Starting phenix.real_space_refine on Mon Dec 30 20:29:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpv_18563/12_2024/8qpv_18563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpv_18563/12_2024/8qpv_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_18563/12_2024/8qpv_18563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpv_18563/12_2024/8qpv_18563.map" model { file = "/net/cci-nas-00/data/ceres_data/8qpv_18563/12_2024/8qpv_18563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpv_18563/12_2024/8qpv_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-5532/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: 8.56, per 1000 atoms: 0.61 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: 3.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 1.74 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: 5.17 Time building geometry restraints manager: 3.59 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.180 Set scattering table: 0.150 Process input model: 33.380 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- 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= 0.231 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 *********************** 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 : 1.667 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: 0.2515 time to fit residues: 89.2019 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 : 1.625 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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= 0.289 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 *********************** 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 : 1.635 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 550 TYR cc_start: 0.8000 (m-10) cc_final: 0.7731 (m-10) REVERT: A 777 MET cc_start: 0.8275 (mmm) cc_final: 0.7956 (mmt) REVERT: A 805 ASN cc_start: 0.7981 (t0) cc_final: 0.7752 (t0) REVERT: B 93 TRP cc_start: 0.8225 (p-90) cc_final: 0.7700 (p-90) REVERT: C 39 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6964 (pp20) REVERT: C 43 GLU cc_start: 0.7876 (mp0) cc_final: 0.7446 (mp0) REVERT: C 201 MET cc_start: 0.7729 (tpp) cc_final: 0.7442 (tpp) REVERT: D 132 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7706 (ttt-90) REVERT: F 403 ASN cc_start: 0.7918 (m-40) cc_final: 0.7602 (t0) outliers start: 28 outliers final: 22 residues processed: 209 average time/residue: 0.2482 time to fit residues: 79.1132 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 : 1.648 ------------------------------------------------------------------------------- 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 88 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 132 optimal weight: 0.0770 chunk 108 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 171 optimal weight: 0.3980 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.2742 ------------------------------------------------------------------------------- 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** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN C 162 GLN F 107 ASN F 163 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14356 Z= 0.170 Angle : 0.550 7.838 19494 Z= 0.288 Chirality : 0.042 0.230 2167 Planarity : 0.004 0.057 2566 Dihedral : 4.340 24.672 1991 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.15 % Allowed : 12.30 % Favored : 85.55 % 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: -0.33 (0.20), residues: 1779 helix: 2.00 (0.24), residues: 472 sheet: -0.28 (0.25), residues: 450 loop : -1.50 (0.21), residues: 857 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 0.022 0.001 PHE A 586 TYR 0.030 0.001 TYR C 197 ARG 0.007 0.000 ARG D 132 *********************** 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 222 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 1.595 Fit side-chains TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. 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 550 TYR cc_start: 0.7970 (m-10) cc_final: 0.7656 (m-10) REVERT: A 565 PHE cc_start: 0.7808 (t80) cc_final: 0.7121 (t80) REVERT: A 805 ASN cc_start: 0.7948 (t0) cc_final: 0.7599 (t0) REVERT: B 32 MET cc_start: 0.5816 (mpp) cc_final: 0.5322 (mtm) REVERT: C 39 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6957 (pp20) REVERT: C 43 GLU cc_start: 0.7891 (mp0) cc_final: 0.7441 (mp0) REVERT: F 140 GLU cc_start: 0.8455 (tp30) cc_final: 0.8152 (tp30) REVERT: F 400 MET cc_start: 0.7330 (tmm) cc_final: 0.7033 (tmm) outliers start: 32 outliers final: 24 residues processed: 211 average time/residue: 0.2350 time to fit residues: 75.8418 Evaluate side-chains 201 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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 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 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 283 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.004 0.053 14356 Z= 0.238 Angle : 0.567 8.718 19494 Z= 0.297 Chirality : 0.043 0.239 2167 Planarity : 0.004 0.053 2566 Dihedral : 4.399 23.789 1991 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.89 % Allowed : 13.51 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.34 (0.20), residues: 1779 helix: 1.99 (0.24), residues: 472 sheet: -0.38 (0.24), residues: 451 loop : -1.45 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 148 HIS 0.003 0.001 HIS A 625 PHE 0.034 0.001 PHE A 586 TYR 0.027 0.002 TYR C 197 ARG 0.006 0.000 ARG D 132 *********************** 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 225 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 1.619 Fit side-chains TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it. 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: 0.7923 (m) cc_final: 0.7650 (m) REVERT: A 550 TYR cc_start: 0.7989 (m-10) cc_final: 0.7628 (m-10) REVERT: A 565 PHE cc_start: 0.7845 (t80) cc_final: 0.7060 (t80) REVERT: A 777 MET cc_start: 0.8172 (mmm) cc_final: 0.7803 (mmp) REVERT: A 805 ASN cc_start: 0.8072 (t0) cc_final: 0.7705 (t0) REVERT: B 32 MET cc_start: 0.5950 (mpp) cc_final: 0.5551 (mtm) REVERT: B 239 THR cc_start: 0.7483 (m) cc_final: 0.7268 (t) REVERT: C 39 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6959 (pp20) REVERT: C 43 GLU cc_start: 0.7918 (mp0) cc_final: 0.7433 (mp0) REVERT: F 403 ASN cc_start: 0.7833 (m-40) cc_final: 0.7515 (t0) outliers start: 43 outliers final: 35 residues processed: 208 average time/residue: 0.2429 time to fit residues: 76.9407 Evaluate side-chains 210 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 222 ASP 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 247 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 283 LEU 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 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 31 ASP 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 140 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 86 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** B 350 ASN C 125 GLN F 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14356 Z= 0.285 Angle : 0.587 7.297 19494 Z= 0.309 Chirality : 0.044 0.252 2167 Planarity : 0.004 0.051 2566 Dihedral : 4.499 22.772 1991 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.09 % Allowed : 14.72 % Favored : 82.19 % 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: -0.38 (0.20), residues: 1779 helix: 1.96 (0.24), residues: 469 sheet: -0.42 (0.24), residues: 451 loop : -1.45 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 148 HIS 0.003 0.001 HIS A 625 PHE 0.039 0.002 PHE A 586 TYR 0.026 0.002 TYR C 197 ARG 0.005 0.000 ARG D 132 *********************** 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 236 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 1.905 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 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 550 TYR cc_start: 0.7989 (m-10) cc_final: 0.7585 (m-10) REVERT: A 777 MET cc_start: 0.8168 (mmm) cc_final: 0.7811 (mmp) REVERT: A 805 ASN cc_start: 0.8120 (t0) cc_final: 0.7734 (t0) REVERT: B 32 MET cc_start: 0.5974 (mpp) cc_final: 0.5622 (mtm) REVERT: C 39 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6992 (pp20) REVERT: C 43 GLU cc_start: 0.7938 (mp0) cc_final: 0.7479 (mp0) REVERT: C 202 MET cc_start: 0.8086 (tpp) cc_final: 0.7780 (tpp) REVERT: F 140 GLU cc_start: 0.8496 (tp30) cc_final: 0.8208 (tp30) REVERT: F 403 ASN cc_start: 0.7843 (m-40) cc_final: 0.7612 (t0) outliers start: 46 outliers final: 36 residues processed: 221 average time/residue: 0.2412 time to fit residues: 82.6271 Evaluate side-chains 213 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 2.402 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 222 ASP 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** B 350 ASN F 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14356 Z= 0.284 Angle : 0.603 8.748 19494 Z= 0.318 Chirality : 0.044 0.263 2167 Planarity : 0.004 0.050 2566 Dihedral : 4.558 22.636 1991 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.56 % Allowed : 15.99 % Favored : 80.44 % 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: 1.78 (0.24), residues: 475 sheet: -0.44 (0.24), residues: 448 loop : -1.48 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 148 HIS 0.004 0.001 HIS A 625 PHE 0.038 0.002 PHE A 586 TYR 0.027 0.002 TYR C 197 ARG 0.006 0.000 ARG D 132 *********************** 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 235 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 182 time to evaluate : 1.518 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 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 165 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7998 (tt) REVERT: A 550 TYR cc_start: 0.8026 (m-10) cc_final: 0.7681 (m-10) REVERT: A 777 MET cc_start: 0.8156 (mmm) cc_final: 0.7804 (mmp) REVERT: A 805 ASN cc_start: 0.8162 (t0) cc_final: 0.7815 (t0) REVERT: B 32 MET cc_start: 0.6008 (mpp) cc_final: 0.5592 (mtm) REVERT: C 39 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7049 (pp20) REVERT: C 43 GLU cc_start: 0.7968 (mp0) cc_final: 0.7541 (mp0) REVERT: C 194 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7372 (mtp) REVERT: F 140 GLU cc_start: 0.8476 (tp30) cc_final: 0.8168 (tp30) REVERT: F 403 ASN cc_start: 0.7854 (m-40) cc_final: 0.7550 (t0) outliers start: 53 outliers final: 39 residues processed: 218 average time/residue: 0.2354 time to fit residues: 79.1111 Evaluate side-chains 214 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 222 ASP 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** F 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14356 Z= 0.204 Angle : 0.583 13.289 19494 Z= 0.301 Chirality : 0.043 0.283 2167 Planarity : 0.004 0.048 2566 Dihedral : 4.378 22.423 1991 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.49 % Allowed : 17.54 % Favored : 78.97 % 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: -0.34 (0.20), residues: 1779 helix: 2.01 (0.24), residues: 472 sheet: -0.31 (0.24), residues: 449 loop : -1.50 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 376 HIS 0.002 0.001 HIS A 625 PHE 0.027 0.001 PHE A 586 TYR 0.025 0.001 TYR C 197 ARG 0.005 0.000 ARG D 132 *********************** 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 229 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 1.698 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. revert: symmetry clash TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 165 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7965 (tt) REVERT: A 304 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7037 (mtp) REVERT: A 550 TYR cc_start: 0.8039 (m-10) cc_final: 0.7748 (m-10) REVERT: A 777 MET cc_start: 0.8167 (mmm) cc_final: 0.7838 (mmp) REVERT: A 805 ASN cc_start: 0.8122 (t0) cc_final: 0.7767 (t0) REVERT: B 32 MET cc_start: 0.5966 (mpp) cc_final: 0.5517 (mtm) REVERT: C 39 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7024 (pp20) REVERT: C 43 GLU cc_start: 0.7953 (mp0) cc_final: 0.7517 (mp0) REVERT: C 194 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7295 (mtp) REVERT: C 202 MET cc_start: 0.8151 (tpp) cc_final: 0.7941 (tpp) REVERT: D 41 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8071 (tp40) REVERT: D 157 SER cc_start: 0.9098 (t) cc_final: 0.8471 (p) REVERT: F 140 GLU cc_start: 0.8482 (tp30) cc_final: 0.8157 (tp30) outliers start: 52 outliers final: 38 residues processed: 214 average time/residue: 0.2407 time to fit residues: 80.6785 Evaluate side-chains 211 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 222 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 479 THR 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 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 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 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 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 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 114 optimal weight: 0.0370 chunk 83 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 132 optimal weight: 0.0000 chunk 153 optimal weight: 4.9990 overall best weight: 3.0068 ------------------------------------------------------------------------------- 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** F 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14356 Z= 0.288 Angle : 0.621 12.085 19494 Z= 0.324 Chirality : 0.044 0.296 2167 Planarity : 0.004 0.048 2566 Dihedral : 4.578 22.561 1991 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.23 % Allowed : 18.01 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.20), residues: 1779 helix: 1.93 (0.24), residues: 469 sheet: -0.42 (0.24), residues: 449 loop : -1.52 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 148 HIS 0.005 0.001 HIS C 51 PHE 0.040 0.002 PHE A 586 TYR 0.027 0.002 TYR C 197 ARG 0.005 0.000 ARG C 160 *********************** 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 228 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 1.764 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. revert: symmetry clash TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it. REVERT: A 165 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7946 (tt) REVERT: A 550 TYR cc_start: 0.8046 (m-10) cc_final: 0.7720 (m-10) REVERT: A 777 MET cc_start: 0.8201 (mmm) cc_final: 0.7858 (mmp) REVERT: A 805 ASN cc_start: 0.8190 (t0) cc_final: 0.7838 (t0) REVERT: B 32 MET cc_start: 0.5954 (mpp) cc_final: 0.5461 (mtm) REVERT: C 39 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7135 (pp20) REVERT: C 43 GLU cc_start: 0.7941 (mp0) cc_final: 0.7729 (mp0) REVERT: C 194 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7429 (mtp) REVERT: C 202 MET cc_start: 0.8089 (tpp) cc_final: 0.7877 (tpp) REVERT: D 157 SER cc_start: 0.9141 (t) cc_final: 0.8505 (p) REVERT: F 140 GLU cc_start: 0.8486 (tp30) cc_final: 0.8159 (tp30) outliers start: 48 outliers final: 42 residues processed: 214 average time/residue: 0.2318 time to fit residues: 77.3473 Evaluate side-chains 221 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 222 ASP 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 479 THR 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 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 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 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 84 ASP 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 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 103 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 70 ASN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN F 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14356 Z= 0.172 Angle : 0.587 12.085 19494 Z= 0.301 Chirality : 0.043 0.313 2167 Planarity : 0.004 0.047 2566 Dihedral : 4.349 22.304 1991 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.09 % Allowed : 18.68 % Favored : 78.23 % 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: -0.29 (0.20), residues: 1779 helix: 2.15 (0.24), residues: 464 sheet: -0.30 (0.24), residues: 449 loop : -1.48 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 145 HIS 0.002 0.001 HIS A 677 PHE 0.021 0.001 PHE A 586 TYR 0.026 0.001 TYR C 197 ARG 0.006 0.000 ARG C 160 *********************** 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 225 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 1.681 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: 0.8289 (OUTLIER) cc_final: 0.7919 (tt) REVERT: A 546 TRP cc_start: 0.7417 (m100) cc_final: 0.6677 (m100) REVERT: A 550 TYR cc_start: 0.8047 (m-10) cc_final: 0.7684 (m-10) REVERT: A 777 MET cc_start: 0.8179 (mmm) cc_final: 0.7844 (mmt) REVERT: A 805 ASN cc_start: 0.8130 (t0) cc_final: 0.7778 (t0) REVERT: B 32 MET cc_start: 0.5963 (mpp) cc_final: 0.5459 (mtm) REVERT: C 39 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7167 (pp20) REVERT: C 43 GLU cc_start: 0.7938 (mp0) cc_final: 0.7723 (mp0) REVERT: C 194 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7362 (mtp) REVERT: C 202 MET cc_start: 0.8103 (tpp) cc_final: 0.7898 (tpp) REVERT: D 67 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.5589 (p90) REVERT: D 157 SER cc_start: 0.9114 (t) cc_final: 0.8477 (p) outliers start: 46 outliers final: 40 residues processed: 214 average time/residue: 0.2263 time to fit residues: 75.7181 Evaluate side-chains 210 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 222 ASP 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 532 VAL Chi-restraints excluded: chain A residue 555 HIS 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 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 245 SER 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 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 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 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 160 optimal weight: 0.0170 chunk 138 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- 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 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 14356 Z= 0.255 Angle : 0.798 59.200 19494 Z= 0.456 Chirality : 0.044 0.452 2167 Planarity : 0.004 0.047 2566 Dihedral : 4.349 22.361 1991 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 2.96 % Allowed : 19.22 % Favored : 77.82 % 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: -0.29 (0.20), residues: 1779 helix: 2.14 (0.24), residues: 464 sheet: -0.30 (0.24), residues: 449 loop : -1.48 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 376 HIS 0.004 0.001 HIS A 280 PHE 0.023 0.001 PHE A 586 TYR 0.025 0.001 TYR C 197 ARG 0.004 0.000 ARG D 132 ********************** 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 211 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 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 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: 0.8281 (OUTLIER) cc_final: 0.7908 (tt) REVERT: A 550 TYR cc_start: 0.8036 (m-10) cc_final: 0.7693 (m-10) REVERT: A 777 MET cc_start: 0.8181 (mmm) cc_final: 0.7858 (mmp) REVERT: A 805 ASN cc_start: 0.8117 (t0) cc_final: 0.7760 (t0) REVERT: B 32 MET cc_start: 0.5966 (mpp) cc_final: 0.5469 (mtm) REVERT: C 39 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7172 (pp20) REVERT: C 43 GLU cc_start: 0.7936 (mp0) cc_final: 0.7723 (mp0) REVERT: C 194 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7366 (mtp) REVERT: C 202 MET cc_start: 0.8105 (tpp) cc_final: 0.7899 (tpp) REVERT: D 67 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.5591 (p90) REVERT: D 157 SER cc_start: 0.9113 (t) cc_final: 0.8484 (p) outliers start: 44 outliers final: 40 residues processed: 199 average time/residue: 0.2266 time to fit residues: 70.3400 Evaluate side-chains 211 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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 222 ASP 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 532 VAL Chi-restraints excluded: chain A residue 555 HIS 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 245 SER 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 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 67 TYR Chi-restraints excluded: chain D residue 84 ASP 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 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.087039 restraints weight = 57245.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085637 restraints weight = 36654.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087119 restraints weight = 32758.153| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 14356 Z= 0.255 Angle : 0.798 59.200 19494 Z= 0.456 Chirality : 0.044 0.452 2167 Planarity : 0.004 0.047 2566 Dihedral : 4.349 22.361 1991 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 2.96 % Allowed : 19.22 % Favored : 77.82 % 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: -0.29 (0.20), residues: 1779 helix: 2.14 (0.24), residues: 464 sheet: -0.30 (0.24), residues: 449 loop : -1.48 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 376 HIS 0.004 0.001 HIS A 280 PHE 0.023 0.001 PHE A 586 TYR 0.025 0.001 TYR C 197 ARG 0.004 0.000 ARG D 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2723.42 seconds wall clock time: 51 minutes 19.88 seconds (3079.88 seconds total)