Starting phenix.real_space_refine on Thu Sep 26 11:23:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/09_2024/7kso_23021.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/09_2024/7kso_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/09_2024/7kso_23021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/09_2024/7kso_23021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/09_2024/7kso_23021.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/09_2024/7kso_23021.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG: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: {'GLU:plan': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 6} 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: {'GLU:plan': 3, 'ASP: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: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 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: 7.66, per 1000 atoms: 0.59 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: 2.94 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.51 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: 3.98 Time building geometry restraints manager: 3.49 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: 0.360 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.450 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- 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 : 0.004 0.055 13374 Z= 0.295 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 : 3.83 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP D 345 HIS 0.004 0.001 HIS B 397 PHE 0.023 0.001 PHE C 86 TYR 0.014 0.001 TYR B 244 ARG 0.002 0.000 ARG D 258 *********************** 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 fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 1.672 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: 0.6321 (tmm) REVERT: A 112 TYR cc_start: 0.7061 (m-80) cc_final: 0.6824 (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: 0.8172 (t80) REVERT: A 643 CYS cc_start: 0.8367 (m) cc_final: 0.8015 (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: 0.7143 (p0) REVERT: B 139 VAL cc_start: 0.8326 (t) cc_final: 0.7749 (t) REVERT: B 240 LEU cc_start: 0.9042 (mt) cc_final: 0.8713 (mm) REVERT: B 252 MET cc_start: 0.8467 (tpp) cc_final: 0.8132 (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: 0.7700 (mttt) REVERT: C 85 LEU cc_start: 0.8219 (tt) cc_final: 0.7949 (tt) REVERT: C 91 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7276 (tm-30) REVERT: C 561 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.7057 (p-80) REVERT: C 657 MET cc_start: 0.8355 (mtm) cc_final: 0.7654 (mpp) REVERT: D 13 GLU cc_start: 0.7564 (tt0) cc_final: 0.7176 (tt0) REVERT: D 44 SER cc_start: 0.9029 (t) cc_final: 0.8825 (p) REVERT: D 49 TRP cc_start: 0.8665 (m100) cc_final: 0.8305 (m100) REVERT: D 185 TRP cc_start: 0.8249 (m100) cc_final: 0.7829 (m100) REVERT: D 194 LEU cc_start: 0.9165 (mt) cc_final: 0.8907 (mt) REVERT: D 203 CYS cc_start: 0.7709 (m) cc_final: 0.7088 (m) REVERT: D 242 LEU cc_start: 0.7863 (pt) cc_final: 0.7572 (pp) REVERT: D 275 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7093 (mp0) REVERT: D 306 LEU cc_start: 0.9256 (mt) cc_final: 0.8979 (mp) REVERT: D 331 THR cc_start: 0.8219 (p) cc_final: 0.7905 (t) REVERT: D 381 SER cc_start: 0.8871 (t) cc_final: 0.8281 (p) REVERT: E 420 GLU cc_start: 0.7300 (mp0) cc_final: 0.6807 (mp0) REVERT: E 430 PHE cc_start: 0.8316 (m-80) cc_final: 0.8082 (m-10) REVERT: E 476 HIS cc_start: 0.7336 (t-90) cc_final: 0.7046 (t70) REVERT: E 492 ILE cc_start: 0.7542 (mt) cc_final: 0.7323 (mt) outliers start: 4 outliers final: 2 residues processed: 425 average time/residue: 0.2432 time to fit residues: 149.8100 Evaluate side-chains 262 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 141 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 130 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.0010 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- 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 669 ASN A 707 HIS 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 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN D 370 HIS F 171 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13374 Z= 0.198 Angle : 0.594 8.584 18141 Z= 0.302 Chirality : 0.046 0.313 2004 Planarity : 0.004 0.084 2348 Dihedral : 4.349 36.149 1796 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.91 % Allowed : 10.82 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.18), residues: 1648 helix: -0.52 (0.26), residues: 321 sheet: -2.31 (0.24), residues: 351 loop : -2.41 (0.17), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 345 HIS 0.009 0.001 HIS D 176 PHE 0.026 0.002 PHE C 656 TYR 0.022 0.002 TYR A 521 ARG 0.007 0.000 ARG A 529 *********************** 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 296 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 270 time to evaluate : 1.351 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 96 HIS cc_start: 0.6661 (OUTLIER) cc_final: 0.6431 (t70) REVERT: A 112 TYR cc_start: 0.7227 (m-80) cc_final: 0.6984 (m-80) REVERT: A 539 MET cc_start: 0.7983 (mtp) cc_final: 0.7382 (mmm) REVERT: A 558 PHE cc_start: 0.8585 (t80) cc_final: 0.8214 (t80) REVERT: A 643 CYS cc_start: 0.8617 (m) cc_final: 0.8169 (t) REVERT: B 240 LEU cc_start: 0.9156 (mt) cc_final: 0.8900 (mm) REVERT: B 252 MET cc_start: 0.8238 (tpp) cc_final: 0.7861 (tpp) REVERT: B 271 MET cc_start: 0.9201 (tpp) cc_final: 0.8754 (mpp) REVERT: B 310 ASP cc_start: 0.8852 (m-30) cc_final: 0.8387 (t0) REVERT: B 375 LYS cc_start: 0.8036 (mttt) cc_final: 0.7808 (mttt) REVERT: C 85 LEU cc_start: 0.8263 (tt) cc_final: 0.7984 (tt) REVERT: C 91 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7869 (tm-30) REVERT: C 643 TYR cc_start: 0.7275 (m-80) cc_final: 0.7060 (m-10) REVERT: C 657 MET cc_start: 0.8333 (mtm) cc_final: 0.7616 (mpp) REVERT: C 663 MET cc_start: 0.8277 (mtm) cc_final: 0.8065 (mtm) REVERT: D 118 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8416 (mt-10) REVERT: D 128 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7881 (t0) REVERT: D 242 LEU cc_start: 0.8331 (pt) cc_final: 0.8025 (pp) REVERT: D 275 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7383 (mp0) REVERT: D 302 ASP cc_start: 0.8003 (t0) cc_final: 0.7781 (t0) REVERT: D 306 LEU cc_start: 0.9343 (mt) cc_final: 0.9083 (mp) REVERT: D 381 SER cc_start: 0.9119 (t) cc_final: 0.8642 (p) REVERT: E 476 HIS cc_start: 0.7223 (t-90) cc_final: 0.5739 (t-90) REVERT: E 492 ILE cc_start: 0.7873 (mt) cc_final: 0.7628 (mt) outliers start: 26 outliers final: 9 residues processed: 284 average time/residue: 0.2188 time to fit residues: 94.3222 Evaluate side-chains 234 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 223 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 546 LYS 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 128 ASN Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 404 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 HIS D 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13374 Z= 0.168 Angle : 0.541 7.281 18141 Z= 0.279 Chirality : 0.044 0.175 2004 Planarity : 0.004 0.061 2348 Dihedral : 4.053 21.894 1790 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.50 % Allowed : 12.30 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.19), residues: 1648 helix: -0.07 (0.27), residues: 334 sheet: -1.86 (0.24), residues: 357 loop : -2.17 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 434 HIS 0.012 0.001 HIS D 176 PHE 0.020 0.001 PHE D 243 TYR 0.021 0.002 TYR A 521 ARG 0.005 0.000 ARG D 172 *********************** 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 289 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 255 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7864 (ptm) REVERT: A 112 TYR cc_start: 0.7232 (m-80) cc_final: 0.6927 (m-80) REVERT: A 283 LYS cc_start: 0.7334 (mttt) cc_final: 0.6915 (pptt) REVERT: A 434 TRP cc_start: 0.7273 (m-10) cc_final: 0.7024 (m-10) REVERT: A 558 PHE cc_start: 0.8633 (t80) cc_final: 0.8248 (t80) REVERT: A 643 CYS cc_start: 0.8770 (m) cc_final: 0.8343 (t) REVERT: B 109 ASP cc_start: 0.7069 (p0) cc_final: 0.6515 (p0) REVERT: B 138 TYR cc_start: 0.8590 (m-80) cc_final: 0.8326 (m-80) REVERT: B 240 LEU cc_start: 0.9178 (mt) cc_final: 0.8963 (mm) REVERT: B 252 MET cc_start: 0.8097 (tpp) cc_final: 0.7577 (tpp) REVERT: B 310 ASP cc_start: 0.8820 (m-30) cc_final: 0.8353 (t0) REVERT: B 366 MET cc_start: 0.9063 (mmm) cc_final: 0.8430 (tpp) REVERT: B 375 LYS cc_start: 0.8085 (mttt) cc_final: 0.7826 (mttt) REVERT: C 85 LEU cc_start: 0.8429 (tt) cc_final: 0.8102 (tt) REVERT: C 91 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7610 (tm-30) REVERT: C 657 MET cc_start: 0.8354 (mtm) cc_final: 0.7658 (mpp) REVERT: D 250 GLN cc_start: 0.8300 (mp10) cc_final: 0.7709 (mp10) REVERT: D 275 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7443 (mp0) REVERT: D 302 ASP cc_start: 0.8115 (t0) cc_final: 0.7774 (t0) REVERT: D 306 LEU cc_start: 0.9366 (mt) cc_final: 0.9140 (mp) REVERT: D 316 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7336 (m170) REVERT: E 420 GLU cc_start: 0.7949 (mp0) cc_final: 0.7537 (mp0) REVERT: F 159 THR cc_start: 0.7717 (p) cc_final: 0.7509 (p) outliers start: 34 outliers final: 20 residues processed: 273 average time/residue: 0.2240 time to fit residues: 92.4336 Evaluate side-chains 242 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 621 VAL 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 44 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 474 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 235 HIS C 577 GLN D 48 GLN D 71 HIS ** D 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13374 Z= 0.238 Angle : 0.574 7.795 18141 Z= 0.297 Chirality : 0.045 0.355 2004 Planarity : 0.004 0.051 2348 Dihedral : 4.175 17.599 1790 Min Nonbonded Distance : 1.423 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.72 % Allowed : 13.70 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1648 helix: 0.22 (0.28), residues: 335 sheet: -1.52 (0.26), residues: 371 loop : -1.93 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 205 HIS 0.031 0.001 HIS D 316 PHE 0.021 0.002 PHE B 299 TYR 0.020 0.002 TYR B 244 ARG 0.006 0.000 ARG B 216 *********************** 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 272 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 1.692 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8321 (t80) cc_final: 0.7893 (t80) REVERT: A 112 TYR cc_start: 0.7593 (m-80) cc_final: 0.7087 (m-80) REVERT: A 283 LYS cc_start: 0.7462 (mttt) cc_final: 0.7022 (pptt) REVERT: A 434 TRP cc_start: 0.6944 (m100) cc_final: 0.6695 (m-10) REVERT: A 558 PHE cc_start: 0.8622 (t80) cc_final: 0.8244 (t80) REVERT: A 643 CYS cc_start: 0.9013 (m) cc_final: 0.8640 (t) REVERT: B 138 TYR cc_start: 0.8615 (m-80) cc_final: 0.8377 (m-80) REVERT: B 347 GLU cc_start: 0.8081 (tp30) cc_final: 0.7813 (tm-30) REVERT: B 375 LYS cc_start: 0.8134 (mttt) cc_final: 0.7870 (mttt) REVERT: C 85 LEU cc_start: 0.8553 (tt) cc_final: 0.8270 (tt) REVERT: C 657 MET cc_start: 0.8509 (mtm) cc_final: 0.7697 (mpp) REVERT: D 13 GLU cc_start: 0.7988 (tt0) cc_final: 0.7439 (tt0) REVERT: D 302 ASP cc_start: 0.8186 (t0) cc_final: 0.7872 (t0) REVERT: D 306 LEU cc_start: 0.9390 (mt) cc_final: 0.9173 (mp) REVERT: D 316 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7925 (m-70) outliers start: 37 outliers final: 26 residues processed: 259 average time/residue: 0.2236 time to fit residues: 87.8968 Evaluate side-chains 236 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 209 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 546 LYS 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 C residue 94 THR Chi-restraints excluded: chain C residue 475 ILE 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 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 170 ASP 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 316 HIS Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 474 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 50.0000 chunk 144 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS C 504 GLN D 78 HIS D 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13374 Z= 0.250 Angle : 0.588 11.996 18141 Z= 0.302 Chirality : 0.045 0.176 2004 Planarity : 0.004 0.050 2348 Dihedral : 4.292 18.206 1790 Min Nonbonded Distance : 1.111 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.24 % Allowed : 13.99 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.20), residues: 1648 helix: 0.35 (0.29), residues: 335 sheet: -1.31 (0.26), residues: 397 loop : -1.79 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 205 HIS 0.034 0.002 HIS A 96 PHE 0.025 0.002 PHE B 147 TYR 0.018 0.002 TYR B 154 ARG 0.011 0.001 ARG C 563 *********************** 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 263 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 219 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8596 (t80) cc_final: 0.8062 (t80) REVERT: A 112 TYR cc_start: 0.7711 (m-80) cc_final: 0.7133 (m-80) REVERT: A 283 LYS cc_start: 0.7504 (mttt) cc_final: 0.7021 (pptt) REVERT: A 434 TRP cc_start: 0.6910 (m100) cc_final: 0.6646 (m-10) REVERT: A 643 CYS cc_start: 0.9125 (m) cc_final: 0.8763 (t) REVERT: B 196 LEU cc_start: 0.9140 (mt) cc_final: 0.8835 (tp) REVERT: B 252 MET cc_start: 0.8240 (tpp) cc_final: 0.7871 (tpp) REVERT: C 85 LEU cc_start: 0.8684 (tt) cc_final: 0.8413 (tt) REVERT: C 460 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8631 (tp) REVERT: C 504 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8373 (tm-30) REVERT: D 13 GLU cc_start: 0.7754 (tt0) cc_final: 0.7408 (tt0) REVERT: D 302 ASP cc_start: 0.8192 (t0) cc_final: 0.7845 (t0) outliers start: 44 outliers final: 32 residues processed: 248 average time/residue: 0.2117 time to fit residues: 79.9246 Evaluate side-chains 232 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 546 LYS 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 240 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 504 GLN 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 671 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 170 ASP 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 279 LEU Chi-restraints excluded: chain D residue 383 ASN Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 39 optimal weight: 0.0980 chunk 161 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 0.0000 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS C 504 GLN C 577 GLN C 634 HIS D 78 HIS D 383 ASN E 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13374 Z= 0.167 Angle : 0.558 7.609 18141 Z= 0.284 Chirality : 0.044 0.321 2004 Planarity : 0.004 0.047 2348 Dihedral : 4.141 18.293 1790 Min Nonbonded Distance : 1.255 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.95 % Allowed : 15.91 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.20), residues: 1648 helix: 0.45 (0.29), residues: 335 sheet: -1.03 (0.27), residues: 381 loop : -1.67 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 389 HIS 0.017 0.001 HIS E 476 PHE 0.027 0.001 PHE D 152 TYR 0.016 0.001 TYR B 154 ARG 0.006 0.000 ARG C 563 *********************** 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 264 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8564 (t80) cc_final: 0.8229 (t80) REVERT: A 112 TYR cc_start: 0.7668 (m-80) cc_final: 0.7078 (m-80) REVERT: A 283 LYS cc_start: 0.7504 (mttt) cc_final: 0.7016 (pptt) REVERT: A 434 TRP cc_start: 0.6826 (m100) cc_final: 0.6601 (m-10) REVERT: B 109 ASP cc_start: 0.7235 (p0) cc_final: 0.6964 (p0) REVERT: B 138 TYR cc_start: 0.8573 (m-80) cc_final: 0.8287 (m-80) REVERT: B 252 MET cc_start: 0.8225 (tpp) cc_final: 0.7892 (tpp) REVERT: B 310 ASP cc_start: 0.8980 (m-30) cc_final: 0.8513 (t0) REVERT: B 347 GLU cc_start: 0.8025 (tp30) cc_final: 0.7808 (tm-30) REVERT: C 85 LEU cc_start: 0.8662 (tt) cc_final: 0.8392 (tt) REVERT: C 504 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8420 (tm-30) REVERT: C 572 LEU cc_start: 0.9419 (mm) cc_final: 0.9200 (mp) REVERT: C 684 MET cc_start: 0.6783 (ppp) cc_final: 0.5991 (ppp) REVERT: D 13 GLU cc_start: 0.7750 (tt0) cc_final: 0.7459 (tt0) REVERT: E 476 HIS cc_start: 0.7658 (t-90) cc_final: 0.7448 (t70) REVERT: F 159 THR cc_start: 0.7794 (p) cc_final: 0.7564 (p) outliers start: 40 outliers final: 24 residues processed: 251 average time/residue: 0.2188 time to fit residues: 83.6317 Evaluate side-chains 226 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 170 ASP 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 279 LEU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 92 optimal weight: 50.0000 chunk 117 optimal weight: 0.5980 chunk 91 optimal weight: 20.0000 chunk 136 optimal weight: 0.0670 chunk 90 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 overall best weight: 1.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 HIS C 504 GLN C 634 HIS D 78 HIS ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13374 Z= 0.218 Angle : 0.580 7.712 18141 Z= 0.298 Chirality : 0.044 0.180 2004 Planarity : 0.004 0.048 2348 Dihedral : 4.196 18.512 1790 Min Nonbonded Distance : 1.183 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.09 % Allowed : 16.27 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1648 helix: 0.53 (0.29), residues: 332 sheet: -0.98 (0.27), residues: 380 loop : -1.55 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 205 HIS 0.015 0.001 HIS A 96 PHE 0.028 0.002 PHE A 312 TYR 0.020 0.001 TYR B 154 ARG 0.004 0.000 ARG C 563 *********************** 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 251 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 209 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8522 (t80) cc_final: 0.8230 (t80) REVERT: A 112 TYR cc_start: 0.7750 (m-80) cc_final: 0.7208 (m-80) REVERT: A 283 LYS cc_start: 0.7531 (mttt) cc_final: 0.7044 (pptt) REVERT: A 643 CYS cc_start: 0.9109 (m) cc_final: 0.8724 (t) REVERT: B 138 TYR cc_start: 0.8606 (m-80) cc_final: 0.8330 (m-80) REVERT: B 252 MET cc_start: 0.8238 (tpp) cc_final: 0.7900 (tpp) REVERT: B 310 ASP cc_start: 0.8980 (m-30) cc_final: 0.8508 (t0) REVERT: B 336 MET cc_start: 0.8276 (pmm) cc_final: 0.7586 (pmm) REVERT: B 347 GLU cc_start: 0.8079 (tp30) cc_final: 0.7847 (tm-30) REVERT: C 85 LEU cc_start: 0.8726 (tt) cc_final: 0.8410 (tt) REVERT: C 198 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7923 (t0) REVERT: C 504 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: C 684 MET cc_start: 0.6842 (ppp) cc_final: 0.6094 (ppp) REVERT: D 174 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7620 (ttm-80) REVERT: D 275 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7222 (mp0) REVERT: E 476 HIS cc_start: 0.7659 (t-90) cc_final: 0.7458 (t-90) REVERT: E 489 ASP cc_start: 0.8642 (t0) cc_final: 0.8086 (t0) REVERT: E 492 ILE cc_start: 0.8517 (mt) cc_final: 0.8177 (mt) REVERT: F 159 THR cc_start: 0.7791 (p) cc_final: 0.7578 (p) outliers start: 42 outliers final: 29 residues processed: 236 average time/residue: 0.2097 time to fit residues: 75.4671 Evaluate side-chains 224 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 546 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 198 ASP 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 475 ILE Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 561 HIS 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 44 SER Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 174 ARG 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 279 LEU Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 498 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 0.0070 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 690 HIS C 577 GLN C 634 HIS D 78 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13374 Z= 0.174 Angle : 0.589 9.770 18141 Z= 0.297 Chirality : 0.045 0.321 2004 Planarity : 0.004 0.043 2348 Dihedral : 4.156 18.532 1790 Min Nonbonded Distance : 1.239 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.02 % Allowed : 16.94 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.20), residues: 1648 helix: 0.58 (0.29), residues: 333 sheet: -0.88 (0.27), residues: 391 loop : -1.51 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 205 HIS 0.009 0.001 HIS E 476 PHE 0.027 0.001 PHE A 312 TYR 0.022 0.001 TYR B 154 ARG 0.006 0.000 ARG E 409 *********************** 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 253 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 212 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8542 (t80) cc_final: 0.8301 (t80) REVERT: A 283 LYS cc_start: 0.7527 (mttt) cc_final: 0.7042 (pptt) REVERT: B 124 TYR cc_start: 0.8285 (m-10) cc_final: 0.7897 (m-10) REVERT: B 138 TYR cc_start: 0.8592 (m-80) cc_final: 0.8351 (m-80) REVERT: B 252 MET cc_start: 0.8237 (tpp) cc_final: 0.8007 (tpp) REVERT: B 310 ASP cc_start: 0.8964 (m-30) cc_final: 0.8522 (t0) REVERT: B 347 GLU cc_start: 0.8044 (tp30) cc_final: 0.7826 (tm-30) REVERT: C 85 LEU cc_start: 0.8671 (tt) cc_final: 0.8386 (tt) REVERT: C 198 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7932 (t0) REVERT: C 684 MET cc_start: 0.6834 (ppp) cc_final: 0.6103 (ppp) REVERT: D 174 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7573 (ttm-80) REVERT: D 275 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7360 (mp0) REVERT: E 476 HIS cc_start: 0.7493 (t-90) cc_final: 0.7265 (t-90) REVERT: E 492 ILE cc_start: 0.8333 (mt) cc_final: 0.8044 (mt) REVERT: F 159 THR cc_start: 0.7766 (p) cc_final: 0.7551 (p) outliers start: 41 outliers final: 27 residues processed: 237 average time/residue: 0.2137 time to fit residues: 76.9188 Evaluate side-chains 228 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 475 ILE 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 671 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 174 ARG 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 279 LEU Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 452 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 135 optimal weight: 0.0970 chunk 141 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 690 HIS C 440 GLN C 504 GLN C 634 HIS D 78 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13374 Z= 0.213 Angle : 0.590 8.859 18141 Z= 0.301 Chirality : 0.044 0.175 2004 Planarity : 0.004 0.046 2348 Dihedral : 4.172 18.139 1790 Min Nonbonded Distance : 1.198 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.43 % Allowed : 17.82 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1648 helix: 0.63 (0.29), residues: 333 sheet: -0.80 (0.27), residues: 381 loop : -1.45 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 205 HIS 0.011 0.001 HIS E 476 PHE 0.027 0.002 PHE A 312 TYR 0.023 0.002 TYR A 319 ARG 0.005 0.000 ARG E 409 *********************** 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 240 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8576 (t80) cc_final: 0.8335 (t80) REVERT: A 283 LYS cc_start: 0.7549 (mttt) cc_final: 0.7065 (pptt) REVERT: A 643 CYS cc_start: 0.9128 (m) cc_final: 0.8744 (t) REVERT: B 109 ASP cc_start: 0.7221 (p0) cc_final: 0.6998 (p0) REVERT: B 138 TYR cc_start: 0.8614 (m-80) cc_final: 0.8383 (m-80) REVERT: B 252 MET cc_start: 0.8211 (tpp) cc_final: 0.7914 (tpp) REVERT: B 336 MET cc_start: 0.8725 (pmm) cc_final: 0.8332 (pmm) REVERT: B 347 GLU cc_start: 0.8061 (tp30) cc_final: 0.7828 (tm-30) REVERT: C 85 LEU cc_start: 0.8767 (tt) cc_final: 0.8435 (tt) REVERT: C 198 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7965 (t0) REVERT: D 174 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7572 (ttm-80) REVERT: E 489 ASP cc_start: 0.8483 (t0) cc_final: 0.8111 (t0) REVERT: E 492 ILE cc_start: 0.8479 (mt) cc_final: 0.8130 (mt) REVERT: F 159 THR cc_start: 0.7793 (p) cc_final: 0.7585 (p) outliers start: 33 outliers final: 27 residues processed: 228 average time/residue: 0.2146 time to fit residues: 74.8141 Evaluate side-chains 225 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 193 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 504 GLN 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 671 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 174 ARG 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 279 LEU Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 110 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 153 optimal weight: 0.1980 chunk 132 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 690 HIS C 577 GLN C 634 HIS D 78 HIS D 272 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13374 Z= 0.162 Angle : 0.596 10.626 18141 Z= 0.299 Chirality : 0.045 0.327 2004 Planarity : 0.004 0.044 2348 Dihedral : 4.113 18.518 1790 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.91 % Allowed : 18.63 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1648 helix: 0.68 (0.29), residues: 334 sheet: -0.83 (0.27), residues: 397 loop : -1.38 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 364 HIS 0.015 0.001 HIS E 476 PHE 0.026 0.001 PHE A 312 TYR 0.023 0.001 TYR B 154 ARG 0.006 0.000 ARG E 409 ********************** 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 240 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 214 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8596 (t80) cc_final: 0.8385 (t80) REVERT: A 283 LYS cc_start: 0.7484 (mttt) cc_final: 0.7058 (pptt) REVERT: B 109 ASP cc_start: 0.7170 (p0) cc_final: 0.6937 (p0) REVERT: B 252 MET cc_start: 0.8228 (tpp) cc_final: 0.7989 (tpp) REVERT: B 310 ASP cc_start: 0.8946 (m-30) cc_final: 0.8502 (t0) REVERT: B 336 MET cc_start: 0.8662 (pmm) cc_final: 0.8282 (pmm) REVERT: B 347 GLU cc_start: 0.8024 (tp30) cc_final: 0.7796 (tm-30) REVERT: B 366 MET cc_start: 0.8854 (mmm) cc_final: 0.8226 (mmm) REVERT: C 85 LEU cc_start: 0.8708 (tt) cc_final: 0.8384 (tt) REVERT: C 684 MET cc_start: 0.6958 (ppp) cc_final: 0.6146 (ppp) REVERT: D 174 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7472 (ttp80) REVERT: E 419 ILE cc_start: 0.8227 (mm) cc_final: 0.7873 (mm) REVERT: E 489 ASP cc_start: 0.8322 (t0) cc_final: 0.8113 (t0) REVERT: E 492 ILE cc_start: 0.7944 (mt) cc_final: 0.7625 (mt) outliers start: 26 outliers final: 22 residues processed: 230 average time/residue: 0.2145 time to fit residues: 75.1282 Evaluate side-chains 225 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 B residue 193 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 475 ILE 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 44 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 174 ARG 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 E residue 402 THR Chi-restraints excluded: chain E residue 452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 19 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.0270 chunk 116 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 overall best weight: 3.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 690 HIS C 607 ASN C 634 HIS E 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104968 restraints weight = 22860.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107748 restraints weight = 14855.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109542 restraints weight = 11363.036| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13374 Z= 0.330 Angle : 0.665 7.762 18141 Z= 0.341 Chirality : 0.047 0.349 2004 Planarity : 0.004 0.054 2348 Dihedral : 4.553 17.094 1790 Min Nonbonded Distance : 1.202 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.06 % Allowed : 18.56 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 1648 helix: 0.51 (0.28), residues: 331 sheet: -0.97 (0.27), residues: 397 loop : -1.37 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 205 HIS 0.013 0.001 HIS B 185 PHE 0.025 0.002 PHE A 312 TYR 0.021 0.002 TYR A 319 ARG 0.005 0.001 ARG B 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2686.36 seconds wall clock time: 48 minutes 48.13 seconds (2928.13 seconds total)