Starting phenix.real_space_refine on Thu Jul 31 01:56:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kso_23021/07_2025/7kso_23021.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kso_23021/07_2025/7kso_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/cci-nas-00/data/ceres_data/7kso_23021/07_2025/7kso_23021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kso_23021/07_2025/7kso_23021.map" model { file = "/net/cci-nas-00/data/ceres_data/7kso_23021/07_2025/7kso_23021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kso_23021/07_2025/7kso_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.73, 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: 3.43 Conformation dependent library (CDL) restraints added in 1.8 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: 1.68 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: 4.11 Time building geometry restraints manager: 3.96 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: 0.750 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.250 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.488 13387 Z= 0.359 Angle : 0.728 8.854 18141 Z= 0.390 Chirality : 0.050 0.544 2004 Planarity : 0.004 0.043 2348 Dihedral : 11.733 86.686 4752 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.83 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 Details of bonding type rmsd hydrogen bonds : bond 0.14017 ( 437) hydrogen bonds : angle 6.81476 ( 1227) metal coordination : bond 0.27586 ( 13) covalent geometry : bond 0.00444 (13374) covalent geometry : angle 0.72845 (18141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 421 time to evaluate : 1.485 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: 0.2614 time to fit residues: 162.2666 Evaluate side-chains 262 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.156424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124305 restraints weight = 23543.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.127537 restraints weight = 14649.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129697 restraints weight = 10784.306| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13387 Z= 0.131 Angle : 0.593 8.595 18141 Z= 0.302 Chirality : 0.046 0.313 2004 Planarity : 0.004 0.084 2348 Dihedral : 4.349 36.169 1796 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.91 % Allowed : 10.68 % Favored : 87.41 % 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: -2.96 (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 0.008 0.000 ARG A 529 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 437) hydrogen bonds : angle 5.34043 ( 1227) metal coordination : bond 0.00443 ( 13) covalent geometry : bond 0.00296 (13374) covalent geometry : angle 0.59349 (18141) *********************** 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 to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 1.487 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 539 MET cc_start: 0.8029 (mtp) cc_final: 0.7421 (mmm) REVERT: A 558 PHE cc_start: 0.8572 (t80) cc_final: 0.8266 (t80) REVERT: A 643 CYS cc_start: 0.8505 (m) cc_final: 0.8095 (t) REVERT: B 240 LEU cc_start: 0.9134 (mt) cc_final: 0.8927 (mm) REVERT: B 252 MET cc_start: 0.8624 (tpp) cc_final: 0.8295 (tpp) REVERT: B 271 MET cc_start: 0.9187 (tpp) cc_final: 0.8838 (mpp) REVERT: B 310 ASP cc_start: 0.8834 (m-30) cc_final: 0.8449 (t0) REVERT: B 375 LYS cc_start: 0.8002 (mttt) cc_final: 0.7761 (mttt) REVERT: C 85 LEU cc_start: 0.8344 (tt) cc_final: 0.8070 (tt) REVERT: C 91 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 657 MET cc_start: 0.8311 (mtm) cc_final: 0.7642 (mpp) REVERT: D 44 SER cc_start: 0.9267 (t) cc_final: 0.8948 (p) REVERT: D 242 LEU cc_start: 0.8175 (pt) cc_final: 0.7852 (pp) REVERT: D 275 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7504 (mp0) REVERT: D 306 LEU cc_start: 0.9202 (mt) cc_final: 0.8946 (mp) REVERT: D 381 SER cc_start: 0.9052 (t) cc_final: 0.8744 (p) REVERT: E 476 HIS cc_start: 0.6938 (t-90) cc_final: 0.5409 (t-90) REVERT: E 492 ILE cc_start: 0.7998 (mt) cc_final: 0.7761 (mt) outliers start: 26 outliers final: 9 residues processed: 284 average time/residue: 0.2242 time to fit residues: 96.2784 Evaluate side-chains 232 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 119 optimal weight: 0.0570 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 106 optimal weight: 0.2980 chunk 147 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 50.0000 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 HIS D 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.154347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121675 restraints weight = 23692.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124744 restraints weight = 15124.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.126770 restraints weight = 11325.671| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13387 Z= 0.107 Angle : 0.540 7.208 18141 Z= 0.279 Chirality : 0.044 0.182 2004 Planarity : 0.004 0.062 2348 Dihedral : 4.053 21.669 1790 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.14 % Allowed : 12.81 % Favored : 85.05 % 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: -2.42 (0.19), residues: 1648 helix: -0.06 (0.27), residues: 333 sheet: -1.83 (0.24), residues: 357 loop : -2.15 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 434 HIS 0.011 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 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 437) hydrogen bonds : angle 5.03485 ( 1227) metal coordination : bond 0.00170 ( 13) covalent geometry : bond 0.00244 (13374) covalent geometry : angle 0.54016 (18141) *********************** 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 284 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 1.666 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: A 111 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7725 (ptm) REVERT: A 283 LYS cc_start: 0.7319 (mttt) cc_final: 0.6899 (pptt) REVERT: A 434 TRP cc_start: 0.7230 (m-10) cc_final: 0.6988 (m-10) REVERT: A 558 PHE cc_start: 0.8624 (t80) cc_final: 0.8300 (t80) REVERT: A 643 CYS cc_start: 0.8653 (m) cc_final: 0.8289 (t) REVERT: B 109 ASP cc_start: 0.6994 (p0) cc_final: 0.6472 (p0) REVERT: B 138 TYR cc_start: 0.8491 (m-80) cc_final: 0.8275 (m-80) REVERT: B 252 MET cc_start: 0.8521 (tpp) cc_final: 0.8063 (tpp) REVERT: B 310 ASP cc_start: 0.8781 (m-30) cc_final: 0.8445 (t0) REVERT: B 375 LYS cc_start: 0.8045 (mttt) cc_final: 0.7746 (mttt) REVERT: C 85 LEU cc_start: 0.8517 (tt) cc_final: 0.8185 (tt) REVERT: C 91 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 486 ARG cc_start: 0.7119 (tmm-80) cc_final: 0.6270 (tpt170) REVERT: C 572 LEU cc_start: 0.9286 (mm) cc_final: 0.8981 (mt) REVERT: C 643 TYR cc_start: 0.7493 (m-10) cc_final: 0.7252 (m-10) REVERT: C 657 MET cc_start: 0.8323 (mtm) cc_final: 0.7658 (mpp) REVERT: D 44 SER cc_start: 0.9335 (t) cc_final: 0.8960 (p) REVERT: D 250 GLN cc_start: 0.8159 (mp10) cc_final: 0.7667 (mp10) REVERT: D 275 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7578 (mp0) REVERT: D 316 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.7569 (m170) REVERT: E 420 GLU cc_start: 0.7850 (mp0) cc_final: 0.7469 (mp0) REVERT: F 159 THR cc_start: 0.7649 (p) cc_final: 0.7407 (p) outliers start: 29 outliers final: 17 residues processed: 271 average time/residue: 0.2174 time to fit residues: 90.2474 Evaluate side-chains 236 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 C residue 94 THR 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 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 103 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 126 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.144981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110667 restraints weight = 22516.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113346 restraints weight = 15003.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115104 restraints weight = 11635.189| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13387 Z= 0.207 Angle : 0.616 7.902 18141 Z= 0.320 Chirality : 0.047 0.357 2004 Planarity : 0.004 0.058 2348 Dihedral : 4.373 18.358 1790 Min Nonbonded Distance : 1.190 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.95 % Allowed : 13.62 % Favored : 83.43 % 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: -2.06 (0.20), residues: 1648 helix: 0.24 (0.28), residues: 335 sheet: -1.68 (0.25), residues: 371 loop : -1.88 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 205 HIS 0.017 0.001 HIS D 316 PHE 0.024 0.002 PHE B 299 TYR 0.021 0.002 TYR C 557 ARG 0.007 0.001 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 437) hydrogen bonds : angle 5.13340 ( 1227) metal coordination : bond 0.00526 ( 13) covalent geometry : bond 0.00475 (13374) covalent geometry : angle 0.61637 (18141) *********************** 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 263 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 1.548 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 42 TYR cc_start: 0.8332 (t80) cc_final: 0.7938 (t80) REVERT: A 283 LYS cc_start: 0.7430 (mttt) cc_final: 0.6957 (pptt) REVERT: A 434 TRP cc_start: 0.6973 (m-10) cc_final: 0.6679 (m-10) REVERT: A 558 PHE cc_start: 0.8681 (t80) cc_final: 0.8368 (t80) REVERT: A 643 CYS cc_start: 0.9004 (m) cc_final: 0.8728 (t) REVERT: B 138 TYR cc_start: 0.8462 (m-80) cc_final: 0.8252 (m-80) REVERT: B 252 MET cc_start: 0.8789 (tpp) cc_final: 0.8586 (tpp) REVERT: B 375 LYS cc_start: 0.8087 (mttt) cc_final: 0.7865 (mttt) REVERT: C 85 LEU cc_start: 0.8676 (tt) cc_final: 0.8427 (tt) REVERT: C 579 MET cc_start: 0.8190 (tpp) cc_final: 0.7975 (tpp) REVERT: C 657 MET cc_start: 0.8550 (mtm) cc_final: 0.7777 (mpp) REVERT: D 13 GLU cc_start: 0.7842 (tt0) cc_final: 0.7237 (tt0) REVERT: D 44 SER cc_start: 0.9488 (t) cc_final: 0.9223 (p) outliers start: 40 outliers final: 27 residues processed: 248 average time/residue: 0.2216 time to fit residues: 83.9046 Evaluate side-chains 221 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 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 240 LEU Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 460 LEU 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 37 THR 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 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 138 optimal weight: 0.0570 chunk 156 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 161 optimal weight: 0.0040 chunk 79 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 126 optimal weight: 5.9990 overall best weight: 0.8512 ------------------------------------------------------------------------------- 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 C 634 HIS D 78 HIS ** D 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112822 restraints weight = 22552.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115787 restraints weight = 14339.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117564 restraints weight = 10809.267| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13387 Z= 0.108 Angle : 0.561 12.605 18141 Z= 0.284 Chirality : 0.044 0.172 2004 Planarity : 0.004 0.050 2348 Dihedral : 4.148 18.084 1790 Min Nonbonded Distance : 1.249 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.43 % Allowed : 15.02 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.20), residues: 1648 helix: 0.40 (0.29), residues: 335 sheet: -1.34 (0.26), residues: 371 loop : -1.72 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 205 HIS 0.013 0.001 HIS E 476 PHE 0.015 0.001 PHE D 368 TYR 0.017 0.001 TYR A 521 ARG 0.010 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 437) hydrogen bonds : angle 4.97393 ( 1227) metal coordination : bond 0.00148 ( 13) covalent geometry : bond 0.00244 (13374) covalent geometry : angle 0.56107 (18141) *********************** 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 261 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 1.592 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 42 TYR cc_start: 0.8463 (t80) cc_final: 0.7962 (t80) REVERT: A 283 LYS cc_start: 0.7402 (mttt) cc_final: 0.6961 (pptt) REVERT: A 434 TRP cc_start: 0.6857 (m100) cc_final: 0.6617 (m-10) REVERT: B 347 GLU cc_start: 0.8048 (tp30) cc_final: 0.7830 (tm-30) REVERT: B 365 TYR cc_start: 0.8225 (t80) cc_final: 0.7999 (t80) REVERT: C 85 LEU cc_start: 0.8649 (tt) cc_final: 0.8396 (tt) REVERT: C 504 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: C 579 MET cc_start: 0.8078 (tpp) cc_final: 0.7771 (tpp) REVERT: C 657 MET cc_start: 0.8494 (mtm) cc_final: 0.7739 (mpp) REVERT: C 684 MET cc_start: 0.6829 (ppp) cc_final: 0.6077 (ppp) REVERT: D 13 GLU cc_start: 0.7593 (tt0) cc_final: 0.6961 (tt0) REVERT: D 44 SER cc_start: 0.9409 (t) cc_final: 0.9153 (p) REVERT: D 174 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7475 (ttm110) outliers start: 33 outliers final: 21 residues processed: 249 average time/residue: 0.2168 time to fit residues: 82.3786 Evaluate side-chains 232 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 193 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 94 THR 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 674 ILE Chi-restraints excluded: chain D residue 16 VAL 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 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 55 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 0.0270 chunk 165 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 504 GLN C 577 GLN C 634 HIS D 78 HIS D 272 HIS D 343 ASN E 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.144205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109453 restraints weight = 22522.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112126 restraints weight = 14894.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113919 restraints weight = 11531.607| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13387 Z= 0.147 Angle : 0.578 7.745 18141 Z= 0.298 Chirality : 0.045 0.300 2004 Planarity : 0.004 0.045 2348 Dihedral : 4.241 18.572 1790 Min Nonbonded Distance : 1.175 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.95 % Allowed : 15.46 % Favored : 81.59 % 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: -1.61 (0.20), residues: 1648 helix: 0.41 (0.28), residues: 340 sheet: -1.16 (0.27), residues: 368 loop : -1.62 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 389 HIS 0.013 0.001 HIS E 476 PHE 0.023 0.002 PHE A 558 TYR 0.016 0.001 TYR B 244 ARG 0.005 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 437) hydrogen bonds : angle 4.91829 ( 1227) metal coordination : bond 0.00265 ( 13) covalent geometry : bond 0.00336 (13374) covalent geometry : angle 0.57829 (18141) *********************** 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 261 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8487 (t80) cc_final: 0.8178 (t80) REVERT: A 283 LYS cc_start: 0.7487 (mttt) cc_final: 0.7002 (pptt) REVERT: A 434 TRP cc_start: 0.6831 (m100) cc_final: 0.6599 (m-10) REVERT: B 252 MET cc_start: 0.8634 (tpp) cc_final: 0.8348 (tpp) REVERT: C 85 LEU cc_start: 0.8753 (tt) cc_final: 0.8469 (tt) REVERT: D 13 GLU cc_start: 0.7587 (tt0) cc_final: 0.7259 (tt0) REVERT: D 44 SER cc_start: 0.9467 (t) cc_final: 0.9232 (p) REVERT: E 420 GLU cc_start: 0.7794 (mp0) cc_final: 0.7494 (mp0) REVERT: E 476 HIS cc_start: 0.7636 (t-90) cc_final: 0.7177 (t70) REVERT: E 488 LEU cc_start: 0.8517 (mp) cc_final: 0.8095 (mt) REVERT: F 159 THR cc_start: 0.7758 (p) cc_final: 0.7539 (p) outliers start: 40 outliers final: 26 residues processed: 248 average time/residue: 0.2149 time to fit residues: 81.9511 Evaluate side-chains 217 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 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 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 621 VAL Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 THR 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 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 52 optimal weight: 0.8980 chunk 30 optimal weight: 0.0370 chunk 165 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 82 optimal weight: 50.0000 chunk 103 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 chunk 126 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 449 HIS C 504 GLN C 634 HIS ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 HIS ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111354 restraints weight = 22340.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114115 restraints weight = 14630.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115878 restraints weight = 11231.891| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13387 Z= 0.116 Angle : 0.577 9.661 18141 Z= 0.293 Chirality : 0.044 0.184 2004 Planarity : 0.004 0.045 2348 Dihedral : 4.135 18.751 1790 Min Nonbonded Distance : 1.238 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.02 % Allowed : 16.27 % Favored : 80.71 % 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: -1.44 (0.20), residues: 1648 helix: 0.48 (0.29), residues: 333 sheet: -1.00 (0.27), residues: 368 loop : -1.49 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 364 HIS 0.010 0.001 HIS E 476 PHE 0.028 0.001 PHE A 312 TYR 0.015 0.001 TYR B 244 ARG 0.005 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 437) hydrogen bonds : angle 4.83583 ( 1227) metal coordination : bond 0.00124 ( 13) covalent geometry : bond 0.00266 (13374) covalent geometry : angle 0.57726 (18141) *********************** 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 259 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8508 (t80) cc_final: 0.8261 (t80) REVERT: A 283 LYS cc_start: 0.7462 (mttt) cc_final: 0.7002 (pptt) REVERT: A 538 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8137 (tt) REVERT: B 252 MET cc_start: 0.8644 (tpp) cc_final: 0.8395 (tpp) REVERT: B 336 MET cc_start: 0.8723 (pmm) cc_final: 0.8121 (pmm) REVERT: C 85 LEU cc_start: 0.8737 (tt) cc_final: 0.8467 (tt) REVERT: C 198 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7812 (t0) REVERT: C 684 MET cc_start: 0.6965 (ppp) cc_final: 0.6161 (ppp) REVERT: D 13 GLU cc_start: 0.7580 (tt0) cc_final: 0.7373 (tt0) REVERT: D 44 SER cc_start: 0.9407 (t) cc_final: 0.9193 (p) REVERT: E 488 LEU cc_start: 0.8500 (mp) cc_final: 0.8202 (mt) REVERT: E 492 ILE cc_start: 0.8722 (mt) cc_final: 0.8424 (mt) outliers start: 41 outliers final: 25 residues processed: 243 average time/residue: 0.2117 time to fit residues: 79.7452 Evaluate side-chains 227 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 538 ILE 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 525 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 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 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 89 optimal weight: 50.0000 chunk 92 optimal weight: 50.0000 chunk 109 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 91 optimal weight: 30.0000 chunk 153 optimal weight: 0.0050 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 50.0000 chunk 148 optimal weight: 5.9990 overall best weight: 3.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN C 440 GLN C 504 GLN C 577 GLN C 634 HIS E 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102315 restraints weight = 22695.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104920 restraints weight = 14840.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106664 restraints weight = 11455.192| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13387 Z= 0.254 Angle : 0.705 7.927 18141 Z= 0.363 Chirality : 0.048 0.340 2004 Planarity : 0.005 0.056 2348 Dihedral : 4.825 18.595 1790 Min Nonbonded Distance : 1.140 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.09 % Allowed : 16.94 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.68 (0.20), residues: 1648 helix: 0.24 (0.27), residues: 333 sheet: -1.35 (0.26), residues: 387 loop : -1.52 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 205 HIS 0.019 0.002 HIS E 476 PHE 0.027 0.002 PHE A 312 TYR 0.019 0.002 TYR B 244 ARG 0.006 0.001 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 437) hydrogen bonds : angle 5.18491 ( 1227) metal coordination : bond 0.00564 ( 13) covalent geometry : bond 0.00579 (13374) covalent geometry : angle 0.70520 (18141) *********************** 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 239 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 1.521 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7563 (mttt) cc_final: 0.7019 (pttp) REVERT: B 252 MET cc_start: 0.8702 (tpp) cc_final: 0.8427 (tpp) REVERT: C 91 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 198 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7958 (t0) REVERT: C 460 LEU cc_start: 0.9030 (tt) cc_final: 0.8629 (tp) outliers start: 42 outliers final: 31 residues processed: 218 average time/residue: 0.2316 time to fit residues: 77.8258 Evaluate side-chains 210 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 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 D residue 16 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 GLU 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 498 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 158 optimal weight: 0.5980 chunk 131 optimal weight: 0.5980 chunk 83 optimal weight: 40.0000 chunk 46 optimal weight: 0.0070 chunk 153 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN C 449 HIS E 408 HIS E 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.143133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108754 restraints weight = 22757.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111488 restraints weight = 14902.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113272 restraints weight = 11394.753| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13387 Z= 0.117 Angle : 0.618 9.715 18141 Z= 0.310 Chirality : 0.045 0.180 2004 Planarity : 0.004 0.052 2348 Dihedral : 4.391 18.827 1790 Min Nonbonded Distance : 1.265 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.06 % Allowed : 18.63 % Favored : 79.31 % 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: -1.41 (0.20), residues: 1648 helix: 0.45 (0.28), residues: 334 sheet: -0.99 (0.26), residues: 394 loop : -1.45 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 205 HIS 0.015 0.001 HIS E 476 PHE 0.027 0.002 PHE A 312 TYR 0.016 0.001 TYR A 521 ARG 0.006 0.000 ARG C 508 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 437) hydrogen bonds : angle 4.94831 ( 1227) metal coordination : bond 0.00077 ( 13) covalent geometry : bond 0.00265 (13374) covalent geometry : angle 0.61757 (18141) *********************** 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 241 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7522 (mttt) cc_final: 0.7036 (pptt) REVERT: B 252 MET cc_start: 0.8826 (tpp) cc_final: 0.8543 (tpp) REVERT: B 310 ASP cc_start: 0.8942 (m-30) cc_final: 0.8574 (t0) REVERT: B 336 MET cc_start: 0.9147 (pmm) cc_final: 0.8789 (pmm) REVERT: C 95 GLN cc_start: 0.8642 (tm-30) cc_final: 0.7979 (tm-30) REVERT: C 98 ARG cc_start: 0.8763 (ttm170) cc_final: 0.8320 (tpp-160) REVERT: C 684 MET cc_start: 0.7011 (ppp) cc_final: 0.6261 (ppp) REVERT: D 242 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7993 (pp) REVERT: E 419 ILE cc_start: 0.8267 (mm) cc_final: 0.7979 (mm) REVERT: E 420 GLU cc_start: 0.7469 (mp0) cc_final: 0.7104 (mp0) REVERT: E 492 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8560 (mt) REVERT: F 159 THR cc_start: 0.8071 (p) cc_final: 0.7707 (p) outliers start: 28 outliers final: 20 residues processed: 227 average time/residue: 0.2330 time to fit residues: 81.1632 Evaluate side-chains 214 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 475 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 59 LYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 242 LEU 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 408 HIS Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.0020 chunk 128 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 130 optimal weight: 0.0270 chunk 157 optimal weight: 4.9990 chunk 12 optimal weight: 0.0270 chunk 44 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 overall best weight: 0.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 HIS C 449 HIS C 577 GLN D 27 ASN D 78 HIS E 408 HIS E 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111287 restraints weight = 22735.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114110 restraints weight = 14711.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115908 restraints weight = 11216.707| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13387 Z= 0.109 Angle : 0.617 11.251 18141 Z= 0.309 Chirality : 0.045 0.355 2004 Planarity : 0.004 0.046 2348 Dihedral : 4.218 18.270 1790 Min Nonbonded Distance : 1.291 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.99 % Allowed : 19.51 % Favored : 78.50 % 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: -1.26 (0.20), residues: 1648 helix: 0.54 (0.29), residues: 333 sheet: -0.85 (0.26), residues: 399 loop : -1.35 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 205 HIS 0.023 0.001 HIS E 408 PHE 0.027 0.002 PHE A 312 TYR 0.020 0.001 TYR C 434 ARG 0.010 0.000 ARG E 407 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 437) hydrogen bonds : angle 4.87164 ( 1227) metal coordination : bond 0.00027 ( 13) covalent geometry : bond 0.00241 (13374) covalent geometry : angle 0.61724 (18141) ********************** 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 242 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7467 (mttt) cc_final: 0.6990 (pptt) REVERT: B 310 ASP cc_start: 0.8909 (m-30) cc_final: 0.8603 (t0) REVERT: B 336 MET cc_start: 0.9125 (pmm) cc_final: 0.8736 (pmm) REVERT: C 85 LEU cc_start: 0.8759 (tt) cc_final: 0.8457 (tt) REVERT: C 95 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 684 MET cc_start: 0.6919 (ppp) cc_final: 0.6213 (ppp) REVERT: E 419 ILE cc_start: 0.8157 (mm) cc_final: 0.7556 (mm) REVERT: E 420 GLU cc_start: 0.7402 (mp0) cc_final: 0.7091 (mm-30) REVERT: E 492 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8035 (mt) REVERT: F 159 THR cc_start: 0.8106 (p) cc_final: 0.7803 (p) outliers start: 27 outliers final: 19 residues processed: 230 average time/residue: 0.2176 time to fit residues: 77.1263 Evaluate side-chains 220 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 475 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 27 ASN 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 202 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 498 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 163 optimal weight: 0.0020 chunk 119 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.0020 chunk 106 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 HIS ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN E 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.144924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111025 restraints weight = 23024.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113817 restraints weight = 14916.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115734 restraints weight = 11368.920| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.274 13387 Z= 0.176 Angle : 0.985 59.136 18141 Z= 0.554 Chirality : 0.045 0.272 2004 Planarity : 0.004 0.104 2348 Dihedral : 4.219 20.782 1790 Min Nonbonded Distance : 1.291 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.69 % Allowed : 20.03 % Favored : 78.28 % Cbeta Deviations : 0.12 % 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: -1.26 (0.20), residues: 1648 helix: 0.50 (0.29), residues: 333 sheet: -0.82 (0.26), residues: 399 loop : -1.36 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 205 HIS 0.040 0.001 HIS C 659 PHE 0.079 0.002 PHE A 303 TYR 0.017 0.001 TYR B 244 ARG 0.013 0.000 ARG C 516 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 437) hydrogen bonds : angle 4.84855 ( 1227) metal coordination : bond 0.00044 ( 13) covalent geometry : bond 0.00436 (13374) covalent geometry : angle 0.98491 (18141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4586.16 seconds wall clock time: 81 minutes 17.46 seconds (4877.46 seconds total)