Starting phenix.real_space_refine on Sun Nov 17 20:28:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3b_29691/11_2024/8g3b_29691.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3b_29691/11_2024/8g3b_29691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3b_29691/11_2024/8g3b_29691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3b_29691/11_2024/8g3b_29691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3b_29691/11_2024/8g3b_29691.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3b_29691/11_2024/8g3b_29691.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 62 5.16 5 C 9348 2.51 5 N 2373 2.21 5 O 2611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14395 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'6OU': 1, 'OLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.23, per 1000 atoms: 0.57 Number of scatterers: 14395 At special positions: 0 Unit cell: (109, 115.104, 198.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 1 15.00 O 2611 8.00 N 2373 7.00 C 9348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 61.3% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.714A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 41 removed outlier: 3.994A pdb=" N VAL A 22 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.726A pdb=" N ASN A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 46 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.626A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.697A pdb=" N ILE A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 removed outlier: 4.118A pdb=" N GLU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.756A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 176 removed outlier: 4.120A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 removed outlier: 4.111A pdb=" N LEU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 268 removed outlier: 3.930A pdb=" N LEU A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 Processing helix chain 'A' and resid 290 through 316 removed outlier: 3.840A pdb=" N SER A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.582A pdb=" N VAL A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 3.866A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.671A pdb=" N GLN A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.566A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 4.152A pdb=" N ALA A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 556 removed outlier: 3.817A pdb=" N VAL A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 removed outlier: 3.826A pdb=" N TYR A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 602 removed outlier: 3.888A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 3.814A pdb=" N VAL A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 removed outlier: 6.054A pdb=" N PHE A 606 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 644 removed outlier: 3.975A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU A 633 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 635 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.623A pdb=" N ASN B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 4.060A pdb=" N ILE B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 113 " --> pdb=" O LEU B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 113' Processing helix chain 'B' and resid 117 through 131 removed outlier: 3.923A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.821A pdb=" N ARG B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 101 through 108 removed outlier: 3.644A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.569A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.636A pdb=" N GLN C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 193 Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 233 through 246 removed outlier: 4.216A pdb=" N LEU C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 9 through 30 removed outlier: 3.746A pdb=" N ILE D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 72 removed outlier: 3.899A pdb=" N LYS D 59 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 79 removed outlier: 3.643A pdb=" N ALA D 78 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE D 79 " --> pdb=" O VAL D 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 75 through 79' Processing helix chain 'D' and resid 84 through 138 Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 142 through 169 Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 183 through 194 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 217 through 235 Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 290 through 300 Processing helix chain 'D' and resid 324 through 327 Processing helix chain 'D' and resid 328 through 334 removed outlier: 3.667A pdb=" N VAL D 334 " --> pdb=" O HIS D 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 11 through 26 Processing helix chain 'E' and resid 35 through 61 removed outlier: 3.753A pdb=" N PHE E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 removed outlier: 3.824A pdb=" N LYS E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 138 removed outlier: 3.612A pdb=" N ALA E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET E 89 " --> pdb=" O PRO E 85 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 143 through 169 Processing helix chain 'E' and resid 171 through 176 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 218 through 235 Processing helix chain 'E' and resid 264 through 271 Proline residue: E 269 - end of helix Processing helix chain 'E' and resid 281 through 286 Processing helix chain 'E' and resid 290 through 300 Processing helix chain 'E' and resid 324 through 327 Processing helix chain 'E' and resid 328 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.620A pdb=" N LEU A 511 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.724A pdb=" N LYS A 354 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.716A pdb=" N LYS A 425 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 363 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N VAL A 458 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA A 386 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 402 through 404 removed outlier: 7.441A pdb=" N ALA A 403 " --> pdb=" O LYS A 438 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 30 removed outlier: 5.739A pdb=" N ILE B 26 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 8 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 6 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 30 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 4 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 63 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 9 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N HIS B 61 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 90 removed outlier: 6.804A pdb=" N ILE B 90 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 212 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 213 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 39 removed outlier: 6.692A pdb=" N SER C 37 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AB1, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.039A pdb=" N GLY C 88 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 167 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 179 through 182 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 209 removed outlier: 3.716A pdb=" N SER D 245 " --> pdb=" O GLN D 208 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D 316 " --> pdb=" O ASP D 258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 178 through 182 removed outlier: 3.820A pdb=" N SER E 216 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 204 through 209 removed outlier: 3.512A pdb=" N ASP E 258 " --> pdb=" O THR E 316 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS E 305 " --> pdb=" O THR E 321 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2370 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2340 1.32 - 1.44: 3760 1.44 - 1.57: 8439 1.57 - 1.69: 10 1.69 - 1.82: 114 Bond restraints: 14663 Sorted by residual: bond pdb=" C10 OLA E 401 " pdb=" C9 OLA E 401 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C10 OLA A 701 " pdb=" C9 OLA A 701 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C16 6OU E 402 " pdb=" O18 6OU E 402 " ideal model delta sigma weight residual 1.327 1.461 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C31 6OU E 402 " pdb=" O30 6OU E 402 " ideal model delta sigma weight residual 1.331 1.418 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C14 6OU E 402 " pdb=" C15 6OU E 402 " ideal model delta sigma weight residual 1.521 1.606 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 14658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 19695 5.06 - 10.12: 29 10.12 - 15.18: 0 15.18 - 20.25: 2 20.25 - 25.31: 1 Bond angle restraints: 19727 Sorted by residual: angle pdb=" C40 6OU E 402 " pdb=" C41 6OU E 402 " pdb=" C42 6OU E 402 " ideal model delta sigma weight residual 127.56 152.87 -25.31 3.00e+00 1.11e-01 7.12e+01 angle pdb=" O22 6OU E 402 " pdb=" P23 6OU E 402 " pdb=" O26 6OU E 402 " ideal model delta sigma weight residual 93.95 109.91 -15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" C39 6OU E 402 " pdb=" C40 6OU E 402 " pdb=" C41 6OU E 402 " ideal model delta sigma weight residual 127.60 112.39 15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N PHE A 124 " pdb=" CA PHE A 124 " pdb=" C PHE A 124 " ideal model delta sigma weight residual 112.54 107.02 5.52 1.22e+00 6.72e-01 2.05e+01 angle pdb=" CA VAL E 42 " pdb=" C VAL E 42 " pdb=" O VAL E 42 " ideal model delta sigma weight residual 120.95 116.72 4.23 1.04e+00 9.25e-01 1.66e+01 ... (remaining 19722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.49: 8560 32.49 - 64.97: 269 64.97 - 97.46: 24 97.46 - 129.95: 0 129.95 - 162.43: 4 Dihedral angle restraints: 8857 sinusoidal: 3645 harmonic: 5212 Sorted by residual: dihedral pdb=" C19 6OU E 402 " pdb=" C20 6OU E 402 " pdb=" C21 6OU E 402 " pdb=" O22 6OU E 402 " ideal model delta sinusoidal sigma weight residual -59.00 103.43 -162.43 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA TRP E 70 " pdb=" C TRP E 70 " pdb=" N GLU E 71 " pdb=" CA GLU E 71 " ideal model delta harmonic sigma weight residual 180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C12 6OU E 402 " pdb=" C13 6OU E 402 " pdb=" C14 6OU E 402 " pdb=" C15 6OU E 402 " ideal model delta sinusoidal sigma weight residual 186.47 34.86 151.61 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 8854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1879 0.055 - 0.110: 314 0.110 - 0.164: 48 0.164 - 0.219: 3 0.219 - 0.274: 1 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C20 6OU E 402 " pdb=" C19 6OU E 402 " pdb=" C21 6OU E 402 " pdb=" O30 6OU E 402 " both_signs ideal model delta sigma weight residual False 2.35 2.62 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA GLU A 557 " pdb=" N GLU A 557 " pdb=" C GLU A 557 " pdb=" CB GLU A 557 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CA ILE A 563 " pdb=" N ILE A 563 " pdb=" C ILE A 563 " pdb=" CB ILE A 563 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 2242 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " -0.143 2.00e-02 2.50e+03 1.12e-01 1.26e+02 pdb=" C11 OLA E 401 " 0.068 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " -0.068 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 701 " 0.116 2.00e-02 2.50e+03 9.08e-02 8.25e+01 pdb=" C11 OLA A 701 " -0.055 2.00e-02 2.50e+03 pdb=" C8 OLA A 701 " 0.055 2.00e-02 2.50e+03 pdb=" C9 OLA A 701 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 128 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO E 129 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " 0.033 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2881 2.78 - 3.31: 13431 3.31 - 3.84: 22351 3.84 - 4.37: 23814 4.37 - 4.90: 43326 Nonbonded interactions: 105803 Sorted by model distance: nonbonded pdb=" O THR B 101 " pdb=" ND2 ASN B 105 " model vdw 2.251 3.120 nonbonded pdb=" O GLY C 45 " pdb=" OG1 THR C 48 " model vdw 2.269 3.040 nonbonded pdb=" N ILE B 3 " pdb=" O ILE B 30 " model vdw 2.278 3.120 nonbonded pdb=" OE2 GLU B 5 " pdb=" ND2 ASN B 7 " model vdw 2.290 3.120 nonbonded pdb=" NH1 ARG C 212 " pdb=" OE1 GLN C 224 " model vdw 2.293 3.120 ... (remaining 105798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.780 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.600 ------------------------------------------------------------------------------- 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= 0.277 Angle : 0.660 25.308 19727 Z= 0.337 Chirality : 0.042 0.274 2245 Planarity : 0.004 0.112 2466 Dihedral : 15.662 162.433 5483 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1779 helix: 2.05 (0.17), residues: 1000 sheet: -0.28 (0.40), residues: 211 loop : -1.85 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 613 HIS 0.003 0.001 HIS D 165 PHE 0.023 0.001 PHE C 35 TYR 0.013 0.001 TYR A 314 ARG 0.006 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 159 time to evaluate : 1.496 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: 0.2660 time to fit residues: 64.1202 Evaluate side-chains 129 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 160 optimal weight: 9.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN C 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14663 Z= 0.274 Angle : 0.563 10.329 19727 Z= 0.300 Chirality : 0.042 0.172 2245 Planarity : 0.004 0.057 2466 Dihedral : 9.485 157.881 1976 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.83 % Allowed : 6.01 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1779 helix: 2.10 (0.17), residues: 1001 sheet: -0.29 (0.39), residues: 211 loop : -1.75 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.005 0.001 HIS A 147 PHE 0.022 0.001 PHE A 529 TYR 0.020 0.002 TYR A 314 ARG 0.004 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.557 Fit side-chains REVERT: A 376 MET cc_start: 0.2650 (pmm) cc_final: 0.1772 (pmm) outliers start: 13 outliers final: 13 residues processed: 135 average time/residue: 0.2680 time to fit residues: 55.1856 Evaluate side-chains 135 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 chunk 109 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 159 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 261 ASN A 585 ASN B 160 HIS C 29 HIS D 163 GLN E 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 14663 Z= 0.605 Angle : 0.759 9.988 19727 Z= 0.402 Chirality : 0.048 0.172 2245 Planarity : 0.005 0.056 2466 Dihedral : 9.966 165.784 1976 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 1.54 % Allowed : 11.52 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1779 helix: 1.49 (0.16), residues: 999 sheet: -0.56 (0.39), residues: 215 loop : -1.96 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 54 HIS 0.007 0.001 HIS A 147 PHE 0.030 0.002 PHE C 35 TYR 0.037 0.003 TYR A 314 ARG 0.006 0.001 ARG C 83 *********************** 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 140 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.530 Fit side-chains REVERT: C 94 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.6818 (p90) REVERT: C 110 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8478 (mp) REVERT: C 130 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8446 (tm-30) outliers start: 24 outliers final: 12 residues processed: 136 average time/residue: 0.2583 time to fit residues: 53.6642 Evaluate side-chains 125 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 208 SER 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 124 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 84 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN B 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14663 Z= 0.296 Angle : 0.566 9.150 19727 Z= 0.303 Chirality : 0.042 0.149 2245 Planarity : 0.004 0.056 2466 Dihedral : 9.625 169.827 1976 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.86 % Allowed : 13.50 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1779 helix: 1.85 (0.17), residues: 1001 sheet: -0.56 (0.40), residues: 207 loop : -1.88 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 54 HIS 0.005 0.001 HIS B 160 PHE 0.045 0.001 PHE B 235 TYR 0.021 0.002 TYR A 314 ARG 0.004 0.000 ARG C 83 *********************** 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 150 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.662 Fit side-chains REVERT: C 94 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.6809 (p90) REVERT: C 110 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8436 (mp) REVERT: D 54 TRP cc_start: 0.7252 (t-100) cc_final: 0.6524 (t60) REVERT: E 23 MET cc_start: 0.7775 (mmm) cc_final: 0.7539 (tmm) REVERT: E 46 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7692 (tp) outliers start: 29 outliers final: 19 residues processed: 144 average time/residue: 0.2563 time to fit residues: 55.8315 Evaluate side-chains 138 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 76 ASN 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 585 ASN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 208 SER 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 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 142 optimal weight: 50.0000 chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 127 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14663 Z= 0.223 Angle : 0.526 9.833 19727 Z= 0.279 Chirality : 0.041 0.155 2245 Planarity : 0.004 0.056 2466 Dihedral : 9.368 172.478 1976 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.30 % Allowed : 14.33 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1779 helix: 2.08 (0.17), residues: 1001 sheet: -0.51 (0.40), residues: 207 loop : -1.82 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 54 HIS 0.004 0.001 HIS B 160 PHE 0.019 0.001 PHE A 529 TYR 0.016 0.001 TYR A 314 ARG 0.003 0.000 ARG C 83 *********************** 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 158 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 1.544 Fit side-chains revert: symmetry clash REVERT: A 503 GLN cc_start: 0.7365 (pp30) cc_final: 0.6799 (pp30) REVERT: C 110 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8404 (mp) REVERT: C 130 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8330 (tm-30) REVERT: C 189 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8625 (mm) REVERT: D 54 TRP cc_start: 0.7235 (t-100) cc_final: 0.6451 (t60) REVERT: E 46 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7671 (tp) outliers start: 36 outliers final: 22 residues processed: 151 average time/residue: 0.2481 time to fit residues: 57.2587 Evaluate side-chains 141 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 486 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 189 LEU 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 44 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.7980 chunk 154 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 142 optimal weight: 50.0000 chunk 79 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN B 51 ASN B 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14663 Z= 0.236 Angle : 0.535 10.111 19727 Z= 0.283 Chirality : 0.041 0.175 2245 Planarity : 0.004 0.056 2466 Dihedral : 9.246 175.430 1976 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.27 % Rotamer: Outliers : 2.43 % Allowed : 15.29 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1779 helix: 2.10 (0.17), residues: 1005 sheet: -0.57 (0.40), residues: 209 loop : -1.75 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 54 HIS 0.004 0.001 HIS B 160 PHE 0.021 0.001 PHE A 529 TYR 0.019 0.002 TYR B 134 ARG 0.003 0.000 ARG C 83 *********************** 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: 38 poor density : 118 time to evaluate : 1.675 Fit side-chains REVERT: A 376 MET cc_start: 0.2228 (pmm) cc_final: 0.1879 (mpp) REVERT: C 94 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.6753 (p90) REVERT: C 110 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8297 (mp) REVERT: E 46 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7680 (tp) outliers start: 38 outliers final: 28 residues processed: 146 average time/residue: 0.2512 time to fit residues: 56.0105 Evaluate side-chains 148 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 LEU 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 165 optimal weight: 40.0000 chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 125 optimal weight: 0.3980 chunk 96 optimal weight: 0.4980 chunk 144 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1793 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= 0.153 Angle : 0.489 10.774 19727 Z= 0.259 Chirality : 0.040 0.161 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.953 179.112 1976 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.12 % Favored : 94.83 % Rotamer: Outliers : 2.18 % Allowed : 15.87 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.21), residues: 1779 helix: 2.30 (0.17), residues: 1002 sheet: -0.50 (0.41), residues: 207 loop : -1.67 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 54 HIS 0.003 0.000 HIS B 160 PHE 0.040 0.001 PHE B 235 TYR 0.015 0.001 TYR A 448 ARG 0.004 0.000 ARG B 10 *********************** 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 160 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 1.617 Fit side-chains REVERT: C 94 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.6730 (p90) REVERT: C 110 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8310 (mp) REVERT: C 130 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8215 (tm-30) REVERT: E 46 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7656 (tp) outliers start: 34 outliers final: 22 residues processed: 149 average time/residue: 0.2555 time to fit residues: 57.9992 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 : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 570 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 107 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 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 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 0.0670 chunk 15 optimal weight: 0.6980 chunk 134 optimal weight: 0.0980 chunk 155 optimal weight: 9.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14663 Z= 0.136 Angle : 0.481 11.452 19727 Z= 0.252 Chirality : 0.039 0.163 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.585 175.116 1976 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 1.66 % Allowed : 16.63 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1779 helix: 2.43 (0.17), residues: 1004 sheet: -0.29 (0.41), residues: 201 loop : -1.63 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 54 HIS 0.003 0.000 HIS B 160 PHE 0.012 0.001 PHE A 529 TYR 0.015 0.001 TYR A 448 ARG 0.005 0.000 ARG A 345 *********************** 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 154 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.583 Fit side-chains REVERT: A 585 ASN cc_start: 0.8530 (t0) cc_final: 0.8310 (t0) REVERT: C 94 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.6708 (p90) REVERT: C 110 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8309 (mp) REVERT: E 46 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7582 (tp) outliers start: 26 outliers final: 18 residues processed: 146 average time/residue: 0.2614 time to fit residues: 57.8303 Evaluate side-chains 142 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 376 MET Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 30.0000 chunk 150 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** A 550 GLN A 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14663 Z= 0.290 Angle : 0.571 13.110 19727 Z= 0.299 Chirality : 0.042 0.143 2245 Planarity : 0.004 0.056 2466 Dihedral : 8.826 170.758 1976 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.21 % Rotamer: Outliers : 1.98 % Allowed : 16.63 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1779 helix: 2.21 (0.17), residues: 1005 sheet: -0.46 (0.41), residues: 203 loop : -1.72 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 54 HIS 0.006 0.001 HIS B 160 PHE 0.026 0.001 PHE A 529 TYR 0.023 0.002 TYR A 314 ARG 0.005 0.000 ARG A 345 *********************** 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 149 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.617 Fit side-chains REVERT: C 28 ILE cc_start: 0.7325 (mp) cc_final: 0.7056 (mp) REVERT: C 94 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.6900 (p90) REVERT: C 110 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8292 (mp) REVERT: C 130 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8274 (tm-30) REVERT: D 41 MET cc_start: 0.5689 (ttm) cc_final: 0.5434 (ttp) REVERT: E 23 MET cc_start: 0.7845 (tpt) cc_final: 0.7232 (tpt) REVERT: E 46 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7713 (tp) outliers start: 31 outliers final: 24 residues processed: 139 average time/residue: 0.2582 time to fit residues: 54.7103 Evaluate side-chains 142 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 77 THR 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 486 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14663 Z= 0.201 Angle : 0.526 13.612 19727 Z= 0.275 Chirality : 0.041 0.150 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.629 165.568 1976 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 1.92 % Allowed : 16.76 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.21), residues: 1779 helix: 2.29 (0.17), residues: 1005 sheet: -0.44 (0.41), residues: 203 loop : -1.70 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 54 HIS 0.004 0.001 HIS B 160 PHE 0.018 0.001 PHE A 529 TYR 0.015 0.001 TYR A 314 ARG 0.007 0.000 ARG A 345 ********************** 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: 30 poor density : 114 time to evaluate : 1.603 Fit side-chains REVERT: C 28 ILE cc_start: 0.7313 (mp) cc_final: 0.7041 (mp) REVERT: C 94 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.6741 (p90) REVERT: C 110 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8249 (mp) REVERT: C 130 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8267 (tm-30) REVERT: E 46 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7673 (tp) outliers start: 30 outliers final: 21 residues processed: 137 average time/residue: 0.2631 time to fit residues: 55.3711 Evaluate side-chains 138 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 376 MET Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 570 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 107 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain D residue 44 LEU 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 43 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4557 r_free = 0.4557 target = 0.231429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.180695 restraints weight = 19329.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.178037 restraints weight = 34724.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.172878 restraints weight = 31003.459| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14663 Z= 0.160 Angle : 0.505 13.635 19727 Z= 0.262 Chirality : 0.040 0.168 2245 Planarity : 0.003 0.056 2466 Dihedral : 8.330 159.048 1976 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.00 % Favored : 94.94 % Rotamer: Outliers : 1.66 % Allowed : 17.27 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1779 helix: 2.41 (0.17), residues: 1004 sheet: -0.44 (0.41), residues: 202 loop : -1.67 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 220 HIS 0.003 0.000 HIS B 160 PHE 0.028 0.001 PHE B 236 TYR 0.015 0.001 TYR A 448 ARG 0.006 0.000 ARG A 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.07 seconds wall clock time: 47 minutes 37.60 seconds (2857.60 seconds total)