Starting phenix.real_space_refine on Fri May 16 03:20:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpv_18563/05_2025/8qpv_18563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpv_18563/05_2025/8qpv_18563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qpv_18563/05_2025/8qpv_18563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpv_18563/05_2025/8qpv_18563.map" model { file = "/net/cci-nas-00/data/ceres_data/8qpv_18563/05_2025/8qpv_18563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpv_18563/05_2025/8qpv_18563.cif" } resolution = 4.0 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= 0.001 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 8844 2.51 5 N 2438 2.21 5 O 2757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14088 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 6038 Classifications: {'peptide': 769} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 29, 'TRANS': 739} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2715 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 1322 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 178, 1319 Classifications: {'peptide': 178} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 33 Conformer: "B" Number of residues, atoms: 178, 1319 Classifications: {'peptide': 178} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 33 bond proxies already assigned to first conformer: 1338 Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1760 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1385 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 175 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 31} Chain breaks: 3 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 23, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 9.20, per 1000 atoms: 0.65 Number of scatterers: 14088 At special positions: 0 Unit cell: (134.68, 125.06, 140.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 2757 8.00 N 2438 7.00 C 8844 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: 3.71 Conformation dependent library (CDL) restraints added in 2.0 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: 3360 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 22 sheets defined 29.0% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.739A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.751A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.007A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 removed outlier: 3.666A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.686A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 378 through 391 removed outlier: 3.918A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.663A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.776A pdb=" N GLU A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 651' Processing helix chain 'B' and resid 136 through 139 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'C' and resid 39 through 43 removed outlier: 3.641A pdb=" N GLU C 43 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.547A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 Processing helix chain 'C' and resid 190 through 211 removed outlier: 3.898A pdb=" N MET C 201 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.829A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.949A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 4.027A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 4.205A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 209 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 4.144A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 47 Processing helix chain 'F' and resid 62 through 88 removed outlier: 3.854A pdb=" N HIS F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN F 69 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET F 87 " --> pdb=" O MET F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 107 Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 124 through 149 removed outlier: 4.004A pdb=" N ARG F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 164 removed outlier: 3.819A pdb=" N SER F 159 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 420 removed outlier: 3.905A pdb=" N ARG F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET F 400 " --> pdb=" O ARG F 396 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA F 411 " --> pdb=" O SER F 407 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F 420 " --> pdb=" O GLU F 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.551A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.433A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 181 removed outlier: 7.500A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 4.724A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.118A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.972A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 493 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 467 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 425 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.335A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.889A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 390 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.640A pdb=" N ALA B 66 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 5.658A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.862A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.572A pdb=" N VAL B 252 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 286 through 292 removed outlier: 5.198A pdb=" N ASP B 288 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 299 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 305 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 4.102A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.418A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 97 through 99 Processing sheet with id=AB9, first strand: chain 'C' and resid 131 through 135 Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 33 removed outlier: 3.942A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AC3, first strand: chain 'F' and resid 36 through 38 Processing sheet with id=AC4, first strand: chain 'F' and resid 445 through 446 672 hydrogen bonds defined for protein. 1901 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: 5.12 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4751 1.34 - 1.46: 2786 1.46 - 1.58: 6726 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 14356 Sorted by residual: bond pdb=" N VAL A 54 " pdb=" CA VAL A 54 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.03e+01 bond pdb=" N GLU B 107 " pdb=" CA GLU B 107 " ideal model delta sigma weight residual 1.456 1.487 -0.031 9.80e-03 1.04e+04 1.02e+01 bond pdb=" N ASP A 56 " pdb=" CA ASP A 56 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.55e+00 bond pdb=" N THR A 53 " pdb=" CA THR A 53 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.27e-02 6.20e+03 8.48e+00 bond pdb=" N VAL F 599 " pdb=" CA VAL F 599 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.32e-02 5.74e+03 8.07e+00 ... (remaining 14351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 18922 1.74 - 3.48: 498 3.48 - 5.22: 60 5.22 - 6.96: 11 6.96 - 8.70: 3 Bond angle restraints: 19494 Sorted by residual: angle pdb=" C ILE C 57 " pdb=" N LEU C 58 " pdb=" CA LEU C 58 " ideal model delta sigma weight residual 121.03 127.45 -6.42 1.60e+00 3.91e-01 1.61e+01 angle pdb=" CA THR A 53 " pdb=" C THR A 53 " pdb=" O THR A 53 " ideal model delta sigma weight residual 121.56 117.68 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" CA VAL F 599 " pdb=" C VAL F 599 " pdb=" O VAL F 599 " ideal model delta sigma weight residual 121.59 118.11 3.48 1.03e+00 9.43e-01 1.14e+01 angle pdb=" N GLU B 107 " pdb=" CA GLU B 107 " pdb=" C GLU B 107 " ideal model delta sigma weight residual 108.13 111.16 -3.03 9.00e-01 1.23e+00 1.13e+01 angle pdb=" C SER F 48 " pdb=" N VAL F 49 " pdb=" CA VAL F 49 " ideal model delta sigma weight residual 122.96 119.78 3.18 9.50e-01 1.11e+00 1.12e+01 ... (remaining 19489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7783 17.94 - 35.88: 634 35.88 - 53.82: 107 53.82 - 71.76: 20 71.76 - 89.70: 14 Dihedral angle restraints: 8558 sinusoidal: 3301 harmonic: 5257 Sorted by residual: dihedral pdb=" CA SER B 191 " pdb=" C SER B 191 " pdb=" N LEU B 192 " pdb=" CA LEU B 192 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA VAL A 480 " pdb=" C VAL A 480 " pdb=" N ASP A 481 " pdb=" CA ASP A 481 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR C 197 " pdb=" C TYR C 197 " pdb=" N SER C 198 " pdb=" CA SER C 198 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 8555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1469 0.039 - 0.077: 491 0.077 - 0.116: 169 0.116 - 0.155: 31 0.155 - 0.194: 7 Chirality restraints: 2167 Sorted by residual: chirality pdb=" CA ASP A 56 " pdb=" N ASP A 56 " pdb=" C ASP A 56 " pdb=" CB ASP A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CB THR B 43 " pdb=" CA THR B 43 " pdb=" OG1 THR B 43 " pdb=" CG2 THR B 43 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA VAL A 54 " pdb=" N VAL A 54 " pdb=" C VAL A 54 " pdb=" CB VAL A 54 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 2164 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 203 " 0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO A 204 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 517 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 518 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 762 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 763 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 763 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 763 " -0.029 5.00e-02 4.00e+02 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 319 2.69 - 3.24: 14153 3.24 - 3.80: 21290 3.80 - 4.35: 27092 4.35 - 4.90: 45837 Nonbonded interactions: 108691 Sorted by model distance: nonbonded pdb=" O THR C 143 " pdb=" NH2 ARG C 160 " model vdw 2.138 3.120 nonbonded pdb=" OD2 ASP F 26 " pdb=" OG SER F 40 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR C 41 " pdb=" OD1 ASP D 162 " model vdw 2.212 3.040 nonbonded pdb=" OE2 GLU A 521 " pdb=" OH TYR E 28 " model vdw 2.228 3.040 nonbonded pdb=" O GLY A 655 " pdb=" OG1 THR A 659 " model vdw 2.231 3.040 ... (remaining 108686 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 1.230 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.180 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.003 0.047 14356 Z= 0.182 Angle : 0.654 8.700 19494 Z= 0.364 Chirality : 0.044 0.194 2167 Planarity : 0.004 0.096 2566 Dihedral : 13.777 89.701 5198 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.30 % Favored : 93.59 % Rotamer: Outliers : 0.34 % Allowed : 0.47 % Favored : 99.19 % 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: -0.37 (0.20), residues: 1779 helix: 1.93 (0.24), residues: 474 sheet: -0.27 (0.25), residues: 448 loop : -1.53 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 117 HIS 0.007 0.001 HIS A 555 PHE 0.033 0.002 PHE A 586 TYR 0.025 0.002 TYR C 197 ARG 0.010 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.13252 ( 664) hydrogen bonds : angle 6.10744 ( 1901) covalent geometry : bond 0.00348 (14356) covalent geometry : angle 0.65434 (19494) *********************** 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 235 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 230 time to evaluate : 1.764 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 54 VAL cc_start: 0.2886 (OUTLIER) cc_final: 0.2661 (p) REVERT: A 413 ASP cc_start: 0.8243 (m-30) cc_final: 0.7964 (m-30) REVERT: A 777 MET cc_start: 0.8225 (mmm) cc_final: 0.7785 (mmp) REVERT: B 32 MET cc_start: 0.5848 (mpp) cc_final: 0.5048 (mpp) REVERT: B 93 TRP cc_start: 0.8366 (p-90) cc_final: 0.7794 (p-90) REVERT: C 39 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6709 (tm-30) REVERT: D 111 MET cc_start: 0.8709 (tpp) cc_final: 0.8253 (tpp) REVERT: F 83 MET cc_start: 0.7539 (tpt) cc_final: 0.7308 (tpt) outliers start: 5 outliers final: 0 residues processed: 234 average time/residue: 0.2447 time to fit residues: 86.6211 Evaluate side-chains 176 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 0.1980 chunk 102 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN F 163 GLN F 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.086284 restraints weight = 39557.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.085015 restraints weight = 35780.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086164 restraints weight = 33756.201| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14356 Z= 0.193 Angle : 0.626 7.909 19494 Z= 0.330 Chirality : 0.045 0.209 2167 Planarity : 0.005 0.069 2566 Dihedral : 4.653 30.042 1991 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.88 % Allowed : 9.34 % Favored : 88.78 % 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: -0.47 (0.20), residues: 1779 helix: 1.80 (0.23), residues: 475 sheet: -0.41 (0.24), residues: 449 loop : -1.50 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 117 HIS 0.004 0.001 HIS A 625 PHE 0.039 0.002 PHE A 586 TYR 0.031 0.002 TYR C 197 ARG 0.008 0.001 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 664) hydrogen bonds : angle 5.11070 ( 1901) covalent geometry : bond 0.00442 (14356) covalent geometry : angle 0.62552 (19494) *********************** 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 220 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 1.810 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 413 ASP cc_start: 0.8541 (m-30) cc_final: 0.8266 (m-30) REVERT: A 550 TYR cc_start: 0.8023 (m-10) cc_final: 0.7747 (m-10) REVERT: A 777 MET cc_start: 0.8336 (mmm) cc_final: 0.8027 (mmt) REVERT: A 805 ASN cc_start: 0.8097 (t0) cc_final: 0.7852 (t0) REVERT: B 32 MET cc_start: 0.6106 (mpp) cc_final: 0.5883 (mpp) REVERT: B 93 TRP cc_start: 0.8236 (p-90) cc_final: 0.7665 (p-90) REVERT: C 39 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6958 (pp20) REVERT: C 43 GLU cc_start: 0.7877 (mp0) cc_final: 0.7395 (mp0) REVERT: C 162 GLN cc_start: 0.7789 (tt0) cc_final: 0.7416 (tm-30) REVERT: C 201 MET cc_start: 0.7771 (tpp) cc_final: 0.7481 (tpp) REVERT: D 132 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7679 (ttt-90) REVERT: F 403 ASN cc_start: 0.8031 (m-40) cc_final: 0.7672 (t0) outliers start: 28 outliers final: 22 residues processed: 209 average time/residue: 0.2311 time to fit residues: 73.5836 Evaluate side-chains 201 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 585 TYR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 407 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 66 optimal weight: 7.9990 chunk 115 optimal weight: 0.0670 chunk 99 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 160 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN D 125 GLN F 107 ASN F 163 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.085526 restraints weight = 35315.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.085532 restraints weight = 28919.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086042 restraints weight = 31100.958| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14356 Z= 0.170 Angle : 0.583 7.092 19494 Z= 0.308 Chirality : 0.044 0.231 2167 Planarity : 0.004 0.059 2566 Dihedral : 4.542 23.129 1991 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.49 % Allowed : 12.70 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1779 helix: 1.81 (0.23), residues: 476 sheet: -0.42 (0.24), residues: 450 loop : -1.56 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 148 HIS 0.004 0.001 HIS A 625 PHE 0.035 0.002 PHE A 586 TYR 0.031 0.002 TYR C 197 ARG 0.009 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 664) hydrogen bonds : angle 4.88758 ( 1901) covalent geometry : bond 0.00391 (14356) covalent geometry : angle 0.58315 (19494) *********************** 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 223 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.569 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 413 ASP cc_start: 0.8565 (m-30) cc_final: 0.8319 (m-30) REVERT: A 550 TYR cc_start: 0.7917 (m-10) cc_final: 0.7559 (m-10) REVERT: A 565 PHE cc_start: 0.7800 (t80) cc_final: 0.7056 (t80) REVERT: A 805 ASN cc_start: 0.8094 (t0) cc_final: 0.7748 (t0) REVERT: B 32 MET cc_start: 0.6155 (mpp) cc_final: 0.5890 (mtm) REVERT: C 39 GLU cc_start: 0.7671 (mt-10) cc_final: 0.6943 (pp20) REVERT: C 43 GLU cc_start: 0.7931 (mp0) cc_final: 0.7417 (mp0) REVERT: D 132 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7759 (ttt-90) REVERT: F 140 GLU cc_start: 0.8441 (tp30) cc_final: 0.8153 (tp30) REVERT: F 403 ASN cc_start: 0.7935 (m-40) cc_final: 0.7656 (t0) outliers start: 37 outliers final: 30 residues processed: 211 average time/residue: 0.2324 time to fit residues: 74.9331 Evaluate side-chains 209 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 585 TYR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 163 GLN Chi-restraints excluded: chain F residue 412 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 57 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN F 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087354 restraints weight = 46018.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.087223 restraints weight = 46444.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088399 restraints weight = 34117.119| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14356 Z= 0.151 Angle : 0.571 7.852 19494 Z= 0.299 Chirality : 0.043 0.240 2167 Planarity : 0.004 0.054 2566 Dihedral : 4.484 23.403 1991 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.09 % Allowed : 13.84 % Favored : 83.06 % 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: -0.43 (0.20), residues: 1779 helix: 1.93 (0.24), residues: 471 sheet: -0.43 (0.24), residues: 451 loop : -1.51 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 148 HIS 0.003 0.001 HIS A 625 PHE 0.033 0.001 PHE A 586 TYR 0.028 0.002 TYR C 197 ARG 0.008 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 664) hydrogen bonds : angle 4.72999 ( 1901) covalent geometry : bond 0.00348 (14356) covalent geometry : angle 0.57085 (19494) *********************** 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 234 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 1.654 Fit side-chains TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 189 THR cc_start: 0.8005 (m) cc_final: 0.7742 (m) REVERT: A 550 TYR cc_start: 0.7967 (m-10) cc_final: 0.7544 (m-10) REVERT: A 777 MET cc_start: 0.8213 (mmm) cc_final: 0.7826 (mmp) REVERT: A 805 ASN cc_start: 0.8185 (t0) cc_final: 0.7816 (t0) REVERT: B 32 MET cc_start: 0.6168 (mpp) cc_final: 0.5918 (mtm) REVERT: C 39 GLU cc_start: 0.7734 (mt-10) cc_final: 0.6959 (pp20) REVERT: C 43 GLU cc_start: 0.7960 (mp0) cc_final: 0.7441 (mp0) REVERT: D 132 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7684 (ttt-90) REVERT: F 140 GLU cc_start: 0.8451 (tp30) cc_final: 0.8100 (tp30) REVERT: F 403 ASN cc_start: 0.7927 (m-40) cc_final: 0.7613 (t0) outliers start: 46 outliers final: 37 residues processed: 219 average time/residue: 0.2395 time to fit residues: 80.1538 Evaluate side-chains 208 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 585 TYR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 412 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 144 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 62 optimal weight: 0.0070 chunk 72 optimal weight: 0.0770 chunk 75 optimal weight: 0.0770 chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.113772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089855 restraints weight = 57111.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.088818 restraints weight = 35424.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.090020 restraints weight = 31058.881| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14356 Z= 0.096 Angle : 0.544 8.149 19494 Z= 0.281 Chirality : 0.042 0.256 2167 Planarity : 0.004 0.050 2566 Dihedral : 4.193 23.537 1991 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.42 % Allowed : 15.59 % Favored : 81.99 % 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: -0.22 (0.20), residues: 1779 helix: 2.22 (0.24), residues: 462 sheet: -0.23 (0.24), residues: 446 loop : -1.47 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 376 HIS 0.003 0.000 HIS A 280 PHE 0.022 0.001 PHE A 426 TYR 0.027 0.001 TYR F 128 ARG 0.006 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 664) hydrogen bonds : angle 4.45473 ( 1901) covalent geometry : bond 0.00210 (14356) covalent geometry : angle 0.54380 (19494) *********************** 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 230 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 1.868 Fit side-chains TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 383 ASP cc_start: 0.7815 (m-30) cc_final: 0.7485 (m-30) REVERT: A 546 TRP cc_start: 0.7345 (m100) cc_final: 0.6537 (m100) REVERT: A 550 TYR cc_start: 0.8051 (m-10) cc_final: 0.7652 (m-10) REVERT: A 777 MET cc_start: 0.8213 (mmm) cc_final: 0.7855 (mmt) REVERT: A 805 ASN cc_start: 0.8150 (t0) cc_final: 0.7750 (t0) REVERT: B 32 MET cc_start: 0.6194 (mpp) cc_final: 0.5928 (mtm) REVERT: C 39 GLU cc_start: 0.7660 (mt-10) cc_final: 0.6896 (pp20) REVERT: C 43 GLU cc_start: 0.7930 (mp0) cc_final: 0.7411 (mp0) REVERT: C 202 MET cc_start: 0.8235 (tpp) cc_final: 0.8011 (tpp) REVERT: D 41 GLN cc_start: 0.8263 (tm-30) cc_final: 0.8040 (tp40) REVERT: D 157 SER cc_start: 0.9059 (t) cc_final: 0.8388 (p) outliers start: 36 outliers final: 25 residues processed: 218 average time/residue: 0.2296 time to fit residues: 77.9305 Evaluate side-chains 195 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 163 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 97 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** 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 = 0.3453 r_free = 0.3453 target = 0.108403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.084485 restraints weight = 39372.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.084795 restraints weight = 37396.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.085356 restraints weight = 33084.510| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14356 Z= 0.248 Angle : 0.648 7.756 19494 Z= 0.344 Chirality : 0.045 0.263 2167 Planarity : 0.005 0.049 2566 Dihedral : 4.647 22.271 1991 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.43 % Allowed : 16.67 % Favored : 79.91 % 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: -0.50 (0.20), residues: 1779 helix: 1.79 (0.23), residues: 473 sheet: -0.44 (0.24), residues: 452 loop : -1.53 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 148 HIS 0.005 0.001 HIS A 625 PHE 0.050 0.002 PHE A 586 TYR 0.026 0.002 TYR C 197 ARG 0.009 0.001 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 664) hydrogen bonds : angle 4.79761 ( 1901) covalent geometry : bond 0.00575 (14356) covalent geometry : angle 0.64752 (19494) *********************** 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 231 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 1.576 Fit side-chains TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 165 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7966 (tt) REVERT: A 550 TYR cc_start: 0.7976 (m-10) cc_final: 0.7601 (m-10) REVERT: A 777 MET cc_start: 0.8283 (mmm) cc_final: 0.7904 (mmp) REVERT: A 805 ASN cc_start: 0.8273 (t0) cc_final: 0.7904 (t0) REVERT: B 32 MET cc_start: 0.6263 (mpp) cc_final: 0.5983 (mtm) REVERT: C 39 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7016 (pp20) REVERT: C 43 GLU cc_start: 0.7902 (mp0) cc_final: 0.7373 (mp0) REVERT: C 194 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7442 (mtp) REVERT: E 64 MET cc_start: 0.8167 (mmm) cc_final: 0.7943 (mtp) REVERT: F 109 MET cc_start: 0.1253 (mmm) cc_final: 0.0600 (tpt) REVERT: F 140 GLU cc_start: 0.8542 (tp30) cc_final: 0.8282 (tp30) REVERT: F 403 ASN cc_start: 0.7990 (m-40) cc_final: 0.7726 (t0) outliers start: 51 outliers final: 40 residues processed: 214 average time/residue: 0.2274 time to fit residues: 75.1921 Evaluate side-chains 210 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 139 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 115 optimal weight: 0.3980 chunk 90 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** 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 = 0.3518 r_free = 0.3518 target = 0.112584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089027 restraints weight = 39184.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.089264 restraints weight = 33669.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.089439 restraints weight = 33644.898| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14356 Z= 0.104 Angle : 0.571 12.704 19494 Z= 0.294 Chirality : 0.043 0.303 2167 Planarity : 0.004 0.048 2566 Dihedral : 4.243 21.960 1991 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.49 % Allowed : 18.21 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1779 helix: 2.18 (0.24), residues: 466 sheet: -0.27 (0.24), residues: 450 loop : -1.49 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 376 HIS 0.002 0.001 HIS A 280 PHE 0.019 0.001 PHE A 428 TYR 0.025 0.001 TYR C 197 ARG 0.006 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 664) hydrogen bonds : angle 4.45902 ( 1901) covalent geometry : bond 0.00229 (14356) covalent geometry : angle 0.57124 (19494) *********************** 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 209 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 1.548 Fit side-chains TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 165 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7924 (tt) REVERT: A 546 TRP cc_start: 0.7362 (m100) cc_final: 0.6575 (m100) REVERT: A 550 TYR cc_start: 0.8019 (m-10) cc_final: 0.7662 (m-10) REVERT: A 777 MET cc_start: 0.8220 (mmm) cc_final: 0.7875 (mmp) REVERT: A 805 ASN cc_start: 0.8176 (t0) cc_final: 0.7804 (t0) REVERT: B 32 MET cc_start: 0.6202 (mpp) cc_final: 0.5835 (mtm) REVERT: C 39 GLU cc_start: 0.7730 (mt-10) cc_final: 0.6996 (pp20) REVERT: C 43 GLU cc_start: 0.7911 (mp0) cc_final: 0.7415 (mp0) REVERT: C 194 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7364 (mtp) REVERT: C 202 MET cc_start: 0.8150 (tpp) cc_final: 0.7937 (tpp) REVERT: D 41 GLN cc_start: 0.8258 (tm-30) cc_final: 0.8011 (tp40) REVERT: D 157 SER cc_start: 0.9082 (t) cc_final: 0.8448 (p) REVERT: E 64 MET cc_start: 0.8090 (mmm) cc_final: 0.7711 (mtp) REVERT: F 140 GLU cc_start: 0.8504 (tp30) cc_final: 0.8220 (tp30) outliers start: 37 outliers final: 30 residues processed: 199 average time/residue: 0.2230 time to fit residues: 68.8966 Evaluate side-chains 198 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 117 optimal weight: 0.0050 chunk 131 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** 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 = 0.3491 r_free = 0.3491 target = 0.110821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087793 restraints weight = 49662.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.087640 restraints weight = 49436.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088502 restraints weight = 36390.028| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14356 Z= 0.147 Angle : 0.582 12.133 19494 Z= 0.302 Chirality : 0.043 0.299 2167 Planarity : 0.004 0.047 2566 Dihedral : 4.303 21.975 1991 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.89 % Allowed : 18.21 % Favored : 78.90 % 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: -0.30 (0.20), residues: 1779 helix: 2.07 (0.24), residues: 470 sheet: -0.33 (0.24), residues: 448 loop : -1.46 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 145 HIS 0.003 0.001 HIS A 625 PHE 0.032 0.001 PHE A 586 TYR 0.027 0.002 TYR F 128 ARG 0.006 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 664) hydrogen bonds : angle 4.47563 ( 1901) covalent geometry : bond 0.00339 (14356) covalent geometry : angle 0.58216 (19494) *********************** 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 212 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 1.757 Fit side-chains TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 165 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7909 (tt) REVERT: A 550 TYR cc_start: 0.8012 (m-10) cc_final: 0.7657 (m-10) REVERT: A 777 MET cc_start: 0.8279 (mmm) cc_final: 0.7915 (mmt) REVERT: A 805 ASN cc_start: 0.8265 (t0) cc_final: 0.7904 (t0) REVERT: B 32 MET cc_start: 0.6299 (mpp) cc_final: 0.5874 (mtm) REVERT: C 39 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7044 (pp20) REVERT: C 43 GLU cc_start: 0.7889 (mp0) cc_final: 0.7384 (mp0) REVERT: C 194 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7433 (mtp) REVERT: D 67 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.5551 (p90) REVERT: D 157 SER cc_start: 0.9112 (t) cc_final: 0.8465 (p) REVERT: E 64 MET cc_start: 0.8121 (mmm) cc_final: 0.7863 (mtp) REVERT: F 140 GLU cc_start: 0.8502 (tp30) cc_final: 0.8195 (tp30) outliers start: 43 outliers final: 35 residues processed: 201 average time/residue: 0.2255 time to fit residues: 71.0428 Evaluate side-chains 202 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 155 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** 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 = 0.3492 r_free = 0.3492 target = 0.110807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.086613 restraints weight = 38843.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087132 restraints weight = 32528.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.087650 restraints weight = 31223.723| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14356 Z= 0.147 Angle : 0.600 11.880 19494 Z= 0.309 Chirality : 0.043 0.315 2167 Planarity : 0.004 0.046 2566 Dihedral : 4.328 21.912 1991 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.89 % Allowed : 18.41 % Favored : 78.70 % 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: -0.28 (0.20), residues: 1779 helix: 2.21 (0.24), residues: 458 sheet: -0.34 (0.24), residues: 448 loop : -1.46 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.003 0.001 HIS A 625 PHE 0.030 0.001 PHE A 586 TYR 0.030 0.001 TYR F 128 ARG 0.007 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 664) hydrogen bonds : angle 4.48844 ( 1901) covalent geometry : bond 0.00339 (14356) covalent geometry : angle 0.59957 (19494) *********************** 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 212 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 1.639 Fit side-chains TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 165 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7897 (tt) REVERT: A 550 TYR cc_start: 0.7973 (m-10) cc_final: 0.7616 (m-10) REVERT: A 777 MET cc_start: 0.8267 (mmm) cc_final: 0.7855 (mmt) REVERT: A 805 ASN cc_start: 0.8232 (t0) cc_final: 0.7869 (t0) REVERT: B 32 MET cc_start: 0.6138 (mpp) cc_final: 0.5678 (mtm) REVERT: C 39 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7113 (pp20) REVERT: C 43 GLU cc_start: 0.7881 (mp0) cc_final: 0.7664 (mp0) REVERT: C 194 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7428 (mtp) REVERT: D 67 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.5522 (p90) REVERT: D 157 SER cc_start: 0.9133 (t) cc_final: 0.8503 (p) REVERT: E 64 MET cc_start: 0.8185 (mmm) cc_final: 0.7847 (mtp) REVERT: F 140 GLU cc_start: 0.8488 (tp30) cc_final: 0.8178 (tp30) outliers start: 43 outliers final: 37 residues processed: 199 average time/residue: 0.2570 time to fit residues: 79.5929 Evaluate side-chains 207 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 37 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.0060 chunk 38 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 108 optimal weight: 0.0020 chunk 27 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** 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 = 0.3517 r_free = 0.3517 target = 0.112455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.088572 restraints weight = 36342.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087472 restraints weight = 27435.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087840 restraints weight = 31028.150| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14356 Z= 0.104 Angle : 0.572 11.680 19494 Z= 0.293 Chirality : 0.042 0.319 2167 Planarity : 0.004 0.046 2566 Dihedral : 4.167 21.543 1991 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.55 % Allowed : 18.75 % Favored : 78.70 % 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: -0.18 (0.20), residues: 1779 helix: 2.35 (0.24), residues: 458 sheet: -0.26 (0.24), residues: 449 loop : -1.44 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 145 HIS 0.002 0.001 HIS A 280 PHE 0.017 0.001 PHE A 802 TYR 0.026 0.001 TYR F 128 ARG 0.005 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 664) hydrogen bonds : angle 4.37069 ( 1901) covalent geometry : bond 0.00232 (14356) covalent geometry : angle 0.57151 (19494) ********************** 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 219 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 1.612 Fit side-chains TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 165 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7886 (tt) REVERT: A 546 TRP cc_start: 0.7565 (m100) cc_final: 0.6746 (m100) REVERT: A 550 TYR cc_start: 0.8041 (m-10) cc_final: 0.7647 (m-10) REVERT: A 777 MET cc_start: 0.8258 (mmm) cc_final: 0.7901 (mmt) REVERT: A 805 ASN cc_start: 0.8158 (t0) cc_final: 0.7786 (t0) REVERT: B 32 MET cc_start: 0.6115 (mpp) cc_final: 0.5592 (mtm) REVERT: C 39 GLU cc_start: 0.7723 (mt-10) cc_final: 0.6992 (pp20) REVERT: C 43 GLU cc_start: 0.7831 (mp0) cc_final: 0.7338 (mp0) REVERT: C 194 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7522 (mtp) REVERT: D 67 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.5503 (p90) REVERT: D 157 SER cc_start: 0.9107 (t) cc_final: 0.8496 (p) REVERT: F 72 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7717 (mt-10) REVERT: F 140 GLU cc_start: 0.8494 (tp30) cc_final: 0.8177 (tp30) outliers start: 38 outliers final: 35 residues processed: 208 average time/residue: 0.2179 time to fit residues: 70.3552 Evaluate side-chains 205 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 163 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.110440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.085880 restraints weight = 57367.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.084720 restraints weight = 39844.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.086081 restraints weight = 32810.884| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14356 Z= 0.169 Angle : 0.614 11.468 19494 Z= 0.318 Chirality : 0.044 0.312 2167 Planarity : 0.004 0.046 2566 Dihedral : 4.341 21.990 1991 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.96 % Allowed : 19.02 % Favored : 78.02 % 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: -0.26 (0.20), residues: 1779 helix: 2.25 (0.24), residues: 458 sheet: -0.34 (0.24), residues: 449 loop : -1.46 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 145 HIS 0.003 0.001 HIS E 83 PHE 0.037 0.002 PHE A 586 TYR 0.028 0.002 TYR F 128 ARG 0.006 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 664) hydrogen bonds : angle 4.50623 ( 1901) covalent geometry : bond 0.00391 (14356) covalent geometry : angle 0.61425 (19494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4465.93 seconds wall clock time: 79 minutes 16.59 seconds (4756.59 seconds total)