Starting phenix.real_space_refine on Wed Mar 4 15:35:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3b_29691/03_2026/8g3b_29691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3b_29691/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g3b_29691/03_2026/8g3b_29691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3b_29691/03_2026/8g3b_29691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3b_29691/03_2026/8g3b_29691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3b_29691/03_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-5986/lib/python3.9/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: 2.85, per 1000 atoms: 0.20 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: 1.23 Conformation dependent library (CDL) restraints added in 520.6 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: 0.34 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: 2.24 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2340 1.32 - 1.44: 3760 1.44 - 1.57: 8439 1.57 - 1.69: 10 1.69 - 1.82: 114 Bond restraints: 14663 Sorted by residual: bond pdb=" C10 OLA E 401 " pdb=" C9 OLA E 401 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C10 OLA A 701 " pdb=" C9 OLA A 701 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C16 6OU E 402 " pdb=" O18 6OU E 402 " ideal model delta sigma weight residual 1.327 1.461 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C31 6OU E 402 " pdb=" O30 6OU E 402 " ideal model delta sigma weight residual 1.331 1.418 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C14 6OU E 402 " pdb=" C15 6OU E 402 " ideal model delta sigma weight residual 1.521 1.606 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 14658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 19695 5.06 - 10.12: 29 10.12 - 15.18: 0 15.18 - 20.25: 2 20.25 - 25.31: 1 Bond angle restraints: 19727 Sorted by residual: angle pdb=" C40 6OU E 402 " pdb=" C41 6OU E 402 " pdb=" C42 6OU E 402 " ideal model delta sigma weight residual 127.56 152.87 -25.31 3.00e+00 1.11e-01 7.12e+01 angle pdb=" O22 6OU E 402 " pdb=" P23 6OU E 402 " pdb=" O26 6OU E 402 " ideal model delta sigma weight residual 93.95 109.91 -15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" C39 6OU E 402 " pdb=" C40 6OU E 402 " pdb=" C41 6OU E 402 " ideal model delta sigma weight residual 127.60 112.39 15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N PHE A 124 " pdb=" CA PHE A 124 " pdb=" C PHE A 124 " ideal model delta sigma weight residual 112.54 107.02 5.52 1.22e+00 6.72e-01 2.05e+01 angle pdb=" CA VAL E 42 " pdb=" C VAL E 42 " pdb=" O VAL E 42 " ideal model delta sigma weight residual 120.95 116.72 4.23 1.04e+00 9.25e-01 1.66e+01 ... (remaining 19722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.49: 8560 32.49 - 64.97: 269 64.97 - 97.46: 24 97.46 - 129.95: 0 129.95 - 162.43: 4 Dihedral angle restraints: 8857 sinusoidal: 3645 harmonic: 5212 Sorted by residual: dihedral pdb=" C19 6OU E 402 " pdb=" C20 6OU E 402 " pdb=" C21 6OU E 402 " pdb=" O22 6OU E 402 " ideal model delta sinusoidal sigma weight residual -59.00 103.43 -162.43 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA TRP E 70 " pdb=" C TRP E 70 " pdb=" N GLU E 71 " pdb=" CA GLU E 71 " ideal model delta harmonic sigma weight residual 180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C12 6OU E 402 " pdb=" C13 6OU E 402 " pdb=" C14 6OU E 402 " pdb=" C15 6OU E 402 " ideal model delta sinusoidal sigma weight residual 186.47 34.86 151.61 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 8854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1879 0.055 - 0.110: 314 0.110 - 0.164: 48 0.164 - 0.219: 3 0.219 - 0.274: 1 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C20 6OU E 402 " pdb=" C19 6OU E 402 " pdb=" C21 6OU E 402 " pdb=" O30 6OU E 402 " both_signs ideal model delta sigma weight residual False 2.35 2.62 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA GLU A 557 " pdb=" N GLU A 557 " pdb=" C GLU A 557 " pdb=" CB GLU A 557 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CA ILE A 563 " pdb=" N ILE A 563 " pdb=" C ILE A 563 " pdb=" CB ILE A 563 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 2242 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " -0.143 2.00e-02 2.50e+03 1.12e-01 1.26e+02 pdb=" C11 OLA E 401 " 0.068 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " -0.068 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 701 " 0.116 2.00e-02 2.50e+03 9.08e-02 8.25e+01 pdb=" C11 OLA A 701 " -0.055 2.00e-02 2.50e+03 pdb=" C8 OLA A 701 " 0.055 2.00e-02 2.50e+03 pdb=" C9 OLA A 701 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 128 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO E 129 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " 0.033 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2881 2.78 - 3.31: 13431 3.31 - 3.84: 22351 3.84 - 4.37: 23814 4.37 - 4.90: 43326 Nonbonded interactions: 105803 Sorted by model distance: nonbonded pdb=" O THR B 101 " pdb=" ND2 ASN B 105 " model vdw 2.251 3.120 nonbonded pdb=" O GLY C 45 " pdb=" OG1 THR C 48 " model vdw 2.269 3.040 nonbonded pdb=" N ILE B 3 " pdb=" O ILE B 30 " model vdw 2.278 3.120 nonbonded pdb=" OE2 GLU B 5 " pdb=" ND2 ASN B 7 " model vdw 2.290 3.120 nonbonded pdb=" NH1 ARG C 212 " pdb=" OE1 GLN C 224 " model vdw 2.293 3.120 ... (remaining 105798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.370 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 14663 Z= 0.226 Angle : 0.660 25.308 19727 Z= 0.337 Chirality : 0.042 0.274 2245 Planarity : 0.004 0.112 2466 Dihedral : 15.662 162.433 5483 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.00431 (14663) covalent geometry : angle 0.65970 (19727) hydrogen bonds : bond 0.16089 ( 817) hydrogen bonds : angle 5.08245 ( 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 : 0.378 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: 0.1155 time to fit residues: 27.9946 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 : 0.528 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN C 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.234066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.183818 restraints weight = 19594.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.179920 restraints weight = 36060.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.175483 restraints weight = 32697.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.172660 restraints weight = 30610.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168809 restraints weight = 30517.832| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14663 Z= 0.131 Angle : 0.514 10.406 19727 Z= 0.272 Chirality : 0.041 0.170 2245 Planarity : 0.003 0.056 2466 Dihedral : 9.319 156.756 1976 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.77 % Allowed : 5.57 % Favored : 93.67 % 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: -0.22 (0.40), residues: 211 loop : -1.68 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 10 TYR 0.013 0.001 TYR E 57 PHE 0.017 0.001 PHE B 235 TRP 0.007 0.001 TRP A 613 HIS 0.003 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00284 (14663) covalent geometry : angle 0.51368 (19727) hydrogen bonds : bond 0.05683 ( 817) hydrogen bonds : angle 4.16421 ( 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 147 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 376 MET cc_start: 0.2654 (pmm) cc_final: 0.1835 (pmm) REVERT: E 23 MET cc_start: 0.7811 (mmm) cc_final: 0.7386 (tpt) outliers start: 12 outliers final: 12 residues processed: 145 average time/residue: 0.1127 time to fit residues: 24.8105 Evaluate side-chains 142 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 8.9990 chunk 122 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 109 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.235319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.186007 restraints weight = 19626.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.183824 restraints weight = 34354.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.178750 restraints weight = 30156.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175227 restraints weight = 33975.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.173112 restraints weight = 29096.766| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14663 Z= 0.108 Angle : 0.465 10.744 19727 Z= 0.244 Chirality : 0.039 0.162 2245 Planarity : 0.003 0.055 2466 Dihedral : 8.730 154.639 1974 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.96 % Allowed : 8.70 % Favored : 90.34 % 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: 1.35 (0.21), residues: 1779 helix: 2.45 (0.17), residues: 1002 sheet: -0.20 (0.40), residues: 211 loop : -1.63 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 10 TYR 0.011 0.001 TYR E 57 PHE 0.014 0.001 PHE A 529 TRP 0.007 0.001 TRP D 54 HIS 0.002 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00224 (14663) covalent geometry : angle 0.46542 (19727) hydrogen bonds : bond 0.04884 ( 817) hydrogen bonds : angle 3.83209 ( 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 155 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: B 134 TYR cc_start: 0.8285 (t80) cc_final: 0.7984 (t80) REVERT: B 241 LYS cc_start: 0.8818 (ttpt) cc_final: 0.8586 (ttpp) REVERT: C 130 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8511 (tm-30) REVERT: E 23 MET cc_start: 0.7703 (mmm) cc_final: 0.7268 (tpt) outliers start: 15 outliers final: 10 residues processed: 150 average time/residue: 0.1211 time to fit residues: 27.2590 Evaluate side-chains 140 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 100 optimal weight: 0.0040 chunk 169 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4583 r_free = 0.4583 target = 0.233061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.182132 restraints weight = 19496.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.180297 restraints weight = 35286.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176246 restraints weight = 28219.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.171966 restraints weight = 31004.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.169337 restraints weight = 29969.727| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14663 Z= 0.135 Angle : 0.493 10.718 19727 Z= 0.258 Chirality : 0.040 0.153 2245 Planarity : 0.003 0.055 2466 Dihedral : 8.524 154.372 1974 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.54 % Allowed : 11.00 % Favored : 87.46 % 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: 1.32 (0.21), residues: 1779 helix: 2.40 (0.17), residues: 1001 sheet: -0.21 (0.39), residues: 216 loop : -1.59 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 10 TYR 0.016 0.001 TYR A 314 PHE 0.031 0.001 PHE B 235 TRP 0.007 0.001 TRP D 54 HIS 0.004 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00308 (14663) covalent geometry : angle 0.49337 (19727) hydrogen bonds : bond 0.05605 ( 817) hydrogen bonds : angle 3.83412 ( 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 149 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 376 MET cc_start: 0.2102 (pmm) cc_final: 0.1611 (mpp) REVERT: B 241 LYS cc_start: 0.8835 (ttpt) cc_final: 0.8615 (ttpp) REVERT: C 110 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8672 (mp) REVERT: C 130 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8465 (tm-30) REVERT: E 23 MET cc_start: 0.7758 (mmm) cc_final: 0.7329 (tpt) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 0.1168 time to fit residues: 25.3801 Evaluate side-chains 137 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 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 83 GLU Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 78 optimal weight: 0.0870 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.228933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.176459 restraints weight = 19401.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.172655 restraints weight = 34788.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168078 restraints weight = 31590.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164549 restraints weight = 35458.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.161974 restraints weight = 30549.589| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14663 Z= 0.205 Angle : 0.576 9.955 19727 Z= 0.302 Chirality : 0.042 0.167 2245 Planarity : 0.004 0.055 2466 Dihedral : 8.649 155.130 1974 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.73 % Allowed : 12.41 % Favored : 85.86 % 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: 1.06 (0.21), residues: 1779 helix: 2.19 (0.17), residues: 1000 sheet: -0.44 (0.39), residues: 221 loop : -1.64 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.025 0.002 TYR A 314 PHE 0.024 0.002 PHE A 529 TRP 0.010 0.001 TRP D 54 HIS 0.005 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00497 (14663) covalent geometry : angle 0.57632 (19727) hydrogen bonds : bond 0.06956 ( 817) hydrogen bonds : angle 4.05327 ( 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 147 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.522 Fit side-chains REVERT: B 241 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8627 (ttpp) REVERT: C 94 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.6405 (p90) REVERT: C 110 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8598 (mp) REVERT: E 46 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7764 (tp) outliers start: 27 outliers final: 16 residues processed: 143 average time/residue: 0.1113 time to fit residues: 24.4425 Evaluate side-chains 138 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** 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 = 0.4567 r_free = 0.4567 target = 0.231523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.181253 restraints weight = 19324.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.176117 restraints weight = 37839.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.172180 restraints weight = 35739.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170683 restraints weight = 34092.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.168046 restraints weight = 28588.979| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14663 Z= 0.136 Angle : 0.503 10.254 19727 Z= 0.264 Chirality : 0.040 0.151 2245 Planarity : 0.003 0.055 2466 Dihedral : 8.394 154.338 1974 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.92 % Allowed : 13.31 % Favored : 84.77 % 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: 1.25 (0.21), residues: 1779 helix: 2.36 (0.17), residues: 998 sheet: -0.34 (0.39), residues: 218 loop : -1.60 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.015 0.001 TYR A 314 PHE 0.020 0.001 PHE B 235 TRP 0.010 0.001 TRP D 54 HIS 0.003 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00309 (14663) covalent geometry : angle 0.50337 (19727) hydrogen bonds : bond 0.05750 ( 817) hydrogen bonds : angle 3.82931 ( 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 156 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.540 Fit side-chains REVERT: B 241 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8572 (ttpp) REVERT: C 94 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.6478 (p90) REVERT: C 110 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8518 (mp) REVERT: C 130 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8323 (tm-30) REVERT: E 23 MET cc_start: 0.7828 (mmm) cc_final: 0.7318 (tpt) REVERT: E 46 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7674 (tp) outliers start: 30 outliers final: 18 residues processed: 147 average time/residue: 0.1112 time to fit residues: 25.1251 Evaluate side-chains 143 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 1 MET 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: 30.0000 chunk 133 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 173 optimal weight: 30.0000 chunk 79 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4552 r_free = 0.4552 target = 0.229691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.179133 restraints weight = 19256.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.175658 restraints weight = 35835.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.170409 restraints weight = 31051.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.166029 restraints weight = 35459.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.163115 restraints weight = 33627.530| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1712 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= 0.175 Angle : 0.549 11.299 19727 Z= 0.288 Chirality : 0.041 0.147 2245 Planarity : 0.003 0.055 2466 Dihedral : 8.463 158.226 1974 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.30 % Allowed : 13.50 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.10 (0.21), residues: 1779 helix: 2.21 (0.17), residues: 1005 sheet: -0.42 (0.39), residues: 218 loop : -1.65 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.021 0.002 TYR A 314 PHE 0.037 0.001 PHE B 235 TRP 0.010 0.001 TRP D 54 HIS 0.005 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00416 (14663) covalent geometry : angle 0.54916 (19727) hydrogen bonds : bond 0.06434 ( 817) hydrogen bonds : angle 3.94252 ( 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 158 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.553 Fit side-chains REVERT: C 94 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.6611 (p90) REVERT: C 110 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8436 (mp) REVERT: E 46 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7488 (tp) outliers start: 36 outliers final: 23 residues processed: 146 average time/residue: 0.1105 time to fit residues: 24.9848 Evaluate side-chains 146 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 537 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 1 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 127 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** 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 = 0.4570 r_free = 0.4570 target = 0.233222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.184318 restraints weight = 19278.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.180806 restraints weight = 35716.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.173779 restraints weight = 35304.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.169430 restraints weight = 36959.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167184 restraints weight = 31847.663| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14663 Z= 0.115 Angle : 0.498 12.774 19727 Z= 0.259 Chirality : 0.040 0.163 2245 Planarity : 0.003 0.055 2466 Dihedral : 8.175 162.919 1974 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.11 % Rotamer: Outliers : 1.47 % Allowed : 14.91 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.34 (0.21), residues: 1779 helix: 2.46 (0.17), residues: 997 sheet: -0.29 (0.40), residues: 205 loop : -1.58 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.012 0.001 TYR D 57 PHE 0.022 0.001 PHE B 236 TRP 0.010 0.001 TRP D 54 HIS 0.004 0.000 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00244 (14663) covalent geometry : angle 0.49840 (19727) hydrogen bonds : bond 0.05015 ( 817) hydrogen bonds : angle 3.71501 ( 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 155 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.423 Fit side-chains REVERT: B 134 TYR cc_start: 0.8290 (t80) cc_final: 0.8054 (t80) REVERT: B 241 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8664 (ttpp) REVERT: C 28 ILE cc_start: 0.7830 (mp) cc_final: 0.7537 (mp) REVERT: E 46 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7540 (tp) outliers start: 23 outliers final: 15 residues processed: 145 average time/residue: 0.1103 time to fit residues: 24.2090 Evaluate side-chains 143 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 153 LEU 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 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 202 HIS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 308 VAL 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: 1.9990 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 164 optimal weight: 30.0000 chunk 106 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.229356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.177215 restraints weight = 19426.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174051 restraints weight = 33399.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167296 restraints weight = 28526.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.163893 restraints weight = 33594.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.161703 restraints weight = 30667.822| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14663 Z= 0.189 Angle : 0.583 13.475 19727 Z= 0.303 Chirality : 0.042 0.140 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.408 171.245 1974 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.62 % Favored : 94.27 % Rotamer: Outliers : 1.92 % Allowed : 14.52 % Favored : 83.56 % 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: 1.11 (0.21), residues: 1779 helix: 2.22 (0.17), residues: 1006 sheet: -0.40 (0.39), residues: 214 loop : -1.64 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 345 TYR 0.022 0.002 TYR A 314 PHE 0.024 0.001 PHE A 529 TRP 0.009 0.001 TRP D 54 HIS 0.004 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00455 (14663) covalent geometry : angle 0.58295 (19727) hydrogen bonds : bond 0.06635 ( 817) hydrogen bonds : angle 3.95393 ( 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 150 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.464 Fit side-chains REVERT: C 28 ILE cc_start: 0.7773 (mp) cc_final: 0.7481 (mp) REVERT: C 94 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.6740 (p90) REVERT: E 23 MET cc_start: 0.7835 (tpt) cc_final: 0.7582 (tpt) REVERT: E 46 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7744 (tp) outliers start: 30 outliers final: 23 residues processed: 142 average time/residue: 0.1114 time to fit residues: 24.2930 Evaluate side-chains 142 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR 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 D residue 308 VAL 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: 0.1980 chunk 68 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 139 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 0.0050 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.233005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.183263 restraints weight = 19333.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.180796 restraints weight = 35163.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.175529 restraints weight = 28578.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.172171 restraints weight = 34264.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.170169 restraints weight = 27395.226| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14663 Z= 0.119 Angle : 0.521 13.728 19727 Z= 0.271 Chirality : 0.040 0.155 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.204 179.160 1974 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Rotamer: Outliers : 1.47 % Allowed : 15.04 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.29 (0.21), residues: 1779 helix: 2.40 (0.17), residues: 1004 sheet: -0.27 (0.41), residues: 200 loop : -1.64 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 345 TYR 0.014 0.001 TYR D 57 PHE 0.014 0.001 PHE A 529 TRP 0.009 0.001 TRP D 54 HIS 0.003 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00252 (14663) covalent geometry : angle 0.52109 (19727) hydrogen bonds : bond 0.05134 ( 817) hydrogen bonds : angle 3.75292 ( 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 144 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.385 Fit side-chains REVERT: B 134 TYR cc_start: 0.8300 (t80) cc_final: 0.8050 (t80) REVERT: B 241 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8590 (ttpp) REVERT: C 28 ILE cc_start: 0.7734 (mp) cc_final: 0.7444 (mp) REVERT: C 94 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.6671 (p90) REVERT: E 23 MET cc_start: 0.7822 (tpt) cc_final: 0.7561 (tpt) REVERT: E 46 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7612 (tp) outliers start: 23 outliers final: 19 residues processed: 137 average time/residue: 0.1130 time to fit residues: 23.4175 Evaluate side-chains 141 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 94 TYR 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: 0.6980 chunk 135 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.227065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.174401 restraints weight = 19327.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171331 restraints weight = 37195.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.166374 restraints weight = 33580.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164847 restraints weight = 32760.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.162395 restraints weight = 28054.977| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14663 Z= 0.260 Angle : 0.644 13.361 19727 Z= 0.337 Chirality : 0.044 0.156 2245 Planarity : 0.004 0.056 2466 Dihedral : 8.671 173.092 1974 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 1.66 % Allowed : 14.78 % Favored : 83.56 % 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: 0.88 (0.21), residues: 1779 helix: 2.03 (0.16), residues: 1004 sheet: -0.47 (0.41), residues: 202 loop : -1.71 (0.26), residues: 573 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 0.012 0.001 TRP D 54 HIS 0.005 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00641 (14663) covalent geometry : angle 0.64450 (19727) hydrogen bonds : bond 0.07527 ( 817) hydrogen bonds : angle 4.14801 ( 2370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2192.76 seconds wall clock time: 38 minutes 42.98 seconds (2322.98 seconds total)