Starting phenix.real_space_refine on Wed Mar 4 10:44:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kso_23021/03_2026/7kso_23021.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kso_23021/03_2026/7kso_23021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kso_23021/03_2026/7kso_23021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kso_23021/03_2026/7kso_23021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kso_23021/03_2026/7kso_23021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kso_23021/03_2026/7kso_23021.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 92 5.16 5 C 8263 2.51 5 N 2322 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13075 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3098 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 375} Chain breaks: 4 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2917 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3109 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 17, 'TRANS': 402} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'HIS:plan': 3, 'GLN:plan1': 11, 'PHE:plan': 7, 'GLU:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 4, 'ARG:plan': 6, 'ASP:plan': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 232 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3054 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 724 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "F" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 165 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 19} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 939 SG CYS A 302 41.272 34.975 42.728 0.99112.68 S ATOM 985 SG CYS A 307 43.600 37.499 41.887 0.87109.30 S ATOM 1591 SG CYS A 531 53.781 18.105 32.983 1.00147.38 S ATOM 1684 SG CYS A 544 53.913 20.388 36.890 1.00127.17 S ATOM 1734 SG CYS A 550 50.230 18.725 34.098 1.00138.70 S ATOM 1591 SG CYS A 531 53.781 18.105 32.983 1.00147.38 S ATOM 1684 SG CYS A 544 53.913 20.388 36.890 1.00127.17 S ATOM 1534 SG CYS A 524 53.362 24.288 32.749 1.00139.61 S ATOM 1719 SG CYS A 548 50.506 22.685 34.072 1.00132.86 S ATOM 1819 SG CYS A 561 46.461 14.460 53.389 1.00122.99 S ATOM 1973 SG CYS A 581 46.466 18.162 54.594 1.00110.26 S ATOM 2031 SG CYS A 589 42.548 15.690 54.701 1.00123.10 S ATOM 1819 SG CYS A 561 46.461 14.460 53.389 1.00122.99 S ATOM 1867 SG CYS A 567 47.437 15.971 57.352 1.00120.66 S ATOM 1906 SG CYS A 572 50.553 14.459 55.048 1.00117.49 S ATOM 1867 SG CYS A 567 47.437 15.971 57.352 1.00120.66 S Time building chain proxies: 2.86, per 1000 atoms: 0.22 Number of scatterers: 13075 At special positions: 0 Unit cell: (97.5, 111.8, 158.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 92 16.00 O 2390 8.00 N 2322 7.00 C 8263 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: 0.87 Conformation dependent library (CDL) restraints added in 583.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 302 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 310 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 307 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 544 " pdb="ZN ZN A 803 " - pdb="ZN ZN A 804 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 531 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 548 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 524 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 567 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 561 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 572 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 567 " pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" NE2 HIS C 471 " 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 23 sheets defined 22.0% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 34 through 62 removed outlier: 3.943A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.984A pdb=" N VAL A 318 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 319' Processing helix chain 'A' and resid 435 through 450 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.722A pdb=" N LYS A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.702A pdb=" N MET A 539 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 4.112A pdb=" N ALA A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 648 through 663 removed outlier: 4.674A pdb=" N LYS A 661 " --> pdb=" O LYS A 657 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 removed outlier: 3.549A pdb=" N ALA A 688 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.612A pdb=" N LYS B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 343 " --> pdb=" O ILE B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'C' and resid 79 through 107 removed outlier: 3.523A pdb=" N HIS C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Proline residue: C 93 - end of helix removed outlier: 3.745A pdb=" N THR C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 126 through 131 removed outlier: 3.919A pdb=" N LYS C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 131' Processing helix chain 'C' and resid 136 through 145 removed outlier: 4.235A pdb=" N LYS C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.576A pdb=" N LEU C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.900A pdb=" N ASP C 505 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 602 removed outlier: 3.941A pdb=" N ARG C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 600 " --> pdb=" O THR C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 624 Processing helix chain 'C' and resid 630 through 649 removed outlier: 4.001A pdb=" N HIS C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET C 637 " --> pdb=" O ASN C 633 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 641 " --> pdb=" O MET C 637 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLN C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS C 646 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.705A pdb=" N PHE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 686 removed outlier: 3.549A pdb=" N ILE C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 28 Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.857A pdb=" N ASP D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.130A pdb=" N TYR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 418 removed outlier: 3.876A pdb=" N ALA E 405 " --> pdb=" O GLN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 470 No H-bonds generated for 'chain 'E' and resid 468 through 470' Processing helix chain 'F' and resid 153 through 164 removed outlier: 3.680A pdb=" N PHE F 157 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.069A pdb=" N ARG A 100 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 134 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU B 125 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 136 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 114 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 100 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 116 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 116 removed outlier: 5.789A pdb=" N SER A 115 " --> pdb=" O GLY A 682 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 removed outlier: 6.537A pdb=" N PHE A 121 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 615 through 619 Processing sheet with id=AA6, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.878A pdb=" N PHE A 638 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 713 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.237A pdb=" N CYS B 84 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASP B 438 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN B 86 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 433 " --> pdb=" O CYS B 429 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN B 415 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.486A pdb=" N THR B 149 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 166 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 184 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN B 176 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS B 182 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 193 through 198 removed outlier: 4.001A pdb=" N GLU B 195 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 215 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE B 228 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 217 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N GLN B 292 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL B 226 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AB2, first strand: chain 'B' and resid 312 through 315 removed outlier: 7.320A pdb=" N LYS B 332 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE B 352 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 368 through 369 Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 234 removed outlier: 4.413A pdb=" N GLN C 356 " --> pdb=" O THR C 162 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N PHE C 164 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR C 354 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ILE E 435 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 203 through 211 removed outlier: 7.012A pdb=" N VAL C 186 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS C 210 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU C 184 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 429 through 431 removed outlier: 3.613A pdb=" N ARG C 486 " --> pdb=" O VAL C 479 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 479 " --> pdb=" O ARG C 486 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 557 through 560 removed outlier: 3.575A pdb=" N ILE C 525 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 47 through 49 removed outlier: 7.331A pdb=" N ASN D 77 " --> pdb=" O ASN D 122 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN D 122 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU D 79 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS D 120 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE D 81 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AC1, first strand: chain 'D' and resid 183 through 185 removed outlier: 3.557A pdb=" N SER D 197 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 230 through 235 removed outlier: 3.756A pdb=" N LYS D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 276 through 281 removed outlier: 3.948A pdb=" N THR D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS D 311 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 320 through 322 removed outlier: 7.021A pdb=" N SER D 336 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP D 346 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU D 366 " --> pdb=" O ASP D 346 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 428 through 431 437 hydrogen bonds defined for protein. 1227 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: 1.90 Time building geometry restraints manager: 1.24 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: 4261 1.34 - 1.46: 2910 1.46 - 1.58: 6076 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 13374 Sorted by residual: bond pdb=" C ARG A 529 " pdb=" N PRO A 530 " ideal model delta sigma weight residual 1.328 1.359 -0.031 1.26e-02 6.30e+03 6.08e+00 bond pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.48e+00 bond pdb=" CA HIS C 561 " pdb=" C HIS C 561 " ideal model delta sigma weight residual 1.520 1.539 -0.018 1.21e-02 6.83e+03 2.23e+00 bond pdb=" C ASN D 282 " pdb=" N PRO D 283 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.21e+00 bond pdb=" CB PHE C 90 " pdb=" CG PHE C 90 " ideal model delta sigma weight residual 1.502 1.536 -0.034 2.30e-02 1.89e+03 2.16e+00 ... (remaining 13369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 17632 1.77 - 3.54: 398 3.54 - 5.31: 71 5.31 - 7.08: 34 7.08 - 8.85: 6 Bond angle restraints: 18141 Sorted by residual: angle pdb=" N ASN F 171 " pdb=" CA ASN F 171 " pdb=" C ASN F 171 " ideal model delta sigma weight residual 111.54 119.01 -7.47 1.36e+00 5.41e-01 3.02e+01 angle pdb=" N PHE F 160 " pdb=" CA PHE F 160 " pdb=" C PHE F 160 " ideal model delta sigma weight residual 111.28 107.36 3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" CA MET A 663 " pdb=" CB MET A 663 " pdb=" CG MET A 663 " ideal model delta sigma weight residual 114.10 121.13 -7.03 2.00e+00 2.50e-01 1.23e+01 angle pdb=" N LEU F 161 " pdb=" CA LEU F 161 " pdb=" C LEU F 161 " ideal model delta sigma weight residual 111.28 114.94 -3.66 1.09e+00 8.42e-01 1.13e+01 angle pdb=" N PHE F 157 " pdb=" CA PHE F 157 " pdb=" C PHE F 157 " ideal model delta sigma weight residual 111.28 114.89 -3.61 1.09e+00 8.42e-01 1.09e+01 ... (remaining 18136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 7488 17.34 - 34.67: 414 34.67 - 52.01: 60 52.01 - 69.35: 17 69.35 - 86.69: 11 Dihedral angle restraints: 7990 sinusoidal: 3039 harmonic: 4951 Sorted by residual: dihedral pdb=" C ASN F 171 " pdb=" N ASN F 171 " pdb=" CA ASN F 171 " pdb=" CB ASN F 171 " ideal model delta harmonic sigma weight residual -122.60 -135.97 13.37 0 2.50e+00 1.60e-01 2.86e+01 dihedral pdb=" N ASN F 171 " pdb=" C ASN F 171 " pdb=" CA ASN F 171 " pdb=" CB ASN F 171 " ideal model delta harmonic sigma weight residual 122.80 136.08 -13.28 0 2.50e+00 1.60e-01 2.82e+01 dihedral pdb=" CA TYR B 244 " pdb=" C TYR B 244 " pdb=" N ASP B 245 " pdb=" CA ASP B 245 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 7987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1906 0.109 - 0.217: 96 0.217 - 0.326: 0 0.326 - 0.435: 1 0.435 - 0.544: 1 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA ASN F 171 " pdb=" N ASN F 171 " pdb=" C ASN F 171 " pdb=" CB ASN F 171 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CA LEU E 447 " pdb=" N LEU E 447 " pdb=" C LEU E 447 " pdb=" CB LEU E 447 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA VAL D 298 " pdb=" N VAL D 298 " pdb=" C VAL D 298 " pdb=" CB VAL D 298 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 2001 not shown) Planarity restraints: 2348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 166 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C SER F 166 " 0.035 2.00e-02 2.50e+03 pdb=" O SER F 166 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO F 167 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 155 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C GLU F 155 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU F 155 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP F 156 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 140 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C LYS C 140 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS C 140 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL C 141 " -0.010 2.00e-02 2.50e+03 ... (remaining 2345 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 382 2.70 - 3.25: 12628 3.25 - 3.80: 19065 3.80 - 4.35: 25310 4.35 - 4.90: 42757 Nonbonded interactions: 100142 Sorted by model distance: nonbonded pdb=" OG1 THR F 154 " pdb=" OE1 GLU F 155 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASP B 431 " pdb=" OG SER B 433 " model vdw 2.202 3.040 nonbonded pdb=" SG CYS A 561 " pdb="ZN ZN A 805 " model vdw 2.233 2.590 nonbonded pdb=" CE2 PHE F 157 " pdb=" CD1 LEU F 161 " model vdw 2.270 3.760 nonbonded pdb=" OG SER D 147 " pdb=" O HIS D 176 " model vdw 2.276 3.040 ... (remaining 100137 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=0.20 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: 0.380 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.080 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.010 0.488 13387 Z= 0.359 Angle : 0.728 8.854 18141 Z= 0.390 Chirality : 0.050 0.544 2004 Planarity : 0.004 0.043 2348 Dihedral : 11.733 86.686 4752 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.29 % Allowed : 1.84 % Favored : 97.86 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.17), residues: 1648 helix: -1.61 (0.23), residues: 308 sheet: -2.99 (0.23), residues: 343 loop : -2.99 (0.16), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 258 TYR 0.014 0.001 TYR B 244 PHE 0.023 0.001 PHE C 86 TRP 0.011 0.001 TRP D 345 HIS 0.004 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00444 (13374) covalent geometry : angle 0.72845 (18141) hydrogen bonds : bond 0.14017 ( 437) hydrogen bonds : angle 6.81476 ( 1227) metal coordination : bond 0.27586 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 421 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 449 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 71 MET cc_start: 0.6625 (tpt) cc_final: 0.6319 (tmm) REVERT: A 112 TYR cc_start: 0.7061 (m-80) cc_final: 0.6825 (m-80) REVERT: A 117 LEU cc_start: 0.8426 (mt) cc_final: 0.8202 (mt) REVERT: A 558 PHE cc_start: 0.8405 (t80) cc_final: 0.8173 (t80) REVERT: A 643 CYS cc_start: 0.8367 (m) cc_final: 0.8014 (t) REVERT: A 666 PHE cc_start: 0.7673 (m-80) cc_final: 0.7411 (m-80) REVERT: B 103 TRP cc_start: 0.8435 (m-10) cc_final: 0.8089 (m-10) REVERT: B 109 ASP cc_start: 0.7355 (p0) cc_final: 0.7142 (p0) REVERT: B 139 VAL cc_start: 0.8326 (t) cc_final: 0.7750 (t) REVERT: B 240 LEU cc_start: 0.9042 (mt) cc_final: 0.8714 (mm) REVERT: B 252 MET cc_start: 0.8467 (tpp) cc_final: 0.8131 (tpp) REVERT: B 265 ILE cc_start: 0.8741 (pt) cc_final: 0.8449 (mm) REVERT: B 375 LYS cc_start: 0.8029 (mttt) cc_final: 0.7699 (mttt) REVERT: C 85 LEU cc_start: 0.8219 (tt) cc_final: 0.7953 (tt) REVERT: C 91 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7260 (tm-30) REVERT: C 561 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.7059 (p-80) REVERT: C 657 MET cc_start: 0.8355 (mtm) cc_final: 0.7653 (mpp) REVERT: D 13 GLU cc_start: 0.7564 (tt0) cc_final: 0.7171 (tt0) REVERT: D 44 SER cc_start: 0.9029 (t) cc_final: 0.8822 (p) REVERT: D 49 TRP cc_start: 0.8665 (m100) cc_final: 0.8300 (m100) REVERT: D 185 TRP cc_start: 0.8249 (m100) cc_final: 0.7824 (m100) REVERT: D 194 LEU cc_start: 0.9165 (mt) cc_final: 0.8906 (mt) REVERT: D 203 CYS cc_start: 0.7709 (m) cc_final: 0.7087 (m) REVERT: D 242 LEU cc_start: 0.7863 (pt) cc_final: 0.7576 (pp) REVERT: D 275 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7101 (mp0) REVERT: D 306 LEU cc_start: 0.9256 (mt) cc_final: 0.8976 (mp) REVERT: D 331 THR cc_start: 0.8219 (p) cc_final: 0.7905 (t) REVERT: D 336 SER cc_start: 0.9186 (p) cc_final: 0.8525 (m) REVERT: D 381 SER cc_start: 0.8871 (t) cc_final: 0.8272 (p) REVERT: E 430 PHE cc_start: 0.8316 (m-80) cc_final: 0.8083 (m-10) REVERT: E 476 HIS cc_start: 0.7336 (t-90) cc_final: 0.7044 (t70) REVERT: E 492 ILE cc_start: 0.7542 (mt) cc_final: 0.7312 (mt) outliers start: 4 outliers final: 2 residues processed: 425 average time/residue: 0.1075 time to fit residues: 67.2337 Evaluate side-chains 262 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 160 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS C 607 ASN D 128 ASN D 370 HIS F 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118660 restraints weight = 23329.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121598 restraints weight = 15062.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123499 restraints weight = 11406.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.124814 restraints weight = 9554.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125504 restraints weight = 8484.605| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13387 Z= 0.165 Angle : 0.620 8.508 18141 Z= 0.317 Chirality : 0.047 0.307 2004 Planarity : 0.005 0.084 2348 Dihedral : 4.497 36.295 1796 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.14 % Allowed : 10.68 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.18), residues: 1648 helix: -0.62 (0.26), residues: 327 sheet: -2.41 (0.23), residues: 370 loop : -2.34 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 529 TYR 0.023 0.002 TYR A 521 PHE 0.028 0.002 PHE C 656 TRP 0.017 0.002 TRP D 345 HIS 0.009 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00375 (13374) covalent geometry : angle 0.61983 (18141) hydrogen bonds : bond 0.03761 ( 437) hydrogen bonds : angle 5.37900 ( 1227) metal coordination : bond 0.00505 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 0.409 Fit side-chains TARDY: cannot create tardy model for: "HIS C 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.6681 (mtpt) cc_final: 0.6369 (mttt) REVERT: A 112 TYR cc_start: 0.7311 (m-80) cc_final: 0.7009 (m-80) REVERT: A 558 PHE cc_start: 0.8731 (t80) cc_final: 0.8409 (t80) REVERT: A 643 CYS cc_start: 0.8777 (m) cc_final: 0.8491 (t) REVERT: B 119 ASN cc_start: 0.6873 (t0) cc_final: 0.6569 (t0) REVERT: B 240 LEU cc_start: 0.9203 (mt) cc_final: 0.8980 (mm) REVERT: B 252 MET cc_start: 0.8678 (tpp) cc_final: 0.8331 (tpp) REVERT: B 310 ASP cc_start: 0.8885 (m-30) cc_final: 0.8451 (t0) REVERT: C 85 LEU cc_start: 0.8449 (tt) cc_final: 0.8188 (tt) REVERT: C 91 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7859 (tm-30) REVERT: C 657 MET cc_start: 0.8356 (mtm) cc_final: 0.7671 (mpp) REVERT: D 15 ARG cc_start: 0.8867 (mpt180) cc_final: 0.8648 (mmt-90) REVERT: D 44 SER cc_start: 0.9348 (t) cc_final: 0.9063 (p) REVERT: D 242 LEU cc_start: 0.8327 (pt) cc_final: 0.8000 (pp) REVERT: D 275 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7764 (mp0) REVERT: D 306 LEU cc_start: 0.9261 (mt) cc_final: 0.9011 (mp) REVERT: D 380 PHE cc_start: 0.9163 (p90) cc_final: 0.8941 (p90) REVERT: D 381 SER cc_start: 0.9092 (t) cc_final: 0.8734 (m) REVERT: E 476 HIS cc_start: 0.7383 (t-90) cc_final: 0.5834 (t-90) REVERT: E 492 ILE cc_start: 0.8311 (mt) cc_final: 0.8089 (mt) outliers start: 29 outliers final: 13 residues processed: 286 average time/residue: 0.0953 time to fit residues: 41.6460 Evaluate side-chains 233 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 220 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 10 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 449 HIS D 27 ASN D 188 ASN E 450 HIS E 498 GLN F 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100760 restraints weight = 22414.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102917 restraints weight = 15293.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104511 restraints weight = 12312.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105405 restraints weight = 10580.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106189 restraints weight = 9653.251| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 13387 Z= 0.365 Angle : 0.796 8.791 18141 Z= 0.414 Chirality : 0.051 0.244 2004 Planarity : 0.006 0.077 2348 Dihedral : 5.426 20.473 1790 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.90 % Allowed : 11.86 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.19), residues: 1648 helix: -0.55 (0.26), residues: 329 sheet: -2.07 (0.25), residues: 382 loop : -2.12 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 340 TYR 0.023 0.003 TYR B 365 PHE 0.028 0.003 PHE C 512 TRP 0.028 0.003 TRP A 434 HIS 0.012 0.002 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00813 (13374) covalent geometry : angle 0.79605 (18141) hydrogen bonds : bond 0.04554 ( 437) hydrogen bonds : angle 5.81194 ( 1227) metal coordination : bond 0.00911 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8585 (t80) cc_final: 0.8150 (t80) REVERT: A 283 LYS cc_start: 0.7509 (mttt) cc_final: 0.7007 (pttp) REVERT: A 319 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6448 (p90) REVERT: B 109 ASP cc_start: 0.7311 (p0) cc_final: 0.7086 (p0) REVERT: B 236 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7910 (mtt-85) REVERT: B 252 MET cc_start: 0.8909 (tpp) cc_final: 0.8668 (tpp) REVERT: B 262 LEU cc_start: 0.9353 (tp) cc_final: 0.9027 (tt) REVERT: C 91 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8095 (tm-30) REVERT: C 95 GLN cc_start: 0.8917 (tp40) cc_final: 0.8582 (tm-30) REVERT: C 117 TYR cc_start: 0.9155 (p90) cc_final: 0.8930 (p90) REVERT: C 493 GLU cc_start: 0.7348 (pm20) cc_final: 0.7103 (pm20) REVERT: C 657 MET cc_start: 0.8534 (mtm) cc_final: 0.7737 (mpp) REVERT: D 44 SER cc_start: 0.9474 (t) cc_final: 0.9193 (p) REVERT: D 242 LEU cc_start: 0.8331 (pt) cc_final: 0.8112 (pp) REVERT: D 250 GLN cc_start: 0.8238 (mp10) cc_final: 0.7670 (mp10) REVERT: D 360 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7459 (tt0) REVERT: E 476 HIS cc_start: 0.7330 (t-90) cc_final: 0.7013 (t-90) REVERT: E 489 ASP cc_start: 0.8900 (t0) cc_final: 0.8687 (t0) REVERT: F 159 THR cc_start: 0.7845 (p) cc_final: 0.7624 (p) outliers start: 53 outliers final: 34 residues processed: 258 average time/residue: 0.1050 time to fit residues: 40.5295 Evaluate side-chains 221 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 156 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 0.0470 chunk 133 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 HIS B 194 ASN D 188 ASN D 316 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.142004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107238 restraints weight = 22526.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110018 restraints weight = 14758.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111774 restraints weight = 11307.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.112956 restraints weight = 9609.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113600 restraints weight = 8659.729| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13387 Z= 0.121 Angle : 0.585 8.892 18141 Z= 0.298 Chirality : 0.046 0.284 2004 Planarity : 0.004 0.049 2348 Dihedral : 4.599 18.437 1790 Min Nonbonded Distance : 1.255 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.65 % Allowed : 14.51 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.19), residues: 1648 helix: -0.13 (0.27), residues: 333 sheet: -1.74 (0.25), residues: 377 loop : -1.91 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 563 TYR 0.018 0.002 TYR A 521 PHE 0.017 0.002 PHE C 86 TRP 0.034 0.002 TRP D 205 HIS 0.009 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00275 (13374) covalent geometry : angle 0.58477 (18141) hydrogen bonds : bond 0.03546 ( 437) hydrogen bonds : angle 5.24799 ( 1227) metal coordination : bond 0.00120 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8447 (t80) cc_final: 0.8076 (t80) REVERT: A 283 LYS cc_start: 0.7491 (mttt) cc_final: 0.6965 (pttp) REVERT: A 319 TYR cc_start: 0.6998 (p90) cc_final: 0.6317 (p90) REVERT: A 558 PHE cc_start: 0.8643 (t80) cc_final: 0.8305 (t80) REVERT: B 336 MET cc_start: 0.8719 (pmm) cc_final: 0.8460 (ppp) REVERT: B 366 MET cc_start: 0.8966 (mmm) cc_final: 0.8677 (mmm) REVERT: C 85 LEU cc_start: 0.8753 (tt) cc_final: 0.8462 (tt) REVERT: C 91 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8059 (tm-30) REVERT: C 95 GLN cc_start: 0.9049 (tp40) cc_final: 0.8655 (tm-30) REVERT: C 117 TYR cc_start: 0.9078 (p90) cc_final: 0.8753 (p90) REVERT: C 657 MET cc_start: 0.8416 (mtm) cc_final: 0.7681 (mpp) REVERT: D 13 GLU cc_start: 0.7675 (tt0) cc_final: 0.7369 (tt0) REVERT: D 44 SER cc_start: 0.9302 (t) cc_final: 0.8980 (p) REVERT: D 316 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.7671 (m170) REVERT: E 452 MET cc_start: 0.6498 (ppp) cc_final: 0.6262 (ppp) REVERT: E 476 HIS cc_start: 0.7276 (t-90) cc_final: 0.6994 (t-90) REVERT: F 159 THR cc_start: 0.7835 (p) cc_final: 0.7618 (p) outliers start: 36 outliers final: 18 residues processed: 267 average time/residue: 0.0991 time to fit residues: 40.1129 Evaluate side-chains 226 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 404 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 103 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.137771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102610 restraints weight = 22956.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105053 restraints weight = 15412.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106703 restraints weight = 12075.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107738 restraints weight = 10330.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108070 restraints weight = 9380.238| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13387 Z= 0.228 Angle : 0.647 10.930 18141 Z= 0.332 Chirality : 0.046 0.211 2004 Planarity : 0.004 0.045 2348 Dihedral : 4.761 19.089 1790 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.17 % Allowed : 16.86 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.20), residues: 1648 helix: -0.12 (0.28), residues: 331 sheet: -1.69 (0.26), residues: 374 loop : -1.77 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 563 TYR 0.014 0.002 TYR B 244 PHE 0.023 0.002 PHE D 152 TRP 0.046 0.002 TRP D 205 HIS 0.011 0.001 HIS D 316 Details of bonding type rmsd covalent geometry : bond 0.00519 (13374) covalent geometry : angle 0.64716 (18141) hydrogen bonds : bond 0.03849 ( 437) hydrogen bonds : angle 5.27617 ( 1227) metal coordination : bond 0.00480 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8552 (t80) cc_final: 0.8008 (t80) REVERT: A 283 LYS cc_start: 0.7548 (mttt) cc_final: 0.7021 (pttp) REVERT: B 252 MET cc_start: 0.8685 (tpp) cc_final: 0.8303 (tpp) REVERT: B 336 MET cc_start: 0.8749 (pmm) cc_final: 0.8463 (ppp) REVERT: C 91 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8058 (tm-30) REVERT: C 95 GLN cc_start: 0.9008 (tp40) cc_final: 0.8733 (tm-30) REVERT: C 98 ARG cc_start: 0.8777 (mmt90) cc_final: 0.8268 (tpp-160) REVERT: C 196 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8674 (ttp-170) REVERT: C 460 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8552 (tp) REVERT: C 657 MET cc_start: 0.8497 (mtm) cc_final: 0.7651 (mpp) REVERT: D 13 GLU cc_start: 0.7922 (tt0) cc_final: 0.7633 (tt0) REVERT: D 44 SER cc_start: 0.9426 (t) cc_final: 0.9149 (p) REVERT: E 452 MET cc_start: 0.6549 (ppp) cc_final: 0.6198 (ppp) outliers start: 43 outliers final: 25 residues processed: 229 average time/residue: 0.0983 time to fit residues: 34.4457 Evaluate side-chains 220 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 484 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 125 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 92 optimal weight: 50.0000 chunk 150 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.100539 restraints weight = 22979.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103164 restraints weight = 14909.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.104888 restraints weight = 11458.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.105863 restraints weight = 9725.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106621 restraints weight = 8825.236| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13387 Z= 0.232 Angle : 0.652 9.847 18141 Z= 0.336 Chirality : 0.047 0.306 2004 Planarity : 0.004 0.049 2348 Dihedral : 4.915 19.764 1790 Min Nonbonded Distance : 1.166 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.90 % Allowed : 17.30 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.20), residues: 1648 helix: -0.18 (0.27), residues: 335 sheet: -1.63 (0.26), residues: 365 loop : -1.79 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.014 0.002 TYR A 521 PHE 0.014 0.002 PHE D 368 TRP 0.034 0.002 TRP D 388 HIS 0.013 0.001 HIS E 476 Details of bonding type rmsd covalent geometry : bond 0.00525 (13374) covalent geometry : angle 0.65230 (18141) hydrogen bonds : bond 0.03914 ( 437) hydrogen bonds : angle 5.32082 ( 1227) metal coordination : bond 0.00547 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7590 (mttt) cc_final: 0.7047 (pttp) REVERT: B 252 MET cc_start: 0.8585 (tpp) cc_final: 0.8253 (tpp) REVERT: C 85 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8567 (tt) REVERT: C 91 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8260 (tm-30) REVERT: C 95 GLN cc_start: 0.9047 (tp40) cc_final: 0.8826 (tm-30) REVERT: C 196 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8661 (ttp-170) REVERT: C 460 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8710 (tp) REVERT: C 493 GLU cc_start: 0.7419 (pm20) cc_final: 0.7068 (pm20) REVERT: D 13 GLU cc_start: 0.8023 (tt0) cc_final: 0.7726 (tt0) REVERT: D 44 SER cc_start: 0.9442 (t) cc_final: 0.9218 (p) REVERT: D 147 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8176 (t) REVERT: E 452 MET cc_start: 0.6791 (ppp) cc_final: 0.6400 (ppp) REVERT: E 476 HIS cc_start: 0.7975 (t-90) cc_final: 0.7659 (t-90) REVERT: E 489 ASP cc_start: 0.8907 (t0) cc_final: 0.8408 (t0) REVERT: E 491 ASN cc_start: 0.8830 (p0) cc_final: 0.8135 (p0) outliers start: 53 outliers final: 38 residues processed: 232 average time/residue: 0.0982 time to fit residues: 34.9836 Evaluate side-chains 234 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 484 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 130 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104105 restraints weight = 22891.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106703 restraints weight = 15117.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108433 restraints weight = 11665.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.109336 restraints weight = 9910.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109879 restraints weight = 9031.030| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13387 Z= 0.140 Angle : 0.596 10.015 18141 Z= 0.305 Chirality : 0.045 0.186 2004 Planarity : 0.004 0.040 2348 Dihedral : 4.655 18.752 1790 Min Nonbonded Distance : 1.208 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.24 % Allowed : 18.48 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.20), residues: 1648 helix: 0.03 (0.28), residues: 333 sheet: -1.47 (0.26), residues: 378 loop : -1.69 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 409 TYR 0.014 0.002 TYR A 521 PHE 0.018 0.001 PHE D 152 TRP 0.036 0.002 TRP D 388 HIS 0.007 0.001 HIS E 476 Details of bonding type rmsd covalent geometry : bond 0.00321 (13374) covalent geometry : angle 0.59619 (18141) hydrogen bonds : bond 0.03594 ( 437) hydrogen bonds : angle 5.11156 ( 1227) metal coordination : bond 0.00239 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7564 (mttt) cc_final: 0.7033 (pttp) REVERT: A 303 PHE cc_start: 0.8899 (m-80) cc_final: 0.8626 (m-10) REVERT: B 252 MET cc_start: 0.8633 (tpp) cc_final: 0.8296 (tpp) REVERT: C 85 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8588 (tt) REVERT: C 95 GLN cc_start: 0.8951 (tp40) cc_final: 0.8745 (tm-30) REVERT: C 493 GLU cc_start: 0.7339 (pm20) cc_final: 0.6995 (pm20) REVERT: C 684 MET cc_start: 0.7019 (ppp) cc_final: 0.6287 (ppp) REVERT: D 13 GLU cc_start: 0.7831 (tt0) cc_final: 0.7572 (tt0) REVERT: D 44 SER cc_start: 0.9417 (t) cc_final: 0.9075 (p) REVERT: D 147 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8203 (t) REVERT: D 242 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8179 (pp) REVERT: E 409 ARG cc_start: 0.8721 (ptp90) cc_final: 0.8433 (ptp90) REVERT: E 419 ILE cc_start: 0.8409 (mm) cc_final: 0.8116 (mm) REVERT: E 452 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.6228 (ppp) REVERT: E 489 ASP cc_start: 0.8643 (t0) cc_final: 0.8388 (t0) REVERT: E 491 ASN cc_start: 0.8641 (p0) cc_final: 0.7942 (p0) REVERT: F 159 THR cc_start: 0.8161 (p) cc_final: 0.7906 (p) outliers start: 44 outliers final: 30 residues processed: 239 average time/residue: 0.0851 time to fit residues: 32.4749 Evaluate side-chains 239 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 492 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 75 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 165 optimal weight: 0.0970 chunk 76 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS C 634 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106048 restraints weight = 22947.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108900 restraints weight = 14592.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110748 restraints weight = 11033.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111736 restraints weight = 9288.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112639 restraints weight = 8392.817| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13387 Z= 0.118 Angle : 0.599 11.101 18141 Z= 0.302 Chirality : 0.045 0.376 2004 Planarity : 0.003 0.041 2348 Dihedral : 4.466 20.011 1790 Min Nonbonded Distance : 1.237 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.72 % Allowed : 20.10 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1648 helix: 0.11 (0.29), residues: 334 sheet: -1.33 (0.26), residues: 393 loop : -1.57 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 409 TYR 0.019 0.002 TYR D 409 PHE 0.030 0.001 PHE A 312 TRP 0.040 0.002 TRP B 364 HIS 0.004 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00269 (13374) covalent geometry : angle 0.59878 (18141) hydrogen bonds : bond 0.03491 ( 437) hydrogen bonds : angle 5.02781 ( 1227) metal coordination : bond 0.00169 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7560 (mttt) cc_final: 0.7062 (pptt) REVERT: A 303 PHE cc_start: 0.8823 (m-80) cc_final: 0.8610 (m-10) REVERT: B 365 TYR cc_start: 0.8163 (t80) cc_final: 0.7847 (t80) REVERT: C 85 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8570 (tt) REVERT: C 95 GLN cc_start: 0.8936 (tp40) cc_final: 0.8677 (tm-30) REVERT: C 493 GLU cc_start: 0.7403 (pm20) cc_final: 0.7067 (pm20) REVERT: C 684 MET cc_start: 0.6980 (ppp) cc_final: 0.6278 (ppp) REVERT: D 13 GLU cc_start: 0.7864 (tt0) cc_final: 0.7583 (tt0) REVERT: D 44 SER cc_start: 0.9365 (t) cc_final: 0.8991 (p) REVERT: D 147 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8259 (t) REVERT: D 242 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8148 (pp) REVERT: E 409 ARG cc_start: 0.8743 (ptp90) cc_final: 0.8447 (ptp90) REVERT: E 419 ILE cc_start: 0.8293 (mm) cc_final: 0.7811 (mm) REVERT: E 420 GLU cc_start: 0.7329 (mp0) cc_final: 0.7011 (mm-30) REVERT: E 452 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.6229 (ppp) REVERT: E 489 ASP cc_start: 0.8620 (t0) cc_final: 0.8354 (t0) REVERT: E 491 ASN cc_start: 0.8663 (p0) cc_final: 0.7912 (p0) REVERT: F 159 THR cc_start: 0.8056 (p) cc_final: 0.7584 (p) outliers start: 37 outliers final: 26 residues processed: 236 average time/residue: 0.0874 time to fit residues: 32.4994 Evaluate side-chains 234 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain F residue 160 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 90 optimal weight: 0.0970 chunk 113 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.142228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107111 restraints weight = 22956.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110014 restraints weight = 14442.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111922 restraints weight = 10828.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112799 restraints weight = 9057.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113769 restraints weight = 8229.810| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13387 Z= 0.112 Angle : 0.599 11.176 18141 Z= 0.301 Chirality : 0.045 0.186 2004 Planarity : 0.003 0.040 2348 Dihedral : 4.364 21.163 1790 Min Nonbonded Distance : 1.240 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.65 % Allowed : 21.13 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.20), residues: 1648 helix: 0.19 (0.28), residues: 334 sheet: -1.22 (0.26), residues: 393 loop : -1.47 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 409 TYR 0.017 0.001 TYR B 244 PHE 0.028 0.001 PHE A 312 TRP 0.032 0.002 TRP B 364 HIS 0.015 0.001 HIS E 476 Details of bonding type rmsd covalent geometry : bond 0.00255 (13374) covalent geometry : angle 0.59916 (18141) hydrogen bonds : bond 0.03380 ( 437) hydrogen bonds : angle 4.92362 ( 1227) metal coordination : bond 0.00146 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7503 (mttt) cc_final: 0.7061 (pptt) REVERT: B 365 TYR cc_start: 0.8109 (t80) cc_final: 0.7811 (t80) REVERT: C 85 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8528 (tt) REVERT: C 95 GLN cc_start: 0.8943 (tp40) cc_final: 0.8687 (tm-30) REVERT: C 493 GLU cc_start: 0.7489 (pm20) cc_final: 0.7173 (pm20) REVERT: C 684 MET cc_start: 0.6962 (ppp) cc_final: 0.6269 (ppp) REVERT: D 13 GLU cc_start: 0.7790 (tt0) cc_final: 0.7576 (tt0) REVERT: D 44 SER cc_start: 0.9370 (t) cc_final: 0.9027 (p) REVERT: D 147 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8285 (t) REVERT: E 419 ILE cc_start: 0.8256 (mm) cc_final: 0.7762 (mm) REVERT: E 420 GLU cc_start: 0.7357 (mp0) cc_final: 0.7045 (mm-30) REVERT: E 452 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.6119 (ppp) REVERT: E 476 HIS cc_start: 0.7742 (t-90) cc_final: 0.7353 (t70) REVERT: E 489 ASP cc_start: 0.8594 (t0) cc_final: 0.8319 (t0) REVERT: E 491 ASN cc_start: 0.8617 (p0) cc_final: 0.7875 (p0) REVERT: F 159 THR cc_start: 0.7980 (p) cc_final: 0.7528 (p) outliers start: 36 outliers final: 27 residues processed: 241 average time/residue: 0.0842 time to fit residues: 32.7334 Evaluate side-chains 238 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain F residue 160 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 31 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 92 optimal weight: 50.0000 chunk 66 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 72 optimal weight: 0.0370 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.140879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106040 restraints weight = 23131.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108673 restraints weight = 15334.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110140 restraints weight = 11710.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111450 restraints weight = 10046.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111973 restraints weight = 9014.881| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13387 Z= 0.142 Angle : 0.612 11.204 18141 Z= 0.309 Chirality : 0.046 0.389 2004 Planarity : 0.004 0.040 2348 Dihedral : 4.404 21.511 1790 Min Nonbonded Distance : 1.209 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.58 % Allowed : 21.35 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.20), residues: 1648 helix: 0.23 (0.28), residues: 335 sheet: -1.24 (0.26), residues: 398 loop : -1.42 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 409 TYR 0.033 0.002 TYR A 42 PHE 0.029 0.002 PHE A 312 TRP 0.034 0.002 TRP B 364 HIS 0.015 0.001 HIS E 476 Details of bonding type rmsd covalent geometry : bond 0.00326 (13374) covalent geometry : angle 0.61237 (18141) hydrogen bonds : bond 0.03442 ( 437) hydrogen bonds : angle 4.93914 ( 1227) metal coordination : bond 0.00233 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7570 (mttt) cc_final: 0.7072 (pptt) REVERT: B 195 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7688 (tm-30) REVERT: C 85 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8543 (tt) REVERT: C 95 GLN cc_start: 0.8926 (tp40) cc_final: 0.8682 (tm-30) REVERT: C 493 GLU cc_start: 0.7375 (pm20) cc_final: 0.7052 (pm20) REVERT: C 504 GLN cc_start: 0.8706 (pp30) cc_final: 0.8356 (pp30) REVERT: C 684 MET cc_start: 0.6989 (ppp) cc_final: 0.6322 (ppp) REVERT: D 13 GLU cc_start: 0.7937 (tt0) cc_final: 0.7674 (tt0) REVERT: D 44 SER cc_start: 0.9412 (t) cc_final: 0.9070 (p) REVERT: D 147 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8333 (t) REVERT: E 419 ILE cc_start: 0.8286 (mm) cc_final: 0.7802 (mm) REVERT: E 420 GLU cc_start: 0.7395 (mp0) cc_final: 0.7090 (mm-30) REVERT: E 452 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.6103 (ppp) REVERT: E 476 HIS cc_start: 0.7770 (t-90) cc_final: 0.7437 (t70) REVERT: E 489 ASP cc_start: 0.8498 (t0) cc_final: 0.8251 (t0) REVERT: E 491 ASN cc_start: 0.8642 (p0) cc_final: 0.7888 (p0) REVERT: F 159 THR cc_start: 0.7991 (p) cc_final: 0.7576 (p) outliers start: 35 outliers final: 28 residues processed: 225 average time/residue: 0.0852 time to fit residues: 30.6634 Evaluate side-chains 235 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain F residue 160 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 163 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 147 optimal weight: 0.0670 chunk 166 optimal weight: 0.4980 chunk 165 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.143650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108838 restraints weight = 22986.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111834 restraints weight = 14389.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113786 restraints weight = 10667.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115050 restraints weight = 8890.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115676 restraints weight = 7912.315| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13387 Z= 0.107 Angle : 0.595 11.504 18141 Z= 0.298 Chirality : 0.045 0.176 2004 Planarity : 0.003 0.039 2348 Dihedral : 4.263 21.279 1790 Min Nonbonded Distance : 1.252 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.36 % Allowed : 21.58 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1648 helix: 0.34 (0.29), residues: 334 sheet: -1.10 (0.26), residues: 400 loop : -1.37 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 409 TYR 0.031 0.001 TYR A 42 PHE 0.029 0.001 PHE A 312 TRP 0.039 0.002 TRP B 364 HIS 0.012 0.001 HIS E 476 Details of bonding type rmsd covalent geometry : bond 0.00242 (13374) covalent geometry : angle 0.59531 (18141) hydrogen bonds : bond 0.03272 ( 437) hydrogen bonds : angle 4.84731 ( 1227) metal coordination : bond 0.00126 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2145.68 seconds wall clock time: 37 minutes 55.88 seconds (2275.88 seconds total)