Starting phenix.real_space_refine on Fri Aug 7 20:46:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k14_61964/08_2026/9k14_61964.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k14_61964/08_2026/9k14_61964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k14_61964/08_2026/9k14_61964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k14_61964/08_2026/9k14_61964.map" model { file = "/net/cci-nas-00/data/ceres_data/9k14_61964/08_2026/9k14_61964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k14_61964/08_2026/9k14_61964.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 6 6.06 5 P 37 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 14520 2.51 5 N 4049 2.21 5 O 4444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23198 Number of models: 1 Model: "" Number of chains: 18 Chain: "T" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 265 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "N" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "P" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 150 Classifications: {'RNA': 7} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 6506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6506 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 27, 'TRANS': 804} Chain breaks: 6 Chain: "C" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "K" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 890 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "H" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "I" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 763 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "E" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1706 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain: "B" Number of atoms: 7645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7645 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 36, 'TRANS': 928} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5734 SG CYS A 989 21.538 72.636 32.051 1.00101.77 S ATOM 5841 SG CYS A1004 23.496 76.019 31.790 1.00 92.02 S ATOM 7975 SG CYS C 90 80.645 43.706 140.990 1.00130.40 S ATOM 7994 SG CYS C 93 82.235 41.657 138.117 1.00152.07 S ATOM 8033 SG CYS C 99 80.731 39.718 141.009 1.00120.88 S ATOM 8059 SG CYS C 102 78.731 41.594 138.451 1.00113.67 S ATOM 10241 SG CYS J 7 51.457 44.244 120.623 1.00 69.31 S ATOM 10265 SG CYS J 10 51.234 45.307 124.201 1.00 72.35 S ATOM 10531 SG CYS J 44 48.456 46.470 121.746 1.00 68.77 S ATOM 10537 SG CYS J 45 48.706 42.912 122.882 1.00 68.41 S ATOM 11629 SG CYS L 12 79.626 16.186 97.082 1.00117.28 S ATOM 11647 SG CYS L 15 79.116 12.895 98.727 1.00113.61 S ATOM 11749 SG CYS L 29 82.154 13.580 96.431 1.00116.76 S ATOM 11775 SG CYS L 32 78.525 12.680 95.312 1.00123.22 S ATOM 13118 SG CYS I 7 30.412 44.808 20.899 1.00108.86 S ATOM 13303 SG CYS I 29 34.106 46.463 19.560 1.00129.80 S ATOM 13328 SG CYS I 32 33.205 44.576 18.496 1.00 91.90 S Time building chain proxies: 4.90, per 1000 atoms: 0.21 Number of scatterers: 23198 At special positions: 0 Unit cell: (117.165, 136.875, 164.25, 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 6 29.99 S 141 16.00 P 37 15.00 Mg 1 11.99 O 4444 8.00 N 4049 7.00 C 14520 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: 1.65 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A 938 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 940 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 989 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1004 " pdb=" ZN C 400 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 90 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " Number of angles added : 20 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5316 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 36 sheets defined 34.7% alpha, 18.1% beta 12 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.686A pdb=" N CYS A 443 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 444' Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.554A pdb=" N LEU A 479 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG A 480 " --> pdb=" O LYS A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 480' Processing helix chain 'A' and resid 492 through 505 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 595 through 613 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 627 through 649 removed outlier: 4.956A pdb=" N SER A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Proline residue: A 644 - end of helix removed outlier: 3.824A pdb=" N SER A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 675 Processing helix chain 'A' and resid 677 through 682 removed outlier: 3.505A pdb=" N ARG A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 682' Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 744 through 748 Processing helix chain 'A' and resid 750 through 771 Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.893A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.612A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 863 removed outlier: 3.548A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 876 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 891 through 904 Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 943 through 949 Processing helix chain 'A' and resid 952 through 970 removed outlier: 4.009A pdb=" N ALA A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.508A pdb=" N THR A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.857A pdb=" N VAL A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A1033 " --> pdb=" O TYR A1029 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A1034 " --> pdb=" O PRO A1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1027 through 1034' Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 3.507A pdb=" N ARG A1089 " --> pdb=" O GLY A1085 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1120 through 1138 removed outlier: 3.888A pdb=" N ALA A1124 " --> pdb=" O GLY A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 3.782A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A1156 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1176 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.809A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.712A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.563A pdb=" N ASP C 124 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 125' Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.588A pdb=" N TRP C 179 " --> pdb=" O HIS C 176 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 180 " --> pdb=" O ALA C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 180' Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 276 through 294 removed outlier: 3.852A pdb=" N VAL C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 Processing helix chain 'F' and resid 96 through 108 Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.510A pdb=" N ALA J 27 " --> pdb=" O ASP J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 37 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.730A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.557A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.875A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'E' and resid 31 through 51 Processing helix chain 'E' and resid 62 through 71 removed outlier: 3.756A pdb=" N PHE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.601A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 removed outlier: 4.267A pdb=" N LEU E 142 " --> pdb=" O LYS E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 162 removed outlier: 3.556A pdb=" N LYS E 161 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 184 removed outlier: 3.764A pdb=" N GLN E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 204 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 21 through 41 Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.674A pdb=" N SER B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.540A pdb=" N ALA B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 300 through 316 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 360 through 380 Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 428 removed outlier: 3.521A pdb=" N VAL B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N HIS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 removed outlier: 4.119A pdb=" N THR B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.525A pdb=" N SER B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.541A pdb=" N TRP B 510 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 551 removed outlier: 3.534A pdb=" N LEU B 548 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 4.001A pdb=" N ALA B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.664A pdb=" N GLU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 660 through 664' Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 707 through 717 Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.571A pdb=" N ILE B 732 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG B 733 " --> pdb=" O PRO B 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 729 through 733' Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 925 through 929 Processing helix chain 'B' and resid 944 through 947 removed outlier: 3.844A pdb=" N PHE B 947 " --> pdb=" O PRO B 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 944 through 947' Processing helix chain 'B' and resid 952 through 966 removed outlier: 4.510A pdb=" N LEU B 956 " --> pdb=" O THR B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1005 removed outlier: 3.507A pdb=" N GLY B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 1046 through 1048 removed outlier: 3.551A pdb=" N SER A 326 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 424 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL A 436 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 327 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE A 438 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR A 329 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.544A pdb=" N ARG A 403 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N CYS A 372 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 375 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 382 " --> pdb=" O TYR A 375 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 377 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 380 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 532 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 529 through 532 current: chain 'H' and resid 119 through 123 removed outlier: 5.731A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 33 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL H 13 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG H 144 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 555 through 556 removed outlier: 3.616A pdb=" N VAL A 562 " --> pdb=" O CYS A 555 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 561 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.632A pdb=" N GLY A 703 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.739A pdb=" N VAL A 797 " --> pdb=" O VAL A 806 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1043 through 1049 Processing sheet with id=AA9, first strand: chain 'A' and resid 906 through 907 removed outlier: 6.793A pdb=" N VAL A 906 " --> pdb=" O ILE A1037 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 983 through 986 removed outlier: 3.511A pdb=" N HIS A 940 " --> pdb=" O GLU A 914 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 914 " --> pdb=" O HIS A 940 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 915 " --> pdb=" O ASN I 46 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN I 46 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR I 44 " --> pdb=" O VAL A 917 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 3.676A pdb=" N GLU A1228 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG F 115 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1230 " --> pdb=" O THR F 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 17 removed outlier: 3.513A pdb=" N LYS C 11 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS C 23 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU C 17 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N ILE C 194 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ASP C 262 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N ASP C 192 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER C 264 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 17 removed outlier: 3.513A pdb=" N LYS C 11 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS C 23 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU C 17 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.208A pdb=" N GLU C 161 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL C 57 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LYS C 163 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE C 55 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG C 165 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 53 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 167 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL L 46 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.810A pdb=" N VAL C 154 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 220 through 223 removed outlier: 3.682A pdb=" N ASP C 221 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 19 through 22 removed outlier: 6.833A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.631A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N GLY B 877 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N VAL B 901 " --> pdb=" O GLY B 877 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.631A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 14 through 16 removed outlier: 3.546A pdb=" N GLU I 36 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 84 through 89 Processing sheet with id=AC4, first strand: chain 'E' and resid 94 through 96 removed outlier: 6.785A pdb=" N LYS E 94 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL E 127 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL E 96 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.574A pdb=" N VAL E 213 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR E 223 " --> pdb=" O TYR E 215 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 68 through 70 removed outlier: 5.790A pdb=" N ASN B 129 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 94 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS B 127 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 96 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG B 125 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ALA B 124 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG B 169 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET B 126 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 167 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC8, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AC9, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.345A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.645A pdb=" N ILE B 245 " --> pdb=" O TYR B 267 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AD3, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD4, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD5, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.623A pdb=" N VAL B 577 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 570 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 579 " --> pdb=" O HIS B 568 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS B 568 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS B 569 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE B 616 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU B 571 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 7.758A pdb=" N MET B 786 " --> pdb=" O GLY B 921 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE B 923 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE B1028 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 823 through 825 removed outlier: 3.566A pdb=" N GLN B 824 " --> pdb=" O CYS B 860 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 855 through 857 removed outlier: 3.874A pdb=" N ILE B 857 " --> pdb=" O VAL B 869 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 931 through 932 858 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4244 1.32 - 1.45: 5985 1.45 - 1.57: 13162 1.57 - 1.70: 69 1.70 - 1.83: 217 Bond restraints: 23677 Sorted by residual: bond pdb=" C1' DT T 10 " pdb=" N1 DT T 10 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.25e+01 bond pdb=" CA PRO B 341 " pdb=" C PRO B 341 " ideal model delta sigma weight residual 1.517 1.494 0.023 6.70e-03 2.23e+04 1.21e+01 bond pdb=" C1' DC N 14 " pdb=" N1 DC N 14 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" C3' DG T 20 " pdb=" C2' DG T 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.88e+00 bond pdb=" C3' DC N 18 " pdb=" C2' DC N 18 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.00e+00 ... (remaining 23672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 31573 2.54 - 5.08: 438 5.08 - 7.62: 52 7.62 - 10.17: 8 10.17 - 12.71: 8 Bond angle restraints: 32079 Sorted by residual: angle pdb=" C3' DT N 24 " pdb=" O3' DT N 24 " pdb=" P DA N 25 " ideal model delta sigma weight residual 119.70 108.55 11.15 1.20e+00 6.94e-01 8.64e+01 angle pdb=" C ILE B 942 " pdb=" N ASN B 943 " pdb=" CA ASN B 943 " ideal model delta sigma weight residual 120.49 132.03 -11.54 1.42e+00 4.96e-01 6.60e+01 angle pdb=" C3' DC N 26 " pdb=" O3' DC N 26 " pdb=" P DT N 27 " ideal model delta sigma weight residual 119.70 111.31 8.39 1.20e+00 6.94e-01 4.89e+01 angle pdb=" CA GLU B 781 " pdb=" CB GLU B 781 " pdb=" CG GLU B 781 " ideal model delta sigma weight residual 114.10 126.81 -12.71 2.00e+00 2.50e-01 4.04e+01 angle pdb=" C3' DA T 8 " pdb=" O3' DA T 8 " pdb=" P DG T 9 " ideal model delta sigma weight residual 119.70 112.13 7.57 1.20e+00 6.94e-01 3.98e+01 ... (remaining 32074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.37: 12449 19.37 - 38.75: 1460 38.75 - 58.12: 346 58.12 - 77.49: 50 77.49 - 96.87: 23 Dihedral angle restraints: 14328 sinusoidal: 6124 harmonic: 8204 Sorted by residual: dihedral pdb=" CA ILE A1049 " pdb=" C ILE A1049 " pdb=" N TRP A1050 " pdb=" CA TRP A1050 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ALA H 61 " pdb=" C ALA H 61 " pdb=" N MET H 62 " pdb=" CA MET H 62 " ideal model delta harmonic sigma weight residual 180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLN E 118 " pdb=" C GLN E 118 " pdb=" N GLU E 119 " pdb=" CA GLU E 119 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 14325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 3567 0.128 - 0.255: 41 0.255 - 0.383: 0 0.383 - 0.511: 4 0.511 - 0.639: 1 Chirality restraints: 3613 Sorted by residual: chirality pdb=" P DT N 24 " pdb=" OP1 DT N 24 " pdb=" OP2 DT N 24 " pdb=" O5' DT N 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DT T 10 " pdb=" OP1 DT T 10 " pdb=" OP2 DT T 10 " pdb=" O5' DT T 10 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" P DG T 9 " pdb=" OP1 DG T 9 " pdb=" OP2 DG T 9 " pdb=" O5' DG T 9 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.50 2.00e-01 2.50e+01 6.15e+00 ... (remaining 3610 not shown) Planarity restraints: 3997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 781 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" CD GLU B 781 " -0.061 2.00e-02 2.50e+03 pdb=" OE1 GLU B 781 " 0.022 2.00e-02 2.50e+03 pdb=" OE2 GLU B 781 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 780 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C GLN B 780 " 0.039 2.00e-02 2.50e+03 pdb=" O GLN B 780 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 781 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 719 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C GLU A 719 " -0.038 2.00e-02 2.50e+03 pdb=" O GLU A 719 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A 720 " 0.013 2.00e-02 2.50e+03 ... (remaining 3994 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 439 2.69 - 3.24: 22887 3.24 - 3.80: 35655 3.80 - 4.35: 46241 4.35 - 4.90: 75127 Nonbonded interactions: 180349 Sorted by model distance: nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A3000 " model vdw 2.141 2.170 nonbonded pdb=" O LYS A 715 " pdb=" OE1 GLU A 719 " model vdw 2.170 3.040 nonbonded pdb=" OD1 ASP A 451 " pdb="MG MG A3000 " model vdw 2.222 2.170 nonbonded pdb=" O ALA J 27 " pdb=" OD1 ASP J 28 " model vdw 2.455 3.040 nonbonded pdb=" O ASN B 393 " pdb=" ND2 ASN B 393 " model vdw 2.455 3.120 ... (remaining 180344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.650 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 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 : 0.005 0.080 23696 Z= 0.253 Angle : 0.838 12.711 32099 Z= 0.491 Chirality : 0.051 0.639 3613 Planarity : 0.005 0.067 3997 Dihedral : 17.446 96.865 9012 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.56 % Favored : 93.41 % Rotamer: Outliers : 1.40 % Allowed : 19.28 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.15), residues: 2776 helix: -0.05 (0.17), residues: 874 sheet: -0.92 (0.24), residues: 489 loop : -1.77 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 70 TYR 0.025 0.002 TYR J 43 PHE 0.024 0.002 PHE A 333 TRP 0.028 0.003 TRP A1050 HIS 0.010 0.001 HIS E 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.25 (23677) covalent geometry : angle 0.82634 / 0.49 (32079) hydrogen bonds : bond 0.20199 / 21.62 ( 876) hydrogen bonds : angle 7.83502 / 7.45 ( 2444) metal coordination : bond 0.00908 / 0.74 ( 19) metal coordination : angle 5.64411 / 9.11 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 GLU cc_start: 0.7578 (tp30) cc_final: 0.7316 (tp30) REVERT: C 200 MET cc_start: 0.6619 (tmm) cc_final: 0.6043 (ttt) REVERT: J 48 MET cc_start: 0.7993 (mmm) cc_final: 0.7446 (mmm) REVERT: H 143 MET cc_start: 0.6408 (ppp) cc_final: 0.5876 (ttp) REVERT: E 46 MET cc_start: 0.4595 (tmm) cc_final: 0.3131 (ptp) REVERT: E 156 LEU cc_start: 0.6810 (mt) cc_final: 0.6520 (mt) REVERT: E 230 TRP cc_start: 0.3984 (t60) cc_final: 0.3590 (t-100) REVERT: B 131 ASP cc_start: 0.6951 (t70) cc_final: 0.6657 (m-30) REVERT: B 850 MET cc_start: 0.6676 (mmm) cc_final: 0.6195 (mmm) REVERT: B 1029 MET cc_start: 0.6130 (ttt) cc_final: 0.5745 (mtt) outliers start: 35 outliers final: 28 residues processed: 214 average time/residue: 0.1645 time to fit residues: 56.1061 Evaluate side-chains 191 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 940 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.0470 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN A 807 GLN K 44 ASN ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.109000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.086906 restraints weight = 94452.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.089003 restraints weight = 59473.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.089340 restraints weight = 36640.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.089645 restraints weight = 31630.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.089741 restraints weight = 28609.924| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23696 Z= 0.135 Angle : 0.633 12.593 32099 Z= 0.334 Chirality : 0.043 0.193 3613 Planarity : 0.004 0.054 3997 Dihedral : 12.488 101.061 3527 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.33 % Allowed : 18.76 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.16), residues: 2776 helix: 0.34 (0.18), residues: 881 sheet: -0.63 (0.24), residues: 487 loop : -1.74 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 875 TYR 0.019 0.001 TYR J 43 PHE 0.015 0.002 PHE B 376 TRP 0.016 0.002 TRP A1050 HIS 0.004 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (23677) covalent geometry : angle 0.62224 / 0.33 (32079) hydrogen bonds : bond 0.05598 / 5.97 ( 876) hydrogen bonds : angle 5.73972 / 5.66 ( 2444) metal coordination : bond 0.00571 / 0.58 ( 19) metal coordination : angle 4.61406 / 7.11 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 170 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.5619 (mmp) cc_final: 0.5392 (mmm) REVERT: A 631 MET cc_start: 0.0765 (mmt) cc_final: -0.0531 (ttt) REVERT: A 858 MET cc_start: 0.5215 (mtm) cc_final: 0.5013 (mtm) REVERT: C 164 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8553 (pp) REVERT: C 200 MET cc_start: 0.6879 (tmm) cc_final: 0.6103 (ttt) REVERT: J 29 TYR cc_start: 0.5777 (OUTLIER) cc_final: 0.5416 (m-10) REVERT: H 62 MET cc_start: 0.7789 (tpt) cc_final: 0.7410 (tpp) REVERT: E 46 MET cc_start: 0.4184 (tmm) cc_final: 0.3089 (ttp) REVERT: E 156 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7232 (mt) REVERT: E 186 GLU cc_start: 0.3338 (OUTLIER) cc_final: 0.3047 (mm-30) REVERT: E 230 TRP cc_start: 0.3720 (t60) cc_final: 0.3448 (t-100) REVERT: B 62 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7374 (t80) REVERT: B 131 ASP cc_start: 0.6628 (t70) cc_final: 0.6385 (m-30) REVERT: B 132 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.7119 (p) outliers start: 83 outliers final: 44 residues processed: 240 average time/residue: 0.1423 time to fit residues: 56.7395 Evaluate side-chains 208 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 940 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 203 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN K 40 HIS ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.106011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.084598 restraints weight = 97286.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.086076 restraints weight = 62163.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.086444 restraints weight = 41199.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.086680 restraints weight = 36432.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.086819 restraints weight = 33012.563| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23696 Z= 0.206 Angle : 0.695 12.330 32099 Z= 0.364 Chirality : 0.045 0.215 3613 Planarity : 0.005 0.056 3997 Dihedral : 12.395 104.727 3510 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.13 % Allowed : 18.80 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.15), residues: 2776 helix: 0.15 (0.17), residues: 883 sheet: -0.72 (0.24), residues: 473 loop : -1.84 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 793 TYR 0.030 0.002 TYR J 43 PHE 0.020 0.002 PHE F 123 TRP 0.018 0.002 TRP B 510 HIS 0.036 0.002 HIS E 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (23677) covalent geometry : angle 0.68381 / 0.36 (32079) hydrogen bonds : bond 0.05499 / 5.88 ( 876) hydrogen bonds : angle 5.45223 / 5.48 ( 2444) metal coordination : bond 0.00838 / 0.77 ( 19) metal coordination : angle 4.95692 / 7.72 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 165 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.5912 (mmp) cc_final: 0.5628 (mmm) REVERT: A 631 MET cc_start: 0.0488 (mmt) cc_final: -0.0719 (ttm) REVERT: A 858 MET cc_start: 0.5828 (mtm) cc_final: 0.5566 (mtm) REVERT: A 1086 ASP cc_start: 0.6278 (OUTLIER) cc_final: 0.6048 (m-30) REVERT: A 1157 CYS cc_start: 0.5782 (OUTLIER) cc_final: 0.5496 (p) REVERT: C 52 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7332 (tp) REVERT: C 200 MET cc_start: 0.7140 (tmm) cc_final: 0.6625 (ttt) REVERT: J 29 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.5606 (m-10) REVERT: K 50 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8269 (mp) REVERT: K 53 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.6065 (t0) REVERT: H 62 MET cc_start: 0.7988 (tpt) cc_final: 0.7635 (tpp) REVERT: E 46 MET cc_start: 0.4903 (tmm) cc_final: 0.4060 (ttp) REVERT: E 156 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7625 (mt) REVERT: E 186 GLU cc_start: 0.3400 (OUTLIER) cc_final: 0.3112 (mm-30) REVERT: E 230 TRP cc_start: 0.4302 (t60) cc_final: 0.4064 (t-100) REVERT: B 62 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7586 (t80) REVERT: B 120 MET cc_start: 0.5498 (OUTLIER) cc_final: 0.5252 (mtm) REVERT: B 983 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8381 (p) outliers start: 128 outliers final: 70 residues processed: 268 average time/residue: 0.1464 time to fit residues: 64.2085 Evaluate side-chains 235 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 154 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 983 THR Chi-restraints excluded: chain B residue 1019 THR Chi-restraints excluded: chain B residue 1034 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 45 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 258 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 276 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS ** B 481 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 = 0.4285 r_free = 0.4285 target = 0.107348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.085641 restraints weight = 96339.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.087394 restraints weight = 61043.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.087989 restraints weight = 38690.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.088258 restraints weight = 33118.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.088379 restraints weight = 30018.339| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23696 Z= 0.120 Angle : 0.596 12.397 32099 Z= 0.312 Chirality : 0.043 0.208 3613 Planarity : 0.004 0.053 3997 Dihedral : 12.170 104.361 3505 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.81 % Allowed : 21.20 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.16), residues: 2776 helix: 0.52 (0.18), residues: 874 sheet: -0.55 (0.24), residues: 488 loop : -1.76 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 116 TYR 0.017 0.001 TYR J 43 PHE 0.018 0.001 PHE F 123 TRP 0.012 0.001 TRP A 539 HIS 0.006 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (23677) covalent geometry : angle 0.58557 / 0.31 (32079) hydrogen bonds : bond 0.04558 / 4.88 ( 876) hydrogen bonds : angle 5.07976 / 5.13 ( 2444) metal coordination : bond 0.00497 / 0.52 ( 19) metal coordination : angle 4.51576 / 7.12 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 165 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 LYS cc_start: 0.6026 (mmtt) cc_final: 0.5734 (mmtt) REVERT: A 631 MET cc_start: 0.0507 (mmt) cc_final: -0.0724 (ttm) REVERT: A 719 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: A 858 MET cc_start: 0.5890 (mtm) cc_final: 0.5376 (mtm) REVERT: A 953 MET cc_start: 0.7740 (ptt) cc_final: 0.7475 (ptp) REVERT: A 1086 ASP cc_start: 0.6069 (OUTLIER) cc_final: 0.5842 (m-30) REVERT: A 1138 LYS cc_start: 0.7292 (mmtt) cc_final: 0.6963 (mmtm) REVERT: A 1157 CYS cc_start: 0.5767 (OUTLIER) cc_final: 0.5507 (p) REVERT: C 164 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8577 (pp) REVERT: C 200 MET cc_start: 0.7008 (tmm) cc_final: 0.6290 (ttt) REVERT: J 29 TYR cc_start: 0.5733 (OUTLIER) cc_final: 0.5490 (m-10) REVERT: K 50 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8095 (mp) REVERT: H 62 MET cc_start: 0.7755 (tpt) cc_final: 0.7469 (tpp) REVERT: E 46 MET cc_start: 0.5030 (tmm) cc_final: 0.4266 (ttp) REVERT: E 156 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7468 (mt) REVERT: E 186 GLU cc_start: 0.3870 (OUTLIER) cc_final: 0.3475 (mm-30) REVERT: E 219 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7384 (tt) REVERT: E 230 TRP cc_start: 0.4349 (t60) cc_final: 0.4108 (t-100) REVERT: B 62 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7460 (t80) REVERT: B 279 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7928 (t80) outliers start: 95 outliers final: 54 residues processed: 238 average time/residue: 0.1344 time to fit residues: 52.9719 Evaluate side-chains 220 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 155 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 913 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 235 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 209 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 197 optimal weight: 0.0470 chunk 46 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN A 582 ASN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN H 94 HIS ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 873 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.107434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.085723 restraints weight = 95269.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.087686 restraints weight = 59118.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.088076 restraints weight = 35744.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.088362 restraints weight = 32330.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.088378 restraints weight = 29063.594| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23696 Z= 0.113 Angle : 0.569 11.999 32099 Z= 0.297 Chirality : 0.042 0.232 3613 Planarity : 0.004 0.053 3997 Dihedral : 12.039 104.744 3501 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.17 % Allowed : 21.56 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2776 helix: 0.72 (0.18), residues: 879 sheet: -0.47 (0.24), residues: 494 loop : -1.71 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 144 TYR 0.016 0.001 TYR J 43 PHE 0.016 0.001 PHE F 123 TRP 0.011 0.001 TRP A 539 HIS 0.005 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (23677) covalent geometry : angle 0.55910 / 0.30 (32079) hydrogen bonds : bond 0.04245 / 4.53 ( 876) hydrogen bonds : angle 4.85285 / 4.92 ( 2444) metal coordination : bond 0.00510 / 0.49 ( 19) metal coordination : angle 4.26160 / 6.80 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 158 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.0375 (OUTLIER) cc_final: -0.0797 (ttm) REVERT: A 719 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: A 858 MET cc_start: 0.6208 (mtm) cc_final: 0.5916 (mtm) REVERT: A 953 MET cc_start: 0.7937 (ptt) cc_final: 0.7628 (ptp) REVERT: A 1086 ASP cc_start: 0.6067 (OUTLIER) cc_final: 0.5837 (m-30) REVERT: A 1157 CYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5743 (p) REVERT: C 164 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8634 (pp) REVERT: C 200 MET cc_start: 0.6832 (tmm) cc_final: 0.6631 (ttt) REVERT: K 50 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7990 (mp) REVERT: H 62 MET cc_start: 0.8004 (tpt) cc_final: 0.7602 (tpp) REVERT: I 97 MET cc_start: 0.0286 (OUTLIER) cc_final: 0.0044 (ttm) REVERT: E 46 MET cc_start: 0.4903 (tmm) cc_final: 0.4241 (ttp) REVERT: E 103 VAL cc_start: 0.2786 (OUTLIER) cc_final: 0.2499 (m) REVERT: E 156 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7462 (mt) REVERT: E 219 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7423 (tt) REVERT: E 230 TRP cc_start: 0.4473 (t60) cc_final: 0.4211 (t-100) REVERT: B 62 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7438 (t80) outliers start: 104 outliers final: 58 residues processed: 242 average time/residue: 0.1320 time to fit residues: 53.2349 Evaluate side-chains 222 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 153 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 913 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 61 optimal weight: 0.2980 chunk 226 optimal weight: 4.9990 chunk 225 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 161 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 ASN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN E 34 HIS ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.106002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.084521 restraints weight = 96634.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.086343 restraints weight = 60920.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.086790 restraints weight = 38447.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.087022 restraints weight = 32333.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.087156 restraints weight = 29565.152| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23696 Z= 0.144 Angle : 0.605 11.575 32099 Z= 0.313 Chirality : 0.043 0.228 3613 Planarity : 0.004 0.052 3997 Dihedral : 12.010 105.594 3500 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.97 % Allowed : 22.32 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.16), residues: 2776 helix: 0.75 (0.18), residues: 874 sheet: -0.49 (0.24), residues: 497 loop : -1.70 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 70 TYR 0.023 0.001 TYR J 43 PHE 0.015 0.002 PHE F 123 TRP 0.012 0.001 TRP B 510 HIS 0.004 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (23677) covalent geometry : angle 0.59594 / 0.31 (32079) hydrogen bonds : bond 0.04395 / 4.70 ( 876) hydrogen bonds : angle 4.83862 / 4.90 ( 2444) metal coordination : bond 0.00597 / 0.58 ( 19) metal coordination : angle 4.30965 / 6.77 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 158 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.0449 (OUTLIER) cc_final: -0.0790 (ttm) REVERT: A 858 MET cc_start: 0.6173 (mtm) cc_final: 0.5938 (mtm) REVERT: A 1086 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.6084 (m-30) REVERT: A 1137 ARG cc_start: 0.7251 (mmm-85) cc_final: 0.6805 (mmt180) REVERT: K 50 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8125 (mp) REVERT: I 97 MET cc_start: 0.0355 (OUTLIER) cc_final: 0.0107 (ttm) REVERT: E 46 MET cc_start: 0.5092 (tmm) cc_final: 0.4471 (ttp) REVERT: E 103 VAL cc_start: 0.2721 (OUTLIER) cc_final: 0.2450 (m) REVERT: E 156 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7514 (mt) REVERT: E 230 TRP cc_start: 0.4731 (t60) cc_final: 0.4487 (t-100) REVERT: B 62 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7514 (t80) REVERT: B 279 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7794 (t80) outliers start: 99 outliers final: 71 residues processed: 234 average time/residue: 0.1366 time to fit residues: 53.1360 Evaluate side-chains 233 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 154 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 939 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 126 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 177 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 ASN ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 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 = 0.4257 r_free = 0.4257 target = 0.105604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.084152 restraints weight = 96328.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.085748 restraints weight = 60803.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.086418 restraints weight = 39168.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.086651 restraints weight = 32053.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.086663 restraints weight = 30698.302| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23696 Z= 0.140 Angle : 0.597 11.841 32099 Z= 0.310 Chirality : 0.042 0.224 3613 Planarity : 0.004 0.052 3997 Dihedral : 11.923 106.386 3497 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.81 % Allowed : 22.93 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.16), residues: 2776 helix: 0.78 (0.18), residues: 876 sheet: -0.48 (0.24), residues: 494 loop : -1.69 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 416 TYR 0.021 0.001 TYR J 43 PHE 0.021 0.002 PHE A 779 TRP 0.011 0.001 TRP B 510 HIS 0.004 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (23677) covalent geometry : angle 0.58715 / 0.31 (32079) hydrogen bonds : bond 0.04300 / 4.60 ( 876) hydrogen bonds : angle 4.77851 / 4.86 ( 2444) metal coordination : bond 0.00579 / 0.56 ( 19) metal coordination : angle 4.32616 / 6.85 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 155 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 858 MET cc_start: 0.6395 (mtm) cc_final: 0.6182 (mtm) REVERT: A 1086 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.6109 (m-30) REVERT: A 1137 ARG cc_start: 0.7248 (mmm-85) cc_final: 0.6784 (mmt180) REVERT: C 200 MET cc_start: 0.6581 (tmm) cc_final: 0.6139 (ttt) REVERT: K 50 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8056 (mp) REVERT: H 62 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6811 (tpt) REVERT: E 46 MET cc_start: 0.5514 (tmm) cc_final: 0.4823 (ttm) REVERT: E 103 VAL cc_start: 0.2736 (OUTLIER) cc_final: 0.2462 (m) REVERT: E 156 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7558 (mt) REVERT: E 177 LYS cc_start: 0.3463 (mttt) cc_final: 0.2683 (tptp) REVERT: E 230 TRP cc_start: 0.4819 (t60) cc_final: 0.4583 (t-100) REVERT: B 62 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7569 (t80) REVERT: B 105 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6913 (p0) REVERT: B 279 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7938 (t80) REVERT: B 503 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7508 (mmt180) outliers start: 95 outliers final: 69 residues processed: 231 average time/residue: 0.1517 time to fit residues: 57.6144 Evaluate side-chains 227 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 150 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 932 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 87 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 184 optimal weight: 0.0050 chunk 66 optimal weight: 0.1980 chunk 205 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 148 optimal weight: 0.0030 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS B 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.107086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.085492 restraints weight = 94933.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.087522 restraints weight = 57575.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.088013 restraints weight = 35044.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.088235 restraints weight = 30824.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.088312 restraints weight = 28731.142| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 23696 Z= 0.106 Angle : 0.581 11.820 32099 Z= 0.300 Chirality : 0.042 0.228 3613 Planarity : 0.004 0.055 3997 Dihedral : 11.791 106.706 3497 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.93 % Allowed : 23.81 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 2776 helix: 0.92 (0.18), residues: 872 sheet: -0.26 (0.24), residues: 472 loop : -1.58 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 167 TYR 0.012 0.001 TYR A1166 PHE 0.016 0.001 PHE A 779 TRP 0.015 0.001 TRP A 539 HIS 0.004 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (23677) covalent geometry : angle 0.57264 / 0.30 (32079) hydrogen bonds : bond 0.03848 / 4.11 ( 876) hydrogen bonds : angle 4.62048 / 4.68 ( 2444) metal coordination : bond 0.00392 / 0.43 ( 19) metal coordination : angle 3.93559 / 6.13 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 170 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 LYS cc_start: 0.5894 (mmtt) cc_final: 0.5663 (mmtt) REVERT: A 631 MET cc_start: 0.0369 (OUTLIER) cc_final: -0.0882 (ttm) REVERT: A 858 MET cc_start: 0.6356 (mtm) cc_final: 0.6126 (mtm) REVERT: A 1086 ASP cc_start: 0.6166 (OUTLIER) cc_final: 0.5885 (m-30) REVERT: C 200 MET cc_start: 0.6682 (tmm) cc_final: 0.6208 (ttt) REVERT: K 50 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7889 (mp) REVERT: E 46 MET cc_start: 0.5563 (tmm) cc_final: 0.5000 (ttp) REVERT: E 103 VAL cc_start: 0.2781 (OUTLIER) cc_final: 0.2525 (m) REVERT: E 177 LYS cc_start: 0.3532 (mttt) cc_final: 0.2806 (tptp) REVERT: E 230 TRP cc_start: 0.4844 (t60) cc_final: 0.4590 (t-100) REVERT: B 62 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7493 (t80) REVERT: B 128 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7378 (p) REVERT: B 182 THR cc_start: 0.7175 (OUTLIER) cc_final: 0.6844 (t) REVERT: B 279 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7715 (t80) REVERT: B 335 ILE cc_start: 0.8079 (tp) cc_final: 0.7868 (mt) REVERT: B 503 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7544 (mmt180) outliers start: 73 outliers final: 50 residues processed: 224 average time/residue: 0.1506 time to fit residues: 55.6692 Evaluate side-chains 215 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 157 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 690 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 224 optimal weight: 2.9990 chunk 252 optimal weight: 0.2980 chunk 96 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 276 optimal weight: 6.9990 chunk 106 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.107033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.085646 restraints weight = 95764.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.087601 restraints weight = 55555.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.087933 restraints weight = 35609.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.088080 restraints weight = 31453.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.088175 restraints weight = 29135.770| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23696 Z= 0.104 Angle : 0.583 11.420 32099 Z= 0.295 Chirality : 0.042 0.242 3613 Planarity : 0.004 0.052 3997 Dihedral : 11.729 107.314 3497 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.44 % Allowed : 24.21 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2776 helix: 0.95 (0.18), residues: 872 sheet: -0.24 (0.24), residues: 473 loop : -1.54 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 167 TYR 0.015 0.001 TYR E 37 PHE 0.016 0.001 PHE A 779 TRP 0.013 0.001 TRP A 855 HIS 0.004 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (23677) covalent geometry : angle 0.57563 / 0.29 (32079) hydrogen bonds : bond 0.03758 / 4.01 ( 876) hydrogen bonds : angle 4.57012 / 4.69 ( 2444) metal coordination : bond 0.00410 / 0.44 ( 19) metal coordination : angle 3.71034 / 5.78 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 164 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 LYS cc_start: 0.5818 (mmtt) cc_final: 0.5592 (mmtt) REVERT: A 858 MET cc_start: 0.6354 (mtm) cc_final: 0.6116 (mtm) REVERT: A 1086 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.5889 (m-30) REVERT: C 200 MET cc_start: 0.6678 (tmm) cc_final: 0.6399 (ttt) REVERT: K 50 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7910 (mp) REVERT: E 46 MET cc_start: 0.5586 (tmm) cc_final: 0.5056 (ttp) REVERT: E 103 VAL cc_start: 0.2953 (OUTLIER) cc_final: 0.2690 (m) REVERT: E 177 LYS cc_start: 0.3605 (mttt) cc_final: 0.2849 (tptp) REVERT: E 230 TRP cc_start: 0.4876 (t60) cc_final: 0.4615 (t-100) REVERT: B 62 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7493 (t80) REVERT: B 128 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7356 (p) REVERT: B 279 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7699 (t80) REVERT: B 335 ILE cc_start: 0.8088 (tp) cc_final: 0.7883 (mt) REVERT: B 503 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7553 (mmt180) REVERT: B 872 LYS cc_start: 0.8218 (tptt) cc_final: 0.7458 (ttmt) outliers start: 61 outliers final: 50 residues processed: 213 average time/residue: 0.1343 time to fit residues: 47.4997 Evaluate side-chains 211 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 155 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 690 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 276 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN B 312 GLN B 892 ASN ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.103618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.082781 restraints weight = 97382.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.083832 restraints weight = 61308.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.084443 restraints weight = 42465.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.084620 restraints weight = 36241.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.084778 restraints weight = 33562.699| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23696 Z= 0.216 Angle : 0.709 11.011 32099 Z= 0.363 Chirality : 0.045 0.254 3613 Planarity : 0.005 0.055 3997 Dihedral : 11.913 109.274 3495 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.77 % Allowed : 23.97 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 2776 helix: 0.57 (0.18), residues: 869 sheet: -0.54 (0.24), residues: 500 loop : -1.72 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 41 TYR 0.031 0.002 TYR K 87 PHE 0.028 0.002 PHE E 66 TRP 0.020 0.002 TRP B 510 HIS 0.007 0.001 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (23677) covalent geometry : angle 0.69947 / 0.36 (32079) hydrogen bonds : bond 0.04926 / 5.27 ( 876) hydrogen bonds : angle 4.96993 / 5.11 ( 2444) metal coordination : bond 0.00836 / 0.78 ( 19) metal coordination : angle 4.73029 / 7.33 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 150 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 MET cc_start: 0.7412 (ppp) cc_final: 0.6451 (ppp) REVERT: A 631 MET cc_start: 0.1132 (mmt) cc_final: -0.0080 (ttt) REVERT: C 238 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7863 (p) REVERT: F 83 MET cc_start: 0.6540 (ppp) cc_final: 0.6333 (ppp) REVERT: K 50 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8246 (mp) REVERT: E 46 MET cc_start: 0.5631 (tmm) cc_final: 0.4932 (ttm) REVERT: E 103 VAL cc_start: 0.2808 (OUTLIER) cc_final: 0.2500 (m) REVERT: E 177 LYS cc_start: 0.3929 (mttt) cc_final: 0.2941 (tptp) REVERT: B 62 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7528 (t80) REVERT: B 105 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6975 (p0) REVERT: B 279 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.8072 (t80) outliers start: 69 outliers final: 55 residues processed: 206 average time/residue: 0.1310 time to fit residues: 44.8409 Evaluate side-chains 208 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 147 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 939 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 10 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 89 optimal weight: 0.0020 chunk 69 optimal weight: 0.5980 chunk 202 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 overall best weight: 1.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.104923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.083876 restraints weight = 95805.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.085492 restraints weight = 58384.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.085842 restraints weight = 37596.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.086105 restraints weight = 34128.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.086213 restraints weight = 30839.562| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23696 Z= 0.126 Angle : 0.614 11.798 32099 Z= 0.313 Chirality : 0.042 0.227 3613 Planarity : 0.004 0.052 3997 Dihedral : 11.784 110.155 3493 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.40 % Allowed : 24.49 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.16), residues: 2776 helix: 0.86 (0.18), residues: 869 sheet: -0.46 (0.24), residues: 489 loop : -1.64 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 167 TYR 0.020 0.001 TYR J 43 PHE 0.024 0.001 PHE E 66 TRP 0.011 0.001 TRP E 230 HIS 0.004 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (23677) covalent geometry : angle 0.60517 / 0.31 (32079) hydrogen bonds : bond 0.04126 / 4.39 ( 876) hydrogen bonds : angle 4.75846 / 4.89 ( 2444) metal coordination : bond 0.00523 / 0.51 ( 19) metal coordination : angle 4.19458 / 6.69 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3660.53 seconds wall clock time: 64 minutes 18.81 seconds (3858.81 seconds total)