Starting phenix.real_space_refine on Fri Jun 20 22:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9isn_60839/06_2025/9isn_60839.cif Found real_map, /net/cci-nas-00/data/ceres_data/9isn_60839/06_2025/9isn_60839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9isn_60839/06_2025/9isn_60839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9isn_60839/06_2025/9isn_60839.map" model { file = "/net/cci-nas-00/data/ceres_data/9isn_60839/06_2025/9isn_60839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9isn_60839/06_2025/9isn_60839.cif" } resolution = 2.97 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= 0.027 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 68 5.49 5 Mg 1 5.21 5 S 83 5.16 5 C 14972 2.51 5 N 4314 2.21 5 O 4779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24219 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 13, 'TRANS': 216} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1246, 9747 Classifications: {'peptide': 1246} Link IDs: {'PTRANS': 55, 'TRANS': 1190} Chain: "F" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 874 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "G" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 648 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 745 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12649 SG CYS D 60 21.476 77.745 77.476 1.00103.67 S ATOM 12667 SG CYS D 62 21.205 79.926 74.560 1.00105.59 S ATOM 12776 SG CYS D 75 19.642 76.528 74.206 1.00103.20 S ATOM 12802 SG CYS D 78 23.275 76.624 74.217 1.00101.57 S ATOM 19201 SG CYS D 886 49.473 22.376 106.117 1.00 62.28 S ATOM 19765 SG CYS D 962 51.081 25.463 104.584 1.00 57.06 S ATOM 19813 SG CYS D 969 49.213 25.701 107.943 1.00 50.08 S ATOM 19832 SG CYS D 972 52.518 23.949 107.762 1.00 55.19 S Time building chain proxies: 14.07, per 1000 atoms: 0.58 Number of scatterers: 24219 At special positions: 0 Unit cell: (126.752, 128.616, 192.924, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 83 16.00 P 68 15.00 Mg 1 11.99 O 4779 8.00 N 4314 7.00 C 14972 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: 6.31 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " Number of angles added : 12 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5394 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 40 sheets defined 40.1% alpha, 15.9% beta 23 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 8.91 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.539A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 4.012A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 203 through 226 removed outlier: 3.841A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 4.446A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.576A pdb=" N GLU B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.250A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 4.010A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 222 through 228 Processing helix chain 'C' and resid 232 through 240 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.546A pdb=" N ARG C 247 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 removed outlier: 3.507A pdb=" N ALA C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 297 through 309 Processing helix chain 'C' and resid 320 through 337 removed outlier: 3.748A pdb=" N VAL C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 393 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.702A pdb=" N LEU C 403 " --> pdb=" O THR C 399 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 399 through 404' Processing helix chain 'C' and resid 406 through 420 Processing helix chain 'C' and resid 430 through 438 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.778A pdb=" N TYR C 466 " --> pdb=" O PRO C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 523 Processing helix chain 'C' and resid 574 through 579 Processing helix chain 'C' and resid 587 through 599 removed outlier: 3.966A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 716 through 720 removed outlier: 4.014A pdb=" N ASP C 719 " --> pdb=" O ASN C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 911 removed outlier: 3.586A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 928 Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 removed outlier: 3.578A pdb=" N HIS C 976 " --> pdb=" O GLY C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1026 removed outlier: 3.592A pdb=" N LYS C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1065 Processing helix chain 'C' and resid 1066 through 1076 removed outlier: 3.669A pdb=" N LEU C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 3.639A pdb=" N TYR C1088 " --> pdb=" O ARG C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1116 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.891A pdb=" N GLU D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.558A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 188 Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 192 through 228 Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.815A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 4.260A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.594A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.590A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 361 removed outlier: 3.851A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.640A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 4.238A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 529 removed outlier: 3.703A pdb=" N VAL D 528 " --> pdb=" O HIS D 525 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS D 529 " --> pdb=" O PRO D 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 525 through 529' Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 606 through 616 Processing helix chain 'D' and resid 663 through 669 Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 721 removed outlier: 3.846A pdb=" N ARG D 721 " --> pdb=" O PHE D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 757 removed outlier: 4.375A pdb=" N LYS D 738 " --> pdb=" O PRO D 734 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU D 739 " --> pdb=" O ASP D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 removed outlier: 3.700A pdb=" N PHE D 788 " --> pdb=" O MET D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 814 removed outlier: 3.558A pdb=" N MET D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 877 removed outlier: 4.190A pdb=" N HIS D 849 " --> pdb=" O PHE D 845 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA D 851 " --> pdb=" O SER D 847 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA D 863 " --> pdb=" O ALA D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 970 through 974 Processing helix chain 'D' and resid 988 through 999 Processing helix chain 'D' and resid 1000 through 1002 No H-bonds generated for 'chain 'D' and resid 1000 through 1002' Processing helix chain 'D' and resid 1022 through 1032 removed outlier: 3.518A pdb=" N ALA D1032 " --> pdb=" O GLU D1028 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1107 Processing helix chain 'D' and resid 1109 through 1129 removed outlier: 3.865A pdb=" N VAL D1124 " --> pdb=" O GLU D1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 3.988A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1165 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1210 removed outlier: 3.685A pdb=" N ALA D1206 " --> pdb=" O SER D1202 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1223 Processing helix chain 'D' and resid 1231 through 1237 removed outlier: 3.926A pdb=" N ILE D1237 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1246 Processing helix chain 'D' and resid 1247 through 1252 removed outlier: 3.551A pdb=" N ASN D1252 " --> pdb=" O SER D1248 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 23 Processing helix chain 'F' and resid 24 through 48 removed outlier: 3.515A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) Proline residue: F 37 - end of helix Processing helix chain 'F' and resid 53 through 56 Processing helix chain 'F' and resid 57 through 73 removed outlier: 3.579A pdb=" N GLU F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 82 through 104 Processing helix chain 'F' and resid 111 through 116 removed outlier: 3.962A pdb=" N GLU F 115 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 111 through 116' Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.930A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.930A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 6.233A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.679A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.808A pdb=" N TYR B 96 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.544A pdb=" N GLY B 103 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR B 127 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 105 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.204A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AB4, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.066A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB6, first strand: chain 'C' and resid 362 through 365 Processing sheet with id=AB7, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.591A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE C 192 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AC1, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.617A pdb=" N ASP C 566 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 548 through 549 Processing sheet with id=AC3, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.905A pdb=" N VAL C 628 " --> pdb=" O LEU C 688 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 653 through 657 removed outlier: 6.806A pdb=" N TYR C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL C 639 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR C 645 " --> pdb=" O GLN C 637 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC6, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.410A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE C 901 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU C 706 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU C 903 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA C 708 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 735 through 745 removed outlier: 3.529A pdb=" N VAL C 857 " --> pdb=" O HIS C 741 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN C 853 " --> pdb=" O ALA C 745 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 854 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 838 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG C 856 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 836 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR C 858 " --> pdb=" O ILE C 834 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 747 through 748 Processing sheet with id=AC9, first strand: chain 'C' and resid 787 through 789 removed outlier: 3.534A pdb=" N VAL C 789 " --> pdb=" O LEU C 823 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1027 through 1028 removed outlier: 6.113A pdb=" N CYS D 441 " --> pdb=" O GLN D 515 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1051 through 1053 removed outlier: 3.778A pdb=" N GLN C1051 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 420 " --> pdb=" O PHE C1053 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1127 through 1128 removed outlier: 3.514A pdb=" N ARG D 11 " --> pdb=" O GLU C1121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.406A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N ALA D 99 " --> pdb=" O CYS D 316 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N CYS D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 135 through 139 removed outlier: 5.401A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE D 138 " --> pdb=" O ASP D 253 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.108A pdb=" N PHE D 335 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 821 removed outlier: 3.523A pdb=" N GLU D 825 " --> pdb=" O ASN D 821 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 881 through 883 Processing sheet with id=AE1, first strand: chain 'D' and resid 892 through 894 Processing sheet with id=AE2, first strand: chain 'D' and resid 924 through 925 removed outlier: 6.936A pdb=" N VAL D 924 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1070 through 1073 Processing sheet with id=AE4, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 4.769A pdb=" N ARG D1147 " --> pdb=" O GLN D1189 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2886 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 10.94 Time building geometry restraints manager: 7.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5237 1.33 - 1.45: 5457 1.45 - 1.58: 13786 1.58 - 1.70: 133 1.70 - 1.82: 149 Bond restraints: 24762 Sorted by residual: bond pdb=" N TYR C 288 " pdb=" CA TYR C 288 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.31e-02 5.83e+03 8.90e+00 bond pdb=" N VAL D1048 " pdb=" CA VAL D1048 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.20e-02 6.94e+03 7.35e+00 bond pdb=" CA ALA B 229 " pdb=" C ALA B 229 " ideal model delta sigma weight residual 1.532 1.500 0.032 1.21e-02 6.83e+03 7.06e+00 bond pdb=" C LYS D 686 " pdb=" O LYS D 686 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.22e-02 6.72e+03 6.34e+00 bond pdb=" N VAL D 68 " pdb=" CA VAL D 68 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.33e-02 5.65e+03 6.30e+00 ... (remaining 24757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 32475 1.70 - 3.41: 1071 3.41 - 5.11: 209 5.11 - 6.81: 28 6.81 - 8.51: 5 Bond angle restraints: 33788 Sorted by residual: angle pdb=" N TYR C 556 " pdb=" CA TYR C 556 " pdb=" C TYR C 556 " ideal model delta sigma weight residual 110.24 118.27 -8.03 1.30e+00 5.92e-01 3.82e+01 angle pdb=" N ASP C 560 " pdb=" CA ASP C 560 " pdb=" C ASP C 560 " ideal model delta sigma weight residual 111.82 105.47 6.35 1.16e+00 7.43e-01 2.99e+01 angle pdb=" N PHE D 788 " pdb=" CA PHE D 788 " pdb=" C PHE D 788 " ideal model delta sigma weight residual 109.64 116.10 -6.46 1.27e+00 6.20e-01 2.59e+01 angle pdb=" N ALA D 534 " pdb=" CA ALA D 534 " pdb=" C ALA D 534 " ideal model delta sigma weight residual 108.41 115.79 -7.38 1.61e+00 3.86e-01 2.10e+01 angle pdb=" N VAL C 573 " pdb=" CA VAL C 573 " pdb=" C VAL C 573 " ideal model delta sigma weight residual 110.21 115.28 -5.07 1.13e+00 7.83e-01 2.01e+01 ... (remaining 33783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 14461 35.29 - 70.58: 500 70.58 - 105.87: 30 105.87 - 141.16: 2 141.16 - 176.45: 4 Dihedral angle restraints: 14997 sinusoidal: 6616 harmonic: 8381 Sorted by residual: dihedral pdb=" CA SER A 44 " pdb=" C SER A 44 " pdb=" N SER A 45 " pdb=" CA SER A 45 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE C 359 " pdb=" C PHE C 359 " pdb=" N GLY C 360 " pdb=" CA GLY C 360 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLU B 24 " pdb=" C GLU B 24 " pdb=" N PRO B 25 " pdb=" CA PRO B 25 " ideal model delta harmonic sigma weight residual -180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 14994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2379 0.033 - 0.066: 956 0.066 - 0.100: 330 0.100 - 0.133: 148 0.133 - 0.166: 25 Chirality restraints: 3838 Sorted by residual: chirality pdb=" CA PRO B 25 " pdb=" N PRO B 25 " pdb=" C PRO B 25 " pdb=" CB PRO B 25 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CB VAL C 506 " pdb=" CA VAL C 506 " pdb=" CG1 VAL C 506 " pdb=" CG2 VAL C 506 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA PHE D 788 " pdb=" N PHE D 788 " pdb=" C PHE D 788 " pdb=" CB PHE D 788 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 3835 not shown) Planarity restraints: 4214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 609 " 0.054 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO C 610 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 610 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 610 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 201 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C GLU C 201 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU C 201 " 0.021 2.00e-02 2.50e+03 pdb=" N MET C 202 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C1053 " 0.017 2.00e-02 2.50e+03 2.25e-02 8.85e+00 pdb=" CG PHE C1053 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE C1053 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C1053 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE C1053 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C1053 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE C1053 " 0.001 2.00e-02 2.50e+03 ... (remaining 4211 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2269 2.74 - 3.28: 24917 3.28 - 3.82: 40834 3.82 - 4.36: 50449 4.36 - 4.90: 84715 Nonbonded interactions: 203184 Sorted by model distance: nonbonded pdb=" OE1 GLN A 185 " pdb=" OG1 THR A 187 " model vdw 2.198 3.040 nonbonded pdb=" O SER D1197 " pdb=" OG1 THR D1200 " model vdw 2.204 3.040 nonbonded pdb=" NH1 ARG D1187 " pdb=" O PRO D1188 " model vdw 2.208 3.120 nonbonded pdb=" OG SER C1125 " pdb=" OD2 ASP D 8 " model vdw 2.209 3.040 nonbonded pdb=" NH2 ARG D 397 " pdb=" O ALA F 110 " model vdw 2.210 3.120 ... (remaining 203179 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 227) selection = (chain 'B' and resid 4 through 227) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 67.230 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24770 Z= 0.215 Angle : 0.744 8.513 33800 Z= 0.422 Chirality : 0.044 0.166 3838 Planarity : 0.006 0.090 4214 Dihedral : 16.807 176.450 9603 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.65 % Allowed : 11.67 % Favored : 87.68 % 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: -1.09 (0.15), residues: 2921 helix: 0.32 (0.16), residues: 1076 sheet: -1.06 (0.25), residues: 392 loop : -1.41 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 718 HIS 0.006 0.001 HIS D 849 PHE 0.048 0.002 PHE C1053 TYR 0.026 0.001 TYR D 130 ARG 0.012 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.14290 ( 1061) hydrogen bonds : angle 6.38847 ( 3008) metal coordination : bond 0.00382 ( 8) metal coordination : angle 3.78913 ( 12) covalent geometry : bond 0.00417 (24762) covalent geometry : angle 0.74047 (33788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 289 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8631 (ptpp) cc_final: 0.8405 (ptpp) REVERT: B 213 LYS cc_start: 0.7146 (mttp) cc_final: 0.6805 (mttp) REVERT: C 84 ILE cc_start: 0.5137 (OUTLIER) cc_final: 0.4749 (pt) REVERT: C 209 MET cc_start: 0.5631 (mmt) cc_final: 0.4163 (ptm) REVERT: C 394 ASP cc_start: 0.5839 (OUTLIER) cc_final: 0.5442 (p0) REVERT: C 771 ASP cc_start: 0.6468 (t0) cc_final: 0.6267 (t0) REVERT: D 276 ARG cc_start: 0.7513 (ptp90) cc_final: 0.7244 (ptp90) REVERT: D 949 HIS cc_start: 0.6952 (m90) cc_final: 0.6734 (m90) outliers start: 16 outliers final: 3 residues processed: 298 average time/residue: 1.2889 time to fit residues: 444.5204 Evaluate side-chains 250 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 245 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 876 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 6.9990 chunk 225 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 232 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 269 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS C 105 ASN C 716 ASN C 875 HIS D 754 GLN D1173 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.190198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139995 restraints weight = 27281.439| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.08 r_work: 0.3578 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24770 Z= 0.155 Angle : 0.627 9.658 33800 Z= 0.331 Chirality : 0.044 0.334 3838 Planarity : 0.005 0.065 4214 Dihedral : 15.220 179.194 3948 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.23 % Allowed : 13.90 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 2921 helix: 0.65 (0.16), residues: 1098 sheet: -0.52 (0.26), residues: 372 loop : -1.23 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.006 0.001 HIS D1182 PHE 0.024 0.002 PHE C1053 TYR 0.022 0.002 TYR B 32 ARG 0.010 0.001 ARG D 595 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 1061) hydrogen bonds : angle 5.03007 ( 3008) metal coordination : bond 0.00409 ( 8) metal coordination : angle 2.72910 ( 12) covalent geometry : bond 0.00362 (24762) covalent geometry : angle 0.62473 (33788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 283 time to evaluate : 2.910 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.7453 (t0) cc_final: 0.6852 (t0) REVERT: A 144 ARG cc_start: 0.7469 (ptt90) cc_final: 0.7185 (ptt90) REVERT: A 203 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6942 (mtm180) REVERT: B 65 THR cc_start: 0.7785 (t) cc_final: 0.7408 (m) REVERT: B 193 ILE cc_start: 0.7643 (mm) cc_final: 0.7400 (mp) REVERT: C 209 MET cc_start: 0.5554 (mmt) cc_final: 0.4043 (ppp) REVERT: C 401 GLN cc_start: 0.7354 (tm-30) cc_final: 0.7145 (tm-30) REVERT: C 555 ASP cc_start: 0.7677 (t70) cc_final: 0.7359 (t0) REVERT: C 616 MET cc_start: 0.6724 (tpt) cc_final: 0.6286 (mmt) REVERT: C 769 ASP cc_start: 0.6689 (t0) cc_final: 0.6412 (t0) REVERT: C 771 ASP cc_start: 0.6561 (t0) cc_final: 0.6324 (t0) REVERT: C 1002 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: D 242 ARG cc_start: 0.6889 (mmp-170) cc_final: 0.6644 (mmp-170) REVERT: D 485 ASP cc_start: 0.7024 (m-30) cc_final: 0.6730 (m-30) REVERT: D 520 LYS cc_start: 0.5046 (mmmt) cc_final: 0.4709 (mmmt) REVERT: D 916 TYR cc_start: 0.7197 (m-10) cc_final: 0.6687 (m-10) REVERT: D 1089 GLU cc_start: 0.6520 (mp0) cc_final: 0.6219 (mm-30) outliers start: 55 outliers final: 20 residues processed: 318 average time/residue: 1.2569 time to fit residues: 469.4600 Evaluate side-chains 273 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1099 THR Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain F residue 104 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 259 optimal weight: 10.0000 chunk 250 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 219 optimal weight: 0.0060 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 254 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN C 589 ASN C 877 ASN D 499 ASN D 754 GLN D 811 GLN D 849 HIS F 93 HIS F 99 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.189482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139873 restraints weight = 27227.267| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.08 r_work: 0.3568 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24770 Z= 0.156 Angle : 0.608 9.403 33800 Z= 0.318 Chirality : 0.044 0.337 3838 Planarity : 0.005 0.063 4214 Dihedral : 15.308 178.586 3939 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.92 % Allowed : 16.13 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2921 helix: 0.82 (0.16), residues: 1091 sheet: -0.42 (0.27), residues: 359 loop : -1.15 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.011 0.001 HIS D 505 PHE 0.026 0.002 PHE D1169 TYR 0.032 0.002 TYR B 32 ARG 0.011 0.000 ARG D 595 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 1061) hydrogen bonds : angle 4.79944 ( 3008) metal coordination : bond 0.00461 ( 8) metal coordination : angle 2.74755 ( 12) covalent geometry : bond 0.00366 (24762) covalent geometry : angle 0.60587 (33788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 273 time to evaluate : 2.848 Fit side-chains revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7378 (tpt90) cc_final: 0.7129 (tmm160) REVERT: A 80 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7133 (mp) REVERT: A 122 ASP cc_start: 0.7451 (t0) cc_final: 0.6845 (t0) REVERT: A 176 TYR cc_start: 0.7276 (p90) cc_final: 0.6761 (p90) REVERT: B 65 THR cc_start: 0.7943 (t) cc_final: 0.7575 (m) REVERT: B 200 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6251 (tp-100) REVERT: C 209 MET cc_start: 0.5595 (mmt) cc_final: 0.4124 (ppp) REVERT: C 401 GLN cc_start: 0.7383 (tm-30) cc_final: 0.7085 (tm-30) REVERT: C 555 ASP cc_start: 0.7722 (t70) cc_final: 0.7485 (t0) REVERT: C 616 MET cc_start: 0.6801 (tpt) cc_final: 0.6416 (mmt) REVERT: C 769 ASP cc_start: 0.6839 (t0) cc_final: 0.6444 (t0) REVERT: C 771 ASP cc_start: 0.6621 (t0) cc_final: 0.6368 (t0) REVERT: C 1002 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: D 485 ASP cc_start: 0.7031 (m-30) cc_final: 0.6700 (m-30) REVERT: D 520 LYS cc_start: 0.5001 (mmmt) cc_final: 0.4698 (mmmt) REVERT: D 916 TYR cc_start: 0.7205 (m-10) cc_final: 0.6818 (m-10) REVERT: D 949 HIS cc_start: 0.7022 (m90) cc_final: 0.6491 (m90) REVERT: D 1089 GLU cc_start: 0.6458 (mp0) cc_final: 0.6227 (mm-30) REVERT: D 1108 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6979 (mm) REVERT: D 1175 ARG cc_start: 0.7194 (ttp80) cc_final: 0.6725 (ttp80) REVERT: D 1201 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7432 (tt0) outliers start: 72 outliers final: 29 residues processed: 314 average time/residue: 1.2502 time to fit residues: 461.8384 Evaluate side-chains 280 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 4.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1009 SER Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain D residue 1245 THR Chi-restraints excluded: chain F residue 104 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 154 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 257 optimal weight: 0.0040 chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 589 ASN D 510 GLN D 622 GLN D 754 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.190510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140556 restraints weight = 27379.107| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.06 r_work: 0.3587 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24770 Z= 0.135 Angle : 0.584 12.526 33800 Z= 0.305 Chirality : 0.043 0.417 3838 Planarity : 0.005 0.060 4214 Dihedral : 15.303 178.063 3939 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.04 % Allowed : 17.67 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 2921 helix: 0.95 (0.16), residues: 1091 sheet: -0.44 (0.27), residues: 371 loop : -1.06 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.007 0.001 HIS D 505 PHE 0.024 0.001 PHE D1169 TYR 0.027 0.001 TYR B 32 ARG 0.005 0.000 ARG D 595 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 1061) hydrogen bonds : angle 4.66369 ( 3008) metal coordination : bond 0.00403 ( 8) metal coordination : angle 2.53681 ( 12) covalent geometry : bond 0.00314 (24762) covalent geometry : angle 0.58221 (33788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 267 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7390 (tpt90) cc_final: 0.7182 (tmm160) REVERT: A 80 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7102 (mp) REVERT: A 122 ASP cc_start: 0.7420 (t0) cc_final: 0.6810 (t0) REVERT: A 131 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8201 (ptmm) REVERT: A 176 TYR cc_start: 0.7219 (p90) cc_final: 0.6724 (p90) REVERT: A 203 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7146 (mtm180) REVERT: C 156 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8068 (mp) REVERT: C 209 MET cc_start: 0.5582 (mmt) cc_final: 0.4207 (ppp) REVERT: C 401 GLN cc_start: 0.7372 (tm-30) cc_final: 0.7053 (tm-30) REVERT: C 555 ASP cc_start: 0.7685 (t70) cc_final: 0.7485 (t0) REVERT: C 616 MET cc_start: 0.6801 (tpt) cc_final: 0.6450 (mmt) REVERT: C 769 ASP cc_start: 0.6824 (t0) cc_final: 0.6474 (t0) REVERT: C 771 ASP cc_start: 0.6522 (t0) cc_final: 0.6278 (t0) REVERT: C 842 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: C 843 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7601 (mp0) REVERT: C 1002 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7049 (mm-30) REVERT: D 244 LEU cc_start: 0.8270 (mp) cc_final: 0.8059 (mp) REVERT: D 485 ASP cc_start: 0.6893 (m-30) cc_final: 0.6523 (m-30) REVERT: D 520 LYS cc_start: 0.4934 (mmmt) cc_final: 0.4623 (mmmt) REVERT: D 749 GLU cc_start: 0.7877 (tp30) cc_final: 0.7389 (tp30) REVERT: D 864 ASP cc_start: 0.7990 (t70) cc_final: 0.7587 (t70) REVERT: D 906 ARG cc_start: 0.7751 (ptm160) cc_final: 0.7371 (pmm-80) REVERT: D 916 TYR cc_start: 0.7187 (m-10) cc_final: 0.6740 (m-10) REVERT: D 949 HIS cc_start: 0.7029 (m90) cc_final: 0.6819 (m90) REVERT: D 1108 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6976 (mm) outliers start: 75 outliers final: 32 residues processed: 316 average time/residue: 1.2001 time to fit residues: 447.2778 Evaluate side-chains 283 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1009 SER Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 754 GLN Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 1099 THR Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1245 THR Chi-restraints excluded: chain F residue 104 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 23 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 589 ASN C 944 GLN D 754 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.187702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137228 restraints weight = 27529.222| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.12 r_work: 0.3543 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24770 Z= 0.186 Angle : 0.633 13.050 33800 Z= 0.327 Chirality : 0.045 0.445 3838 Planarity : 0.005 0.062 4214 Dihedral : 15.349 176.836 3939 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.49 % Allowed : 18.85 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2921 helix: 0.78 (0.16), residues: 1097 sheet: -0.58 (0.26), residues: 396 loop : -1.07 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.007 0.001 HIS D 849 PHE 0.027 0.002 PHE D1169 TYR 0.029 0.002 TYR B 32 ARG 0.006 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.04480 ( 1061) hydrogen bonds : angle 4.73235 ( 3008) metal coordination : bond 0.00515 ( 8) metal coordination : angle 2.54888 ( 12) covalent geometry : bond 0.00448 (24762) covalent geometry : angle 0.63128 (33788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 259 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.7513 (t0) cc_final: 0.6877 (t0) REVERT: A 131 LYS cc_start: 0.8626 (ptpp) cc_final: 0.8149 (ptmm) REVERT: B 21 PHE cc_start: 0.7198 (m-80) cc_final: 0.6996 (m-80) REVERT: B 82 GLN cc_start: 0.7497 (tm-30) cc_final: 0.7276 (tm-30) REVERT: B 200 GLN cc_start: 0.6474 (mm-40) cc_final: 0.5985 (tp-100) REVERT: C 156 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8109 (mp) REVERT: C 209 MET cc_start: 0.5678 (mmt) cc_final: 0.4232 (pmm) REVERT: C 401 GLN cc_start: 0.7474 (tm-30) cc_final: 0.7105 (tm-30) REVERT: C 593 MET cc_start: 0.7696 (mtp) cc_final: 0.7271 (mtp) REVERT: C 616 MET cc_start: 0.6890 (tpt) cc_final: 0.6520 (mmt) REVERT: C 769 ASP cc_start: 0.6874 (t0) cc_final: 0.6462 (t0) REVERT: C 771 ASP cc_start: 0.6705 (t0) cc_final: 0.6450 (t0) REVERT: C 843 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7615 (mp0) REVERT: C 944 GLN cc_start: 0.8336 (pt0) cc_final: 0.8117 (pt0) REVERT: C 1002 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: C 1062 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7671 (mt-10) REVERT: D 244 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7919 (mp) REVERT: D 485 ASP cc_start: 0.6899 (m-30) cc_final: 0.6510 (m-30) REVERT: D 520 LYS cc_start: 0.5104 (mmmt) cc_final: 0.4809 (mmmt) REVERT: D 749 GLU cc_start: 0.7884 (tp30) cc_final: 0.7345 (tp30) REVERT: D 906 ARG cc_start: 0.7727 (ptm160) cc_final: 0.7444 (pmm-80) REVERT: D 949 HIS cc_start: 0.7031 (m90) cc_final: 0.6700 (m90) REVERT: D 1108 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6898 (mm) outliers start: 86 outliers final: 38 residues processed: 318 average time/residue: 1.1840 time to fit residues: 444.4357 Evaluate side-chains 287 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1009 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 1094 LEU Chi-restraints excluded: chain D residue 1099 THR Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain D residue 1235 VAL Chi-restraints excluded: chain D residue 1245 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 125 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 291 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 243 optimal weight: 0.0970 chunk 115 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 589 ASN D 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.190209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140534 restraints weight = 27273.245| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.04 r_work: 0.3585 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24770 Z= 0.133 Angle : 0.585 15.460 33800 Z= 0.303 Chirality : 0.042 0.178 3838 Planarity : 0.005 0.058 4214 Dihedral : 15.324 177.500 3939 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.00 % Allowed : 19.74 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 2921 helix: 0.97 (0.16), residues: 1099 sheet: -0.54 (0.26), residues: 395 loop : -1.01 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.005 0.001 HIS D 505 PHE 0.024 0.001 PHE C1053 TYR 0.024 0.001 TYR B 32 ARG 0.008 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 1061) hydrogen bonds : angle 4.60620 ( 3008) metal coordination : bond 0.00369 ( 8) metal coordination : angle 2.37534 ( 12) covalent geometry : bond 0.00310 (24762) covalent geometry : angle 0.58341 (33788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 263 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: A 80 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7016 (mp) REVERT: A 122 ASP cc_start: 0.7496 (t0) cc_final: 0.6850 (t0) REVERT: A 131 LYS cc_start: 0.8641 (ptpp) cc_final: 0.8189 (ptmm) REVERT: A 176 TYR cc_start: 0.7286 (p90) cc_final: 0.6668 (p90) REVERT: B 82 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7227 (tm-30) REVERT: B 200 GLN cc_start: 0.6504 (mm-40) cc_final: 0.5980 (tp-100) REVERT: C 156 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8052 (mp) REVERT: C 209 MET cc_start: 0.5483 (mmt) cc_final: 0.4104 (pmm) REVERT: C 401 GLN cc_start: 0.7449 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 616 MET cc_start: 0.6831 (tpt) cc_final: 0.6500 (mmt) REVERT: C 769 ASP cc_start: 0.6975 (t0) cc_final: 0.6542 (t0) REVERT: C 771 ASP cc_start: 0.6533 (t0) cc_final: 0.6286 (t0) REVERT: C 842 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: C 843 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7504 (mp0) REVERT: C 944 GLN cc_start: 0.8280 (pt0) cc_final: 0.8064 (pt0) REVERT: C 1062 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7516 (mt-10) REVERT: D 244 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7975 (mp) REVERT: D 276 ARG cc_start: 0.7554 (ptp-110) cc_final: 0.7350 (ptp90) REVERT: D 485 ASP cc_start: 0.7053 (m-30) cc_final: 0.6724 (m-30) REVERT: D 520 LYS cc_start: 0.4902 (mmmt) cc_final: 0.4694 (mmmt) REVERT: D 749 GLU cc_start: 0.7878 (tp30) cc_final: 0.7321 (tp30) REVERT: D 809 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7810 (mpm) REVERT: D 864 ASP cc_start: 0.8012 (t70) cc_final: 0.7565 (t70) REVERT: D 906 ARG cc_start: 0.7750 (ptm160) cc_final: 0.7384 (pmm-80) REVERT: D 916 TYR cc_start: 0.7246 (m-10) cc_final: 0.6850 (m-10) REVERT: D 949 HIS cc_start: 0.7105 (m90) cc_final: 0.6870 (m90) REVERT: D 1200 THR cc_start: 0.8980 (m) cc_final: 0.8760 (p) outliers start: 74 outliers final: 35 residues processed: 315 average time/residue: 1.1981 time to fit residues: 446.1822 Evaluate side-chains 282 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1009 SER Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 754 GLN Chi-restraints excluded: chain D residue 809 MET Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain D residue 1099 THR Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain D residue 1245 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 48 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 chunk 135 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.189837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140096 restraints weight = 27340.309| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.05 r_work: 0.3580 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24770 Z= 0.139 Angle : 0.599 15.496 33800 Z= 0.309 Chirality : 0.043 0.344 3838 Planarity : 0.005 0.059 4214 Dihedral : 15.324 177.271 3939 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.55 % Allowed : 20.88 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 2921 helix: 1.01 (0.16), residues: 1097 sheet: -0.48 (0.26), residues: 396 loop : -0.98 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.006 0.001 HIS D 949 PHE 0.047 0.001 PHE C1053 TYR 0.014 0.001 TYR B 32 ARG 0.012 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 1061) hydrogen bonds : angle 4.56603 ( 3008) metal coordination : bond 0.00391 ( 8) metal coordination : angle 2.33135 ( 12) covalent geometry : bond 0.00329 (24762) covalent geometry : angle 0.59766 (33788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 253 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: A 80 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.7048 (mp) REVERT: A 122 ASP cc_start: 0.7466 (t0) cc_final: 0.7238 (t0) REVERT: A 131 LYS cc_start: 0.8647 (ptpp) cc_final: 0.8187 (ptmm) REVERT: A 176 TYR cc_start: 0.7334 (p90) cc_final: 0.6663 (p90) REVERT: B 82 GLN cc_start: 0.7652 (tm-30) cc_final: 0.7270 (tm-30) REVERT: B 200 GLN cc_start: 0.6536 (mm-40) cc_final: 0.6056 (tp-100) REVERT: C 156 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8054 (mp) REVERT: C 209 MET cc_start: 0.5406 (mmt) cc_final: 0.3968 (ppp) REVERT: C 401 GLN cc_start: 0.7407 (tm-30) cc_final: 0.7005 (tm-30) REVERT: C 553 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6622 (pp20) REVERT: C 593 MET cc_start: 0.7593 (mtp) cc_final: 0.7195 (mtp) REVERT: C 616 MET cc_start: 0.6817 (tpt) cc_final: 0.6501 (mmt) REVERT: C 730 ASP cc_start: 0.6843 (t70) cc_final: 0.6575 (m-30) REVERT: C 769 ASP cc_start: 0.6958 (t0) cc_final: 0.6542 (t0) REVERT: C 771 ASP cc_start: 0.6560 (t0) cc_final: 0.6310 (t0) REVERT: C 842 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: C 843 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7490 (mp0) REVERT: C 944 GLN cc_start: 0.8276 (pt0) cc_final: 0.8048 (pt0) REVERT: D 276 ARG cc_start: 0.7541 (ptp-110) cc_final: 0.7299 (ptp90) REVERT: D 445 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7978 (mmtp) REVERT: D 485 ASP cc_start: 0.6970 (m-30) cc_final: 0.6640 (m-30) REVERT: D 520 LYS cc_start: 0.4897 (mmmt) cc_final: 0.4685 (mmmt) REVERT: D 749 GLU cc_start: 0.7870 (tp30) cc_final: 0.7274 (tp30) REVERT: D 809 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7839 (mpm) REVERT: D 864 ASP cc_start: 0.7987 (t70) cc_final: 0.7524 (t70) REVERT: D 892 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6438 (mm) REVERT: D 906 ARG cc_start: 0.7764 (ptm160) cc_final: 0.7415 (pmm-80) REVERT: D 916 TYR cc_start: 0.7228 (m-10) cc_final: 0.6835 (m-10) REVERT: D 949 HIS cc_start: 0.7391 (m90) cc_final: 0.7079 (m90) REVERT: D 1006 MET cc_start: 0.6505 (tpt) cc_final: 0.6241 (mmt) REVERT: D 1200 THR cc_start: 0.8992 (m) cc_final: 0.8783 (p) REVERT: D 1201 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7188 (tt0) outliers start: 63 outliers final: 39 residues processed: 296 average time/residue: 1.3080 time to fit residues: 455.1667 Evaluate side-chains 286 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1009 SER Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 809 MET Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain D residue 1099 THR Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain D residue 1245 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 210 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 199 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 289 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 885 ASN D 35 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.189531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140090 restraints weight = 27243.097| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.06 r_work: 0.3573 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24770 Z= 0.145 Angle : 0.611 15.883 33800 Z= 0.313 Chirality : 0.043 0.337 3838 Planarity : 0.005 0.059 4214 Dihedral : 15.328 177.230 3939 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.63 % Allowed : 21.61 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2921 helix: 0.98 (0.16), residues: 1097 sheet: -0.52 (0.25), residues: 419 loop : -0.96 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.005 0.001 HIS D 849 PHE 0.047 0.001 PHE C1053 TYR 0.020 0.001 TYR B 32 ARG 0.009 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 1061) hydrogen bonds : angle 4.57126 ( 3008) metal coordination : bond 0.00415 ( 8) metal coordination : angle 2.32057 ( 12) covalent geometry : bond 0.00343 (24762) covalent geometry : angle 0.60932 (33788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 255 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: A 80 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7107 (mp) REVERT: A 122 ASP cc_start: 0.7433 (t0) cc_final: 0.7200 (t0) REVERT: A 131 LYS cc_start: 0.8662 (ptpp) cc_final: 0.8437 (ptpp) REVERT: A 176 TYR cc_start: 0.7342 (p90) cc_final: 0.6684 (p90) REVERT: B 82 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7295 (tm-30) REVERT: B 200 GLN cc_start: 0.6547 (mm-40) cc_final: 0.6042 (tp-100) REVERT: C 156 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8080 (mp) REVERT: C 209 MET cc_start: 0.5406 (mmt) cc_final: 0.4005 (ppp) REVERT: C 401 GLN cc_start: 0.7417 (tm-30) cc_final: 0.7014 (tm-30) REVERT: C 553 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6779 (pp20) REVERT: C 593 MET cc_start: 0.7623 (mtp) cc_final: 0.7288 (mtp) REVERT: C 616 MET cc_start: 0.6894 (tpt) cc_final: 0.6572 (mmt) REVERT: C 730 ASP cc_start: 0.6862 (t70) cc_final: 0.6573 (m-30) REVERT: C 769 ASP cc_start: 0.7005 (t0) cc_final: 0.6578 (t0) REVERT: C 771 ASP cc_start: 0.6583 (t0) cc_final: 0.6335 (t0) REVERT: C 843 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7602 (mp0) REVERT: C 994 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7722 (mtt-85) REVERT: D 276 ARG cc_start: 0.7529 (ptp-110) cc_final: 0.7283 (ptp90) REVERT: D 445 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7878 (mmtp) REVERT: D 485 ASP cc_start: 0.7012 (m-30) cc_final: 0.6671 (m-30) REVERT: D 520 LYS cc_start: 0.4840 (mmmt) cc_final: 0.4636 (mmmt) REVERT: D 749 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: D 864 ASP cc_start: 0.7973 (t70) cc_final: 0.7548 (t70) REVERT: D 892 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6442 (mm) REVERT: D 906 ARG cc_start: 0.7799 (ptm160) cc_final: 0.7466 (pmm-80) REVERT: D 916 TYR cc_start: 0.7241 (m-10) cc_final: 0.6867 (m-10) REVERT: D 949 HIS cc_start: 0.7358 (m90) cc_final: 0.7107 (m90) REVERT: D 1006 MET cc_start: 0.6615 (tpt) cc_final: 0.6389 (mmt) outliers start: 65 outliers final: 40 residues processed: 299 average time/residue: 1.2028 time to fit residues: 423.0110 Evaluate side-chains 289 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 994 ARG Chi-restraints excluded: chain C residue 1009 SER Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 754 GLN Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain D residue 1099 THR Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain D residue 1235 VAL Chi-restraints excluded: chain D residue 1245 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 234 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 290 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 203 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 589 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.189757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140083 restraints weight = 27371.452| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.06 r_work: 0.3581 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24770 Z= 0.140 Angle : 0.604 13.452 33800 Z= 0.312 Chirality : 0.043 0.322 3838 Planarity : 0.005 0.064 4214 Dihedral : 15.329 177.429 3939 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.47 % Allowed : 21.89 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 2921 helix: 1.00 (0.16), residues: 1097 sheet: -0.49 (0.25), residues: 408 loop : -0.95 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.005 0.001 HIS D 505 PHE 0.045 0.001 PHE C1053 TYR 0.020 0.001 TYR B 32 ARG 0.009 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 1061) hydrogen bonds : angle 4.55329 ( 3008) metal coordination : bond 0.00403 ( 8) metal coordination : angle 2.16820 ( 12) covalent geometry : bond 0.00332 (24762) covalent geometry : angle 0.60236 (33788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 248 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: A 80 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.7073 (mp) REVERT: A 122 ASP cc_start: 0.7437 (t0) cc_final: 0.7206 (t0) REVERT: A 137 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 176 TYR cc_start: 0.7328 (p90) cc_final: 0.6644 (p90) REVERT: B 82 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 200 GLN cc_start: 0.6548 (mm-40) cc_final: 0.6051 (tp-100) REVERT: C 156 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8022 (mp) REVERT: C 209 MET cc_start: 0.5349 (mmt) cc_final: 0.3990 (ppp) REVERT: C 401 GLN cc_start: 0.7506 (tm-30) cc_final: 0.7081 (tm-30) REVERT: C 553 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6721 (pp20) REVERT: C 593 MET cc_start: 0.7629 (mtp) cc_final: 0.7250 (mtp) REVERT: C 616 MET cc_start: 0.6833 (tpt) cc_final: 0.6512 (mmt) REVERT: C 730 ASP cc_start: 0.6871 (t70) cc_final: 0.6576 (m-30) REVERT: C 769 ASP cc_start: 0.6977 (t0) cc_final: 0.6631 (t0) REVERT: C 771 ASP cc_start: 0.6522 (t0) cc_final: 0.6263 (t0) REVERT: C 843 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7619 (mp0) REVERT: C 994 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7727 (mtt-85) REVERT: C 1036 MET cc_start: 0.6060 (mmm) cc_final: 0.5714 (mtm) REVERT: C 1076 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7612 (tp) REVERT: D 276 ARG cc_start: 0.7518 (ptp-110) cc_final: 0.7271 (ptp90) REVERT: D 445 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7889 (mmtp) REVERT: D 485 ASP cc_start: 0.7030 (m-30) cc_final: 0.6676 (m-30) REVERT: D 749 GLU cc_start: 0.7808 (tp30) cc_final: 0.7198 (tp30) REVERT: D 807 MET cc_start: 0.6305 (pmm) cc_final: 0.5066 (tmm) REVERT: D 864 ASP cc_start: 0.7989 (t70) cc_final: 0.7540 (t70) REVERT: D 892 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6534 (mm) REVERT: D 906 ARG cc_start: 0.7800 (ptm160) cc_final: 0.7473 (pmm-80) REVERT: D 916 TYR cc_start: 0.7193 (m-10) cc_final: 0.6812 (m-10) REVERT: D 1200 THR cc_start: 0.9034 (m) cc_final: 0.8829 (p) REVERT: D 1201 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7228 (tt0) outliers start: 61 outliers final: 43 residues processed: 292 average time/residue: 1.2608 time to fit residues: 434.3046 Evaluate side-chains 287 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 994 ARG Chi-restraints excluded: chain C residue 1009 SER Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain D residue 1099 THR Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain D residue 1235 VAL Chi-restraints excluded: chain D residue 1245 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 174 optimal weight: 30.0000 chunk 179 optimal weight: 0.8980 chunk 180 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 GLN ** D1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.188389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138842 restraints weight = 27247.114| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.05 r_work: 0.3555 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24770 Z= 0.169 Angle : 0.638 13.028 33800 Z= 0.328 Chirality : 0.044 0.312 3838 Planarity : 0.005 0.061 4214 Dihedral : 15.352 176.862 3939 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.23 % Allowed : 22.46 % Favored : 75.31 % 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: -0.33 (0.15), residues: 2921 helix: 0.89 (0.16), residues: 1098 sheet: -0.54 (0.25), residues: 410 loop : -0.99 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 773 HIS 0.006 0.001 HIS D 849 PHE 0.051 0.002 PHE C1053 TYR 0.025 0.002 TYR B 32 ARG 0.009 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 1061) hydrogen bonds : angle 4.62003 ( 3008) metal coordination : bond 0.00510 ( 8) metal coordination : angle 2.21263 ( 12) covalent geometry : bond 0.00405 (24762) covalent geometry : angle 0.63654 (33788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: A 122 ASP cc_start: 0.7448 (t0) cc_final: 0.7217 (t0) REVERT: A 137 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 82 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7380 (tm-30) REVERT: B 200 GLN cc_start: 0.6611 (mm-40) cc_final: 0.6028 (tp-100) REVERT: C 156 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8118 (mp) REVERT: C 209 MET cc_start: 0.5501 (mmt) cc_final: 0.4035 (ppp) REVERT: C 401 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7124 (tm-30) REVERT: C 553 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6706 (pp20) REVERT: C 593 MET cc_start: 0.7658 (mtp) cc_final: 0.7269 (mtp) REVERT: C 616 MET cc_start: 0.6956 (tpt) cc_final: 0.6619 (mmt) REVERT: C 730 ASP cc_start: 0.6945 (t70) cc_final: 0.6642 (m-30) REVERT: C 769 ASP cc_start: 0.7013 (t0) cc_final: 0.6575 (t0) REVERT: C 771 ASP cc_start: 0.6653 (t0) cc_final: 0.6385 (t0) REVERT: C 843 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7632 (mp0) REVERT: C 994 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7719 (mtt-85) REVERT: C 1036 MET cc_start: 0.6077 (mmm) cc_final: 0.5742 (mtm) REVERT: C 1076 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7607 (tp) REVERT: D 276 ARG cc_start: 0.7541 (ptp-110) cc_final: 0.7292 (ptp90) REVERT: D 445 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7933 (mmtp) REVERT: D 485 ASP cc_start: 0.6893 (m-30) cc_final: 0.6550 (m-30) REVERT: D 749 GLU cc_start: 0.7807 (tp30) cc_final: 0.7204 (tp30) REVERT: D 864 ASP cc_start: 0.7977 (t70) cc_final: 0.7529 (t70) REVERT: D 892 LEU cc_start: 0.6629 (mp) cc_final: 0.6383 (mm) REVERT: D 916 TYR cc_start: 0.7238 (m-10) cc_final: 0.6882 (m-10) REVERT: D 1201 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7277 (tt0) outliers start: 55 outliers final: 44 residues processed: 284 average time/residue: 1.2371 time to fit residues: 412.9350 Evaluate side-chains 288 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 994 ARG Chi-restraints excluded: chain C residue 1009 SER Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 754 GLN Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain D residue 1099 THR Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain D residue 1235 VAL Chi-restraints excluded: chain D residue 1245 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 268 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 212 optimal weight: 0.2980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 GLN C 589 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.189001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139216 restraints weight = 27313.911| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.04 r_work: 0.3566 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24770 Z= 0.152 Angle : 0.632 13.489 33800 Z= 0.323 Chirality : 0.044 0.306 3838 Planarity : 0.005 0.061 4214 Dihedral : 15.339 176.992 3939 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.43 % Allowed : 22.33 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 2921 helix: 0.92 (0.16), residues: 1098 sheet: -0.51 (0.25), residues: 409 loop : -0.98 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.005 0.001 HIS D 849 PHE 0.055 0.001 PHE C1053 TYR 0.024 0.002 TYR D 130 ARG 0.009 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 1061) hydrogen bonds : angle 4.61272 ( 3008) metal coordination : bond 0.00443 ( 8) metal coordination : angle 2.12252 ( 12) covalent geometry : bond 0.00361 (24762) covalent geometry : angle 0.63082 (33788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18270.16 seconds wall clock time: 315 minutes 42.31 seconds (18942.31 seconds total)