pdb=" C08 6OU E 402 " pdb=" C09 6OU E 402 " pdb=" C10 6OU E 402 " ideal model delta sinusoidal sigma weight residual 179.90 -32.51 -147.59 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 8843 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: 4.330 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.240 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 15.462 151.615 5472 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG B 10 TYR 0.013 0.001 TYR A 314 PHE 0.023 0.001 PHE C 35 TRP 0.009 0.001 TRP A 613 HIS 0.003 0.001 HIS D 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.23 (14663) covalent geometry : angle 0.65970 / 0.34 (19727) hydrogen bonds : bond 0.16089 / 10.48 ( 817) hydrogen bonds : angle 5.08245 / 3.64 ( 2370) *********************** 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 : 0.525 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: 0.0991 time to fit residues: 24.2820 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 : 0.364 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4590 r_free = 0.4590 target = 0.234017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.183466 restraints weight = 19581.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.179508 restraints weight = 36334.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.175019 restraints weight = 32436.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.172710 restraints weight = 32946.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.170289 restraints weight = 27081.833| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0859 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= 0.131 Angle : 0.512 10.318 19727 Z= 0.271 Chirality : 0.041 0.168 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.425 143.590 1965 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.77 % Allowed : 5.63 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1779 helix: 2.27 (0.17), residues: 999 sheet: -0.23 (0.40), residues: 211 loop : -1.68 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.013 0.001 TYR E 57 PHE 0.017 0.001 PHE A 529 TRP 0.007 0.001 TRP A 613 HIS 0.004 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14663) covalent geometry : angle 0.51184 / 0.27 (19727) hydrogen bonds : bond 0.05695 / 3.74 ( 817) hydrogen bonds : angle 4.15276 / 2.94 ( 2370) *********************** 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 146 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 376 MET cc_start: 0.2606 (pmm) cc_final: 0.1757 (pmm) REVERT: E 23 MET cc_start: 0.7793 (mmm) cc_final: 0.7376 (tpt) outliers start: 12 outliers final: 12 residues processed: 144 average time/residue: 0.0964 time to fit residues: 21.5734 Evaluate side-chains 140 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 499 GLU 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 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 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 97 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 149 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 29 HIS 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 = 0.233685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.183777 restraints weight = 19569.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.181364 restraints weight = 36307.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.177574 restraints weight = 28995.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174138 restraints weight = 32348.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171879 restraints weight = 31639.149| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1087 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= 0.122 Angle : 0.481 10.612 19727 Z= 0.254 Chirality : 0.040 0.161 2245 Planarity : 0.003 0.055 2466 Dihedral : 8.009 141.150 1963 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.22 % Allowed : 8.57 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1779 helix: 2.36 (0.17), residues: 1004 sheet: -0.29 (0.39), residues: 217 loop : -1.63 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 10 TYR 0.013 0.001 TYR A 314 PHE 0.017 0.001 PHE A 529 TRP 0.007 0.001 TRP D 54 HIS 0.003 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14663) covalent geometry : angle 0.48099 / 0.25 (19727) hydrogen bonds : bond 0.05370 / 3.52 ( 817) hydrogen bonds : angle 3.90541 / 2.76 ( 2370) *********************** 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 152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: B 241 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8533 (ttpp) REVERT: C 130 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8500 (tm-30) REVERT: E 23 MET cc_start: 0.7720 (mmm) cc_final: 0.7315 (tpt) outliers start: 19 outliers final: 14 residues processed: 147 average time/residue: 0.0941 time to fit residues: 20.8540 Evaluate side-chains 139 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 499 GLU 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 202 HIS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 83 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 100 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN D 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.234011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.182787 restraints weight = 19598.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.177830 restraints weight = 34345.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.171978 restraints weight = 35180.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170577 restraints weight = 32428.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.168687 restraints weight = 23470.757| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1275 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= 0.118 Angle : 0.472 10.891 19727 Z= 0.247 Chirality : 0.039 0.161 2245 Planarity : 0.003 0.055 2466 Dihedral : 7.690 133.526 1963 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.28 % Allowed : 11.07 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.21), residues: 1779 helix: 2.47 (0.17), residues: 999 sheet: -0.20 (0.39), residues: 216 loop : -1.59 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 10 TYR 0.012 0.001 TYR A 314 PHE 0.038 0.001 PHE B 235 TRP 0.007 0.001 TRP D 54 HIS 0.003 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (14663) covalent geometry : angle 0.47182 / 0.25 (19727) hydrogen bonds : bond 0.05183 / 3.40 ( 817) hydrogen bonds : angle 3.78979 / 2.67 ( 2370) *********************** 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 147 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: B 241 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8556 (ttpp) REVERT: C 110 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8606 (mp) REVERT: C 130 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8449 (tm-30) REVERT: E 23 MET cc_start: 0.7763 (mmm) cc_final: 0.7317 (tpt) outliers start: 20 outliers final: 15 residues processed: 142 average time/residue: 0.0978 time to fit residues: 21.3256 Evaluate side-chains 140 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 612 VAL 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 110 LEU Chi-restraints excluded: chain C residue 202 HIS 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 96 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 50 optimal weight: 0.0570 chunk 78 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.234251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.184687 restraints weight = 19545.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.180500 restraints weight = 37986.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175290 restraints weight = 35601.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.172637 restraints weight = 35523.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.170037 restraints weight = 28330.292| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14663 Z= 0.110 Angle : 0.466 10.643 19727 Z= 0.243 Chirality : 0.039 0.165 2245 Planarity : 0.003 0.054 2466 Dihedral : 7.351 126.475 1963 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.41 % Allowed : 11.84 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.21), residues: 1779 helix: 2.53 (0.17), residues: 999 sheet: -0.14 (0.40), residues: 216 loop : -1.57 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.011 0.001 TYR A 314 PHE 0.015 0.001 PHE A 529 TRP 0.008 0.001 TRP D 54 HIS 0.003 0.000 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (14663) covalent geometry : angle 0.46568 / 0.24 (19727) hydrogen bonds : bond 0.04928 / 3.24 ( 817) hydrogen bonds : angle 3.69838 / 2.60 ( 2370) *********************** 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: 22 poor density : 132 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 376 MET cc_start: 0.2264 (pmm) cc_final: 0.1988 (mpp) REVERT: B 240 MET cc_start: 0.7643 (tpp) cc_final: 0.7433 (tpp) REVERT: B 241 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8640 (ttpp) REVERT: C 110 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8645 (mp) REVERT: C 130 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8500 (tm-30) REVERT: C 189 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8533 (mm) REVERT: E 46 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7631 (tp) REVERT: E 98 THR cc_start: 0.8291 (m) cc_final: 0.8080 (p) outliers start: 22 outliers final: 14 residues processed: 148 average time/residue: 0.0931 time to fit residues: 21.2297 Evaluate side-chains 145 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 612 VAL 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 110 LEU Chi-restraints excluded: chain C residue 189 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 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 52 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.229842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.172592 restraints weight = 19280.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169824 restraints weight = 33793.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.165976 restraints weight = 31768.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.161510 restraints weight = 31279.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.159923 restraints weight = 30039.287| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14663 Z= 0.184 Angle : 0.554 10.737 19727 Z= 0.290 Chirality : 0.042 0.143 2245 Planarity : 0.003 0.055 2466 Dihedral : 7.517 136.845 1963 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.92 % Allowed : 12.35 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.21), residues: 1779 helix: 2.30 (0.17), residues: 1000 sheet: -0.34 (0.39), residues: 221 loop : -1.58 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.023 0.002 TYR A 314 PHE 0.024 0.001 PHE A 529 TRP 0.009 0.001 TRP D 54 HIS 0.005 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (14663) covalent geometry : angle 0.55413 / 0.29 (19727) hydrogen bonds : bond 0.06573 / 4.29 ( 817) hydrogen bonds : angle 3.94480 / 2.78 ( 2370) *********************** 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 152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.465 Fit side-chains REVERT: B 241 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8703 (ttpp) REVERT: C 94 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.6417 (p90) REVERT: C 110 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8593 (mp) REVERT: E 23 MET cc_start: 0.7877 (tpt) cc_final: 0.7654 (tpt) REVERT: E 46 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7354 (tp) REVERT: E 98 THR cc_start: 0.8321 (m) cc_final: 0.8090 (p) outliers start: 30 outliers final: 18 residues processed: 146 average time/residue: 0.0948 time to fit residues: 21.2969 Evaluate side-chains 139 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 141 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 167 optimal weight: 0.0970 chunk 115 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 173 optimal weight: 30.0000 chunk 79 optimal weight: 0.3980 chunk 89 optimal weight: 8.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN E 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.234539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.185714 restraints weight = 19345.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.183343 restraints weight = 34801.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.177687 restraints weight = 29027.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.172614 restraints weight = 34081.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.170795 restraints weight = 30198.247| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1622 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= 0.107 Angle : 0.481 11.521 19727 Z= 0.250 Chirality : 0.039 0.163 2245 Planarity : 0.003 0.055 2466 Dihedral : 7.136 135.117 1963 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 1.66 % Allowed : 13.24 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.21), residues: 1779 helix: 2.52 (0.17), residues: 1001 sheet: -0.31 (0.39), residues: 221 loop : -1.47 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.011 0.001 TYR D 57 PHE 0.028 0.001 PHE B 235 TRP 0.009 0.001 TRP D 54 HIS 0.003 0.000 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (14663) covalent geometry : angle 0.48113 / 0.25 (19727) hydrogen bonds : bond 0.04849 / 3.19 ( 817) hydrogen bonds : angle 3.66777 / 2.57 ( 2370) *********************** 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 159 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: B 134 TYR cc_start: 0.8281 (t80) cc_final: 0.8013 (t80) REVERT: B 241 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8651 (ttpp) REVERT: C 94 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.6285 (p90) REVERT: C 110 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8534 (mp) REVERT: C 130 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8365 (tm-30) REVERT: E 23 MET cc_start: 0.7815 (tpt) cc_final: 0.7561 (tpt) REVERT: E 46 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7442 (tp) REVERT: E 98 THR cc_start: 0.8283 (m) cc_final: 0.8070 (p) outliers start: 26 outliers final: 16 residues processed: 151 average time/residue: 0.0927 time to fit residues: 21.5872 Evaluate side-chains 149 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 376 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 127 optimal weight: 30.0000 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 HIS E 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.232667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.183088 restraints weight = 19337.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.177732 restraints weight = 37485.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.173652 restraints weight = 37447.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173159 restraints weight = 33310.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170650 restraints weight = 29347.952| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1683 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= 0.133 Angle : 0.511 13.188 19727 Z= 0.265 Chirality : 0.040 0.146 2245 Planarity : 0.003 0.055 2466 Dihedral : 7.092 137.712 1963 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.00 % Favored : 94.94 % Rotamer: Outliers : 1.86 % Allowed : 13.76 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.21), residues: 1779 helix: 2.47 (0.17), residues: 1001 sheet: -0.31 (0.39), residues: 219 loop : -1.50 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 345 TYR 0.016 0.001 TYR A 314 PHE 0.019 0.001 PHE B 236 TRP 0.008 0.001 TRP D 54 HIS 0.004 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (14663) covalent geometry : angle 0.51149 / 0.27 (19727) hydrogen bonds : bond 0.05489 / 3.60 ( 817) hydrogen bonds : angle 3.73630 / 2.63 ( 2370) *********************** 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 153 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: B 241 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8595 (ttpp) REVERT: C 94 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.6436 (p90) REVERT: C 110 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8464 (mp) REVERT: C 130 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8362 (tm-30) REVERT: E 23 MET cc_start: 0.7921 (tpt) cc_final: 0.7681 (tpt) REVERT: E 46 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7643 (tp) outliers start: 29 outliers final: 20 residues processed: 144 average time/residue: 0.1034 time to fit residues: 22.7527 Evaluate side-chains 142 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 376 MET 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 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 135 GLU 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 87 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 164 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.233696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.185076 restraints weight = 19261.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.179673 restraints weight = 35500.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.174691 restraints weight = 37271.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.174130 restraints weight = 35259.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.171396 restraints weight = 29150.328| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1774 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= 0.118 Angle : 0.497 13.354 19727 Z= 0.258 Chirality : 0.040 0.154 2245 Planarity : 0.003 0.055 2466 Dihedral : 6.928 138.773 1963 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 1.92 % Allowed : 13.76 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.21), residues: 1779 helix: 2.51 (0.17), residues: 1002 sheet: -0.30 (0.39), residues: 219 loop : -1.50 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 345 TYR 0.013 0.001 TYR D 57 PHE 0.023 0.001 PHE B 236 TRP 0.008 0.001 TRP D 54 HIS 0.003 0.000 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (14663) covalent geometry : angle 0.49719 / 0.26 (19727) hydrogen bonds : bond 0.05037 / 3.31 ( 817) hydrogen bonds : angle 3.66141 / 2.58 ( 2370) *********************** 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 156 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.498 Fit side-chains REVERT: B 241 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8594 (ttpp) REVERT: C 28 ILE cc_start: 0.7671 (mp) cc_final: 0.7375 (mp) REVERT: C 94 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.6430 (p90) REVERT: C 110 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8403 (mp) REVERT: E 23 MET cc_start: 0.7946 (tpt) cc_final: 0.7698 (tpt) REVERT: E 46 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7482 (tp) outliers start: 30 outliers final: 21 residues processed: 147 average time/residue: 0.0997 time to fit residues: 22.7404 Evaluate side-chains 147 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 376 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER 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 30 ILE 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 135 GLU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 202 HIS 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 40 optimal weight: 0.0040 chunk 68 optimal weight: 0.0470 chunk 76 optimal weight: 0.6980 chunk 139 optimal weight: 40.0000 chunk 152 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 overall best weight: 0.6892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4580 r_free = 0.4580 target = 0.234231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.184011 restraints weight = 19168.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.180433 restraints weight = 37594.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.175610 restraints weight = 36283.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.174120 restraints weight = 33599.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.171365 restraints weight = 27700.452| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14663 Z= 0.113 Angle : 0.506 13.736 19727 Z= 0.260 Chirality : 0.040 0.157 2245 Planarity : 0.003 0.055 2466 Dihedral : 6.835 138.259 1963 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.11 % Rotamer: Outliers : 1.66 % Allowed : 14.08 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.21), residues: 1779 helix: 2.54 (0.17), residues: 1001 sheet: -0.24 (0.39), residues: 214 loop : -1.47 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 345 TYR 0.013 0.001 TYR D 57 PHE 0.024 0.001 PHE B 236 TRP 0.007 0.001 TRP E 220 HIS 0.003 0.000 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (14663) covalent geometry : angle 0.50624 / 0.26 (19727) hydrogen bonds : bond 0.04878 / 3.21 ( 817) hydrogen bonds : angle 3.62445 / 2.55 ( 2370) ********************** 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 151 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.580 Fit side-chains REVERT: B 241 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8619 (ttpp) REVERT: C 28 ILE cc_start: 0.7797 (mp) cc_final: 0.7504 (mp) REVERT: C 94 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.6470 (p90) REVERT: C 110 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 130 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8346 (tm-30) REVERT: E 23 MET cc_start: 0.7877 (tpt) cc_final: 0.7624 (tpt) REVERT: E 46 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7503 (tp) outliers start: 26 outliers final: 21 residues processed: 143 average time/residue: 0.1143 time to fit residues: 25.2134 Evaluate side-chains 147 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 376 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER 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 135 GLU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 202 HIS 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 44 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4536 r_free = 0.4536 target = 0.227656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.173819 restraints weight = 19302.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.170947 restraints weight = 37318.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167958 restraints weight = 33408.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165969 restraints weight = 31551.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.163540 restraints weight = 27634.819| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14663 Z= 0.251 Angle : 0.642 13.519 19727 Z= 0.334 Chirality : 0.044 0.163 2245 Planarity : 0.004 0.055 2466 Dihedral : 7.686 157.995 1963 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.07 % Favored : 93.87 % Rotamer: Outliers : 1.98 % Allowed : 13.76 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.21), residues: 1779 helix: 2.05 (0.16), residues: 1005 sheet: -0.21 (0.40), residues: 206 loop : -1.63 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 345 TYR 0.032 0.002 TYR A 314 PHE 0.025 0.002 PHE A 529 TRP 0.011 0.001 TRP D 54 HIS 0.005 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.25 (14663) covalent geometry : angle 0.64185 / 0.33 (19727) hydrogen bonds : bond 0.07539 / 4.91 ( 817) hydrogen bonds : angle 4.10818 / 2.89 ( 2370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2008.25 seconds wall clock time: 35 minutes 40.87 seconds (2140.87 seconds total)