Starting phenix.real_space_refine on Wed Nov 19 18:40:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6drd_7997/11_2025/6drd_7997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6drd_7997/11_2025/6drd_7997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6drd_7997/11_2025/6drd_7997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6drd_7997/11_2025/6drd_7997.map" model { file = "/net/cci-nas-00/data/ceres_data/6drd_7997/11_2025/6drd_7997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6drd_7997/11_2025/6drd_7997.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 151 5.16 5 C 16923 2.51 5 N 4627 2.21 5 O 5002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26708 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7989 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 42, 'TRANS': 957} Chain breaks: 7 Chain: "B" Number of atoms: 8079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 8079 Classifications: {'peptide': 1009} Link IDs: {'PTRANS': 47, 'TRANS': 961} Chain breaks: 4 Chain: "C" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2104 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 15, 'TRANS': 246} Chain breaks: 1 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1529 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain breaks: 3 Chain: "F" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 549 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain breaks: 1 Chain: "G" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 157} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1176 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "I" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 897 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 890 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "L" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 312 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain breaks: 1 Chain: "M" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 359 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'UNK:plan-1': 45} Unresolved non-hydrogen planarities: 45 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: "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} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16763 SG CYS C 88 99.801 36.940 128.868 1.00 84.15 S ATOM 16776 SG CYS C 90 96.454 35.917 128.184 1.00 89.78 S ATOM 16811 SG CYS C 94 98.126 36.350 131.926 1.00 78.59 S ATOM 16833 SG CYS C 97 98.165 39.753 130.643 1.00 73.17 S ATOM 23785 SG CYS I 17 42.579 136.778 80.632 1.00 69.69 S ATOM 23809 SG CYS I 20 39.738 133.044 79.865 1.00 68.56 S ATOM 23970 SG CYS I 39 43.235 134.520 77.311 1.00 73.34 S ATOM 23995 SG CYS I 42 40.314 136.635 77.836 1.00 84.81 S ATOM 24347 SG CYS I 86 69.457 140.598 116.497 1.00 65.29 S ATOM 24545 SG CYS I 114 68.914 137.101 117.996 1.00 54.00 S ATOM 24580 SG CYS I 119 66.073 138.928 116.679 1.00 68.30 S ATOM 24690 SG CYS J 7 95.450 70.934 133.476 1.00 37.11 S ATOM 24714 SG CYS J 10 98.559 70.831 135.285 1.00 38.91 S ATOM 24978 SG CYS J 44 96.874 72.793 133.252 1.00 44.13 S ATOM 24984 SG CYS J 45 96.316 72.102 137.919 1.00 44.37 S ATOM 26074 SG CYS L 19 55.153 54.977 123.109 1.00 73.63 S ATOM 26093 SG CYS L 22 53.527 52.917 126.072 1.00 75.85 S ATOM 26176 SG CYS L 39 51.712 54.031 123.183 1.00 80.79 S Time building chain proxies: 6.31, per 1000 atoms: 0.24 Number of scatterers: 26708 At special positions: 0 Unit cell: (170.3, 167.68, 168.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 5 29.99 S 151 16.00 O 5002 8.00 N 4627 7.00 C 16923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 18 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6346 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 41 sheets defined 30.5% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 397 through 400 removed outlier: 3.870A pdb=" N ASP A 400 " --> pdb=" O PHE A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 397 through 400' Processing helix chain 'A' and resid 401 through 409 removed outlier: 4.078A pdb=" N LEU A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.828A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.691A pdb=" N ALA A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.669A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.585A pdb=" N ASP A 614 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 615 " --> pdb=" O ASP A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.591A pdb=" N SER A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 676 removed outlier: 3.880A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 672 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.824A pdb=" N GLU A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 4.209A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 removed outlier: 3.871A pdb=" N GLN A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 710 removed outlier: 3.868A pdb=" N ILE A 706 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 721 removed outlier: 3.769A pdb=" N ILE A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'A' and resid 747 through 760 removed outlier: 3.840A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 Processing helix chain 'A' and resid 781 through 786 removed outlier: 3.921A pdb=" N ILE A 785 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 853 removed outlier: 3.726A pdb=" N ARG A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 849 " --> pdb=" O GLU A 845 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 868 removed outlier: 3.874A pdb=" N GLN A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.856A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 920 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 940 through 945 removed outlier: 4.049A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 951 through 970 removed outlier: 3.801A pdb=" N ARG A 958 " --> pdb=" O ARG A 954 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 966 " --> pdb=" O ASP A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 991 Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.694A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1036 removed outlier: 3.807A pdb=" N GLN A1032 " --> pdb=" O PRO A1028 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A1036 " --> pdb=" O GLN A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1048 removed outlier: 3.665A pdb=" N HIS A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A1046 " --> pdb=" O ASN A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.512A pdb=" N ASP A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP A1067 " --> pdb=" O GLU A1063 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A1070 " --> pdb=" O ASP A1066 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN A1078 " --> pdb=" O SER A1074 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1093 removed outlier: 3.601A pdb=" N LEU A1090 " --> pdb=" O MET A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1125 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.530A pdb=" N ASP A1150 " --> pdb=" O SER A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1159 Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 3.756A pdb=" N THR A1184 " --> pdb=" O PRO A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 3.522A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1293 removed outlier: 3.608A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1367 removed outlier: 3.572A pdb=" N THR A1367 " --> pdb=" O VAL A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1383 Processing helix chain 'A' and resid 1386 through 1390 Processing helix chain 'A' and resid 1394 through 1398 Processing helix chain 'A' and resid 1401 through 1406 removed outlier: 3.694A pdb=" N MET A1405 " --> pdb=" O LEU A1401 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A1406 " --> pdb=" O CYS A1402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1401 through 1406' Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 4.574A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 30 removed outlier: 3.622A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 37 Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.562A pdb=" N ILE B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 109 through 116 removed outlier: 4.114A pdb=" N LEU B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.608A pdb=" N CYS B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 removed outlier: 4.123A pdb=" N LYS B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS B 249 " --> pdb=" O GLY B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 249' Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.708A pdb=" N VAL B 272 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.562A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 4.002A pdb=" N ASP B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 removed outlier: 3.622A pdb=" N LEU B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.530A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 341 " --> pdb=" O LYS B 337 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 377 removed outlier: 4.112A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 421 removed outlier: 4.095A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 447 removed outlier: 4.918A pdb=" N LYS B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.737A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 546 removed outlier: 3.580A pdb=" N LEU B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE B 544 " --> pdb=" O PRO B 540 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 556 removed outlier: 3.840A pdb=" N ILE B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 592 removed outlier: 3.778A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 590 " --> pdb=" O THR B 586 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 644 removed outlier: 3.592A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 642 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.507A pdb=" N VAL B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 729 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 897 through 900 removed outlier: 4.222A pdb=" N GLU B 900 " --> pdb=" O ARG B 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 897 through 900' Processing helix chain 'B' and resid 979 through 990 removed outlier: 3.607A pdb=" N CYS B 984 " --> pdb=" O HIS B 980 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 985 " --> pdb=" O LEU B 981 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1016 Processing helix chain 'C' and resid 27 through 39 removed outlier: 4.098A pdb=" N ARG C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 4.095A pdb=" N HIS C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.674A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 259 through 268 removed outlier: 3.622A pdb=" N SER C 264 " --> pdb=" O GLN C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'D' and resid 37 through 50 removed outlier: 3.786A pdb=" N GLU D 42 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS D 43 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 47 " --> pdb=" O HIS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.537A pdb=" N ARG D 70 " --> pdb=" O ASN D 66 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 102 removed outlier: 4.064A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 123 through 135 removed outlier: 3.654A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 24 removed outlier: 5.150A pdb=" N ILE E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 removed outlier: 4.175A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS E 91 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 116 through 121 removed outlier: 3.631A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 removed outlier: 4.280A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA E 161 " --> pdb=" O SER E 157 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'F' and resid 60 through 75 removed outlier: 3.804A pdb=" N LEU F 71 " --> pdb=" O GLY F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 99 removed outlier: 3.610A pdb=" N LYS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 34 removed outlier: 3.720A pdb=" N GLN G 28 " --> pdb=" O ASN G 24 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 3.626A pdb=" N THR I 66 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 23 removed outlier: 3.760A pdb=" N GLY J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 35 removed outlier: 3.642A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 39 Processing helix chain 'J' and resid 42 through 47 removed outlier: 3.636A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG J 47 " --> pdb=" O TYR J 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 42 through 47' Processing helix chain 'J' and resid 55 through 60 removed outlier: 3.538A pdb=" N LEU J 59 " --> pdb=" O LEU J 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.638A pdb=" N GLU K 8 " --> pdb=" O PRO K 5 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 5 through 10' Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.091A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 90 removed outlier: 3.985A pdb=" N PHE K 87 " --> pdb=" O PRO K 83 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR K 88 " --> pdb=" O GLN K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 106 removed outlier: 3.637A pdb=" N LEU K 94 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU K 102 " --> pdb=" O LEU K 98 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU K 103 " --> pdb=" O SER K 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 63 Processing helix chain 'M' and resid 79 through 84 Processing helix chain 'M' and resid 305 through 311 Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 369 removed outlier: 5.907A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 379 removed outlier: 5.536A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 390 through 393 removed outlier: 3.891A pdb=" N ARG A 448 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA5, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.972A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 631 " --> pdb=" O GLU A 634 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.471A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AA8, first strand: chain 'A' and resid 1336 through 1337 Processing sheet with id=AA9, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 3.656A pdb=" N LEU A1211 " --> pdb=" O TYR A1176 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1319 through 1320 Processing sheet with id=AB2, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.281A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE G 59 " --> pdb=" O LEU A1473 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS G 9 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR G 3 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.281A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE G 59 " --> pdb=" O LEU A1473 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR G 50 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 83 through 92 removed outlier: 6.101A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB6, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB7, first strand: chain 'B' and resid 196 through 197 Processing sheet with id=AB8, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AB9, first strand: chain 'B' and resid 206 through 207 removed outlier: 3.731A pdb=" N VAL B 237 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 572 through 573 removed outlier: 6.061A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 602 " --> pdb=" O TYR B 615 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 632 through 633 removed outlier: 3.668A pdb=" N LYS B 632 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 632 through 633 removed outlier: 3.668A pdb=" N LYS B 632 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 749 through 751 removed outlier: 3.778A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 904 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 858 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 749 through 751 removed outlier: 3.778A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 759 through 760 removed outlier: 3.930A pdb=" N THR B 760 " --> pdb=" O GLY B 997 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 935 through 936 removed outlier: 4.459A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N TYR B 949 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET B 796 " --> pdb=" O TYR B 949 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 935 through 936 Processing sheet with id=AC9, first strand: chain 'B' and resid 827 through 829 removed outlier: 3.771A pdb=" N VAL B 828 " --> pdb=" O THR B 870 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 870 " --> pdb=" O VAL B 828 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 869 " --> pdb=" O CYS B 892 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 8 through 15 removed outlier: 3.571A pdb=" N THR C 8 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 44 through 55 removed outlier: 5.234A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP C 49 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 157 " --> pdb=" O CYS C 107 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 44 through 55 removed outlier: 5.234A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP C 49 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 163 " --> pdb=" O PHE C 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD5, first strand: chain 'E' and resid 61 through 62 removed outlier: 6.826A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 148 through 150 removed outlier: 3.549A pdb=" N TYR E 203 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 85 through 88 removed outlier: 3.783A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 99 through 101 removed outlier: 7.393A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.710A pdb=" N GLU G 118 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 113 through 117 removed outlier: 3.770A pdb=" N SER H 113 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 25 through 29 removed outlier: 3.517A pdb=" N TYR I 37 " --> pdb=" O GLN I 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN I 46 " --> pdb=" O TYR I 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 80 through 81 removed outlier: 4.459A pdb=" N LEU I 110 " --> pdb=" O GLU I 125 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU I 125 " --> pdb=" O LEU I 110 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 22 through 23 removed outlier: 3.593A pdb=" N ILE K 73 " --> pdb=" O PHE K 33 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 16 through 17 660 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8081 1.33 - 1.45: 4319 1.45 - 1.57: 14556 1.57 - 1.69: 0 1.69 - 1.81: 238 Bond restraints: 27194 Sorted by residual: bond pdb=" CZ ARG A 483 " pdb=" NH2 ARG A 483 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.94e+00 bond pdb=" CB ARG A 483 " pdb=" CG ARG A 483 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.48e+00 bond pdb=" CB VAL B 809 " pdb=" CG2 VAL B 809 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.03e+00 bond pdb=" CG LEU B 751 " pdb=" CD1 LEU B 751 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.04e+00 bond pdb=" CB VAL B 780 " pdb=" CG2 VAL B 780 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.00e+00 ... (remaining 27189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 34641 2.22 - 4.44: 1797 4.44 - 6.66: 228 6.66 - 8.88: 64 8.88 - 11.10: 13 Bond angle restraints: 36743 Sorted by residual: angle pdb=" N ILE A 676 " pdb=" CA ILE A 676 " pdb=" C ILE A 676 " ideal model delta sigma weight residual 113.42 107.16 6.26 1.17e+00 7.31e-01 2.86e+01 angle pdb=" C ASN B 649 " pdb=" N ASN B 650 " pdb=" CA ASN B 650 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C GLN I 18 " pdb=" N GLU I 19 " pdb=" CA GLU I 19 " ideal model delta sigma weight residual 122.61 129.55 -6.94 1.56e+00 4.11e-01 1.98e+01 angle pdb=" C GLU B 629 " pdb=" N LYS B 630 " pdb=" CA LYS B 630 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C GLN B 790 " pdb=" N GLU B 791 " pdb=" CA GLU B 791 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.92e+01 ... (remaining 36738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 15592 15.70 - 31.39: 887 31.39 - 47.09: 144 47.09 - 62.79: 9 62.79 - 78.49: 12 Dihedral angle restraints: 16644 sinusoidal: 6864 harmonic: 9780 Sorted by residual: dihedral pdb=" CA SER A 374 " pdb=" C SER A 374 " pdb=" N ILE A 375 " pdb=" CA ILE A 375 " ideal model delta harmonic sigma weight residual 180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ASP B 428 " pdb=" C ASP B 428 " pdb=" N PHE B 429 " pdb=" CA PHE B 429 " ideal model delta harmonic sigma weight residual 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA LYS C 171 " pdb=" C LYS C 171 " pdb=" N GLU C 172 " pdb=" CA GLU C 172 " ideal model delta harmonic sigma weight residual 180.00 150.59 29.41 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 16641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2907 0.065 - 0.129: 1055 0.129 - 0.194: 164 0.194 - 0.258: 18 0.258 - 0.323: 4 Chirality restraints: 4148 Sorted by residual: chirality pdb=" CB VAL J 14 " pdb=" CA VAL J 14 " pdb=" CG1 VAL J 14 " pdb=" CG2 VAL J 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB VAL B 673 " pdb=" CA VAL B 673 " pdb=" CG1 VAL B 673 " pdb=" CG2 VAL B 673 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB ILE B 621 " pdb=" CA ILE B 621 " pdb=" CG1 ILE B 621 " pdb=" CG2 ILE B 621 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 4145 not shown) Planarity restraints: 4742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1048 " -0.029 2.00e-02 2.50e+03 2.68e-02 1.44e+01 pdb=" CG TYR B1048 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR B1048 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B1048 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B1048 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B1048 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B1048 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B1048 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 479 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C TRP A 479 " -0.063 2.00e-02 2.50e+03 pdb=" O TRP A 479 " 0.024 2.00e-02 2.50e+03 pdb=" N SER A 480 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 118 " 0.028 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP F 118 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP F 118 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP F 118 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 118 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 118 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 118 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 118 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 118 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP F 118 " 0.002 2.00e-02 2.50e+03 ... (remaining 4739 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1639 2.72 - 3.26: 24895 3.26 - 3.81: 40272 3.81 - 4.35: 50483 4.35 - 4.90: 85555 Nonbonded interactions: 202844 Sorted by model distance: nonbonded pdb=" N CYS L 22 " pdb="ZN ZN L 101 " model vdw 2.169 2.310 nonbonded pdb=" O SER A 656 " pdb=" OG1 THR A 665 " model vdw 2.209 3.040 nonbonded pdb=" N CYS C 94 " pdb="ZN ZN C 301 " model vdw 2.234 2.310 nonbonded pdb=" NH1 ARG B 803 " pdb=" O PHE J 8 " model vdw 2.238 3.120 nonbonded pdb=" OG SER B 31 " pdb=" OH TYR B 766 " model vdw 2.265 3.040 ... (remaining 202839 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.700 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 : 0.012 0.532 27212 Z= 0.488 Angle : 1.265 54.852 36761 Z= 0.620 Chirality : 0.064 0.323 4148 Planarity : 0.007 0.081 4742 Dihedral : 10.405 78.486 10298 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.14 % Favored : 88.73 % Rotamer: Outliers : 0.68 % Allowed : 3.07 % Favored : 96.25 % 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: -5.06 (0.12), residues: 3240 helix: -4.46 (0.08), residues: 963 sheet: -2.88 (0.21), residues: 479 loop : -2.87 (0.13), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 807 TYR 0.065 0.004 TYR B1048 PHE 0.043 0.004 PHE B 806 TRP 0.055 0.005 TRP F 118 HIS 0.016 0.003 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.01022 (27194) covalent geometry : angle 1.12854 (36743) hydrogen bonds : bond 0.31414 ( 634) hydrogen bonds : angle 10.99067 ( 1782) metal coordination : bond 0.26020 ( 18) metal coordination : angle 25.84651 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 763 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 PHE cc_start: 0.8453 (m-80) cc_final: 0.8116 (m-80) REVERT: A 601 ASN cc_start: 0.8142 (m-40) cc_final: 0.7631 (m-40) REVERT: A 634 GLU cc_start: 0.8174 (tt0) cc_final: 0.7487 (mt-10) REVERT: A 733 LEU cc_start: 0.8556 (tm) cc_final: 0.8285 (mt) REVERT: A 779 ILE cc_start: 0.8461 (tt) cc_final: 0.8106 (tt) REVERT: A 845 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: A 930 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8048 (mm) REVERT: A 1097 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7152 (mt-10) REVERT: A 1119 LEU cc_start: 0.8987 (mt) cc_final: 0.8778 (mt) REVERT: A 1202 PHE cc_start: 0.7544 (m-80) cc_final: 0.7132 (m-80) REVERT: A 1248 ASN cc_start: 0.7944 (m-40) cc_final: 0.6949 (m-40) REVERT: A 1284 PHE cc_start: 0.8618 (t80) cc_final: 0.8241 (t80) REVERT: A 1337 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6844 (pt0) REVERT: A 1384 HIS cc_start: 0.7742 (t70) cc_final: 0.7503 (t-170) REVERT: A 1401 LEU cc_start: 0.8992 (tp) cc_final: 0.8780 (tp) REVERT: B 22 TRP cc_start: 0.8329 (t-100) cc_final: 0.7944 (t-100) REVERT: B 85 LEU cc_start: 0.7545 (mt) cc_final: 0.7257 (tt) REVERT: B 108 MET cc_start: 0.8681 (ptm) cc_final: 0.8416 (ptp) REVERT: B 119 THR cc_start: 0.8926 (m) cc_final: 0.8700 (p) REVERT: B 147 THR cc_start: 0.9272 (m) cc_final: 0.9041 (p) REVERT: B 160 TYR cc_start: 0.7321 (m-10) cc_final: 0.7118 (m-80) REVERT: B 169 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7852 (mpt180) REVERT: B 174 LEU cc_start: 0.8824 (mt) cc_final: 0.8486 (mt) REVERT: B 337 LYS cc_start: 0.8811 (tttm) cc_final: 0.8533 (tppt) REVERT: B 508 MET cc_start: 0.8093 (mmt) cc_final: 0.7618 (mmt) REVERT: B 621 ILE cc_start: 0.8536 (tt) cc_final: 0.8223 (tt) REVERT: B 697 GLU cc_start: 0.8151 (pt0) cc_final: 0.7906 (pt0) REVERT: B 724 TYR cc_start: 0.8841 (t80) cc_final: 0.8452 (t80) REVERT: B 764 MET cc_start: 0.8640 (mmt) cc_final: 0.8245 (mmt) REVERT: B 910 THR cc_start: 0.8421 (p) cc_final: 0.8169 (p) REVERT: C 81 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8462 (mmmt) REVERT: C 196 VAL cc_start: 0.8998 (t) cc_final: 0.8620 (p) REVERT: C 258 ASP cc_start: 0.8061 (t0) cc_final: 0.7820 (t70) REVERT: E 115 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8342 (mmtm) REVERT: E 198 GLU cc_start: 0.7490 (pt0) cc_final: 0.7114 (tm-30) REVERT: F 75 MET cc_start: 0.7894 (mtp) cc_final: 0.7678 (mtt) REVERT: F 92 ILE cc_start: 0.8592 (mt) cc_final: 0.8251 (mt) REVERT: F 115 TYR cc_start: 0.7923 (p90) cc_final: 0.7614 (p90) REVERT: G 117 MET cc_start: 0.2278 (mmm) cc_final: 0.1919 (tpp) REVERT: H 13 LYS cc_start: 0.7904 (mttt) cc_final: 0.7621 (mtpp) REVERT: H 113 SER cc_start: 0.8148 (p) cc_final: 0.7575 (p) REVERT: I 64 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7592 (mm-30) REVERT: I 71 ASP cc_start: 0.7847 (m-30) cc_final: 0.7527 (t0) REVERT: K 24 ASP cc_start: 0.7387 (t0) cc_final: 0.7135 (t0) REVERT: L 24 THR cc_start: 0.7945 (p) cc_final: 0.7420 (p) REVERT: L 42 ARG cc_start: 0.6733 (mtt-85) cc_final: 0.6398 (tpt170) REVERT: L 46 LYS cc_start: 0.8288 (tptp) cc_final: 0.7916 (tptp) outliers start: 20 outliers final: 7 residues processed: 781 average time/residue: 0.2077 time to fit residues: 243.8552 Evaluate side-chains 451 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 442 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 8 PHE Chi-restraints excluded: chain M residue 312 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS A 662 HIS A 671 ASN A 721 HIS A 792 ASN A 991 GLN ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN A1163 HIS A1194 ASN A1220 HIS A1230 GLN A1310 HIS B 164 ASN B 452 ASN B 500 GLN B 552 ASN B 649 ASN B 699 HIS B 731 GLN B 749 HIS B 817 GLN B 825 GLN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS I 22 ASN I 41 ASN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN K 84 GLN L 23 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.149381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.123039 restraints weight = 42870.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122023 restraints weight = 59016.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123212 restraints weight = 51407.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123537 restraints weight = 36094.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.123622 restraints weight = 33070.554| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27212 Z= 0.176 Angle : 0.737 21.635 36761 Z= 0.375 Chirality : 0.048 0.188 4148 Planarity : 0.005 0.059 4742 Dihedral : 6.566 57.454 3656 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 2.53 % Allowed : 9.86 % Favored : 87.61 % 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: -4.10 (0.13), residues: 3240 helix: -3.36 (0.12), residues: 977 sheet: -2.33 (0.21), residues: 529 loop : -2.44 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 109 TYR 0.018 0.002 TYR J 43 PHE 0.022 0.002 PHE A 592 TRP 0.016 0.002 TRP F 118 HIS 0.008 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00408 (27194) covalent geometry : angle 0.71280 (36743) hydrogen bonds : bond 0.05188 ( 634) hydrogen bonds : angle 6.52548 ( 1782) metal coordination : bond 0.01322 ( 18) metal coordination : angle 8.57503 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 514 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8532 (tpp) cc_final: 0.7997 (tpp) REVERT: A 566 PHE cc_start: 0.8317 (m-80) cc_final: 0.8110 (m-80) REVERT: A 634 GLU cc_start: 0.8182 (tt0) cc_final: 0.7483 (mt-10) REVERT: A 645 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8216 (tt) REVERT: A 733 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8230 (mt) REVERT: A 734 ARG cc_start: 0.7521 (tpp-160) cc_final: 0.7255 (tpp80) REVERT: A 853 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.6907 (mptt) REVERT: A 894 ASP cc_start: 0.8171 (p0) cc_final: 0.7924 (p0) REVERT: A 1097 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7258 (mt-10) REVERT: A 1117 VAL cc_start: 0.7959 (t) cc_final: 0.7694 (p) REVERT: A 1199 MET cc_start: 0.7511 (ppp) cc_final: 0.6788 (ppp) REVERT: A 1202 PHE cc_start: 0.6841 (m-80) cc_final: 0.6434 (m-80) REVERT: A 1384 HIS cc_start: 0.7644 (t70) cc_final: 0.7358 (t-170) REVERT: A 1401 LEU cc_start: 0.8724 (tp) cc_final: 0.8477 (tp) REVERT: B 119 THR cc_start: 0.8675 (m) cc_final: 0.8446 (p) REVERT: B 500 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8185 (tp40) REVERT: B 508 MET cc_start: 0.8065 (mmt) cc_final: 0.7644 (mmm) REVERT: B 529 MET cc_start: 0.8532 (mmm) cc_final: 0.7762 (mtm) REVERT: B 621 ILE cc_start: 0.8646 (tt) cc_final: 0.8406 (tt) REVERT: B 668 LEU cc_start: 0.8775 (pp) cc_final: 0.7722 (tt) REVERT: B 674 MET cc_start: 0.8802 (tpt) cc_final: 0.8264 (tpt) REVERT: B 692 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7728 (t) REVERT: B 796 MET cc_start: 0.8034 (mtp) cc_final: 0.7277 (mmm) REVERT: B 802 ASP cc_start: 0.8331 (m-30) cc_final: 0.8111 (m-30) REVERT: B 870 THR cc_start: 0.8662 (p) cc_final: 0.8437 (t) REVERT: B 908 MET cc_start: 0.7792 (tmm) cc_final: 0.7361 (tmm) REVERT: B 954 MET cc_start: 0.8569 (tpp) cc_final: 0.8219 (mmt) REVERT: C 81 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8448 (mmmt) REVERT: C 196 VAL cc_start: 0.9063 (t) cc_final: 0.8749 (p) REVERT: C 258 ASP cc_start: 0.7273 (t0) cc_final: 0.6997 (t0) REVERT: E 198 GLU cc_start: 0.7238 (pt0) cc_final: 0.7018 (tm-30) REVERT: F 92 ILE cc_start: 0.8009 (mt) cc_final: 0.7763 (mt) REVERT: G 117 MET cc_start: 0.2389 (mmm) cc_final: 0.1993 (tpp) REVERT: H 9 ILE cc_start: 0.9260 (mm) cc_final: 0.8940 (mm) REVERT: H 13 LYS cc_start: 0.7984 (mttt) cc_final: 0.6997 (ttpt) REVERT: I 57 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7704 (mttt) REVERT: I 64 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7215 (mm-30) REVERT: L 46 LYS cc_start: 0.8387 (tptp) cc_final: 0.8180 (tptp) outliers start: 74 outliers final: 46 residues processed: 566 average time/residue: 0.1795 time to fit residues: 161.2132 Evaluate side-chains 468 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 417 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 312 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 79 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 GLN B 144 HIS B 410 ASN B 452 ASN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 HIS D 93 HIS H 130 ASN I 41 ASN I 98 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.148647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119781 restraints weight = 42876.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.119134 restraints weight = 42385.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.120536 restraints weight = 39472.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120846 restraints weight = 27924.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121104 restraints weight = 25636.204| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 27212 Z= 0.197 Angle : 0.692 15.380 36761 Z= 0.356 Chirality : 0.048 0.267 4148 Planarity : 0.005 0.058 4742 Dihedral : 6.069 55.597 3645 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 3.86 % Allowed : 11.43 % Favored : 84.71 % 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: -3.70 (0.13), residues: 3240 helix: -2.88 (0.13), residues: 989 sheet: -2.15 (0.22), residues: 520 loop : -2.27 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 932 TYR 0.018 0.002 TYR J 43 PHE 0.022 0.002 PHE A 592 TRP 0.030 0.002 TRP B 236 HIS 0.015 0.002 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00468 (27194) covalent geometry : angle 0.67910 (36743) hydrogen bonds : bond 0.04547 ( 634) hydrogen bonds : angle 6.02235 ( 1782) metal coordination : bond 0.00978 ( 18) metal coordination : angle 6.11070 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 437 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8568 (tpp) cc_final: 0.8100 (tpp) REVERT: A 634 GLU cc_start: 0.8313 (tt0) cc_final: 0.7426 (mt-10) REVERT: A 645 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8341 (tt) REVERT: A 733 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8289 (tm) REVERT: A 853 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.6943 (tttt) REVERT: A 1097 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7179 (mt-10) REVERT: A 1202 PHE cc_start: 0.7076 (m-80) cc_final: 0.6659 (m-80) REVERT: A 1284 PHE cc_start: 0.8399 (t80) cc_final: 0.8153 (t80) REVERT: A 1384 HIS cc_start: 0.7685 (t70) cc_final: 0.7432 (t-170) REVERT: A 1401 LEU cc_start: 0.8857 (tp) cc_final: 0.8632 (tp) REVERT: B 119 THR cc_start: 0.8842 (m) cc_final: 0.8557 (p) REVERT: B 264 LYS cc_start: 0.8584 (pttp) cc_final: 0.8309 (pttm) REVERT: B 296 GLU cc_start: 0.7915 (mp0) cc_final: 0.7645 (mp0) REVERT: B 448 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8547 (tt) REVERT: B 500 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8323 (tp40) REVERT: B 508 MET cc_start: 0.8110 (mmt) cc_final: 0.7766 (mmm) REVERT: B 520 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8660 (p) REVERT: B 621 ILE cc_start: 0.8739 (tt) cc_final: 0.8494 (tt) REVERT: B 668 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.7676 (tt) REVERT: B 674 MET cc_start: 0.8847 (tpt) cc_final: 0.8252 (tpt) REVERT: B 692 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7731 (t) REVERT: B 796 MET cc_start: 0.8129 (mtp) cc_final: 0.7810 (mmm) REVERT: B 802 ASP cc_start: 0.8358 (m-30) cc_final: 0.8080 (m-30) REVERT: B 870 THR cc_start: 0.8678 (p) cc_final: 0.8453 (t) REVERT: B 908 MET cc_start: 0.7664 (tmm) cc_final: 0.7251 (tmm) REVERT: B 954 MET cc_start: 0.8662 (tpp) cc_final: 0.8365 (mmt) REVERT: C 258 ASP cc_start: 0.7321 (t0) cc_final: 0.7086 (t0) REVERT: E 198 GLU cc_start: 0.7354 (pt0) cc_final: 0.6975 (tm-30) REVERT: G 117 MET cc_start: 0.2465 (mmm) cc_final: 0.1782 (tpp) REVERT: H 9 ILE cc_start: 0.9207 (mm) cc_final: 0.8992 (mm) REVERT: H 10 PHE cc_start: 0.8590 (m-80) cc_final: 0.8364 (m-80) REVERT: I 43 ASP cc_start: 0.7903 (m-30) cc_final: 0.7048 (t0) REVERT: I 57 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7661 (mttt) REVERT: I 64 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7386 (mm-30) REVERT: J 55 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8248 (tt) REVERT: K 24 ASP cc_start: 0.7637 (t0) cc_final: 0.7334 (t70) REVERT: L 46 LYS cc_start: 0.8392 (tptp) cc_final: 0.8128 (tptp) outliers start: 113 outliers final: 71 residues processed: 515 average time/residue: 0.1795 time to fit residues: 148.9248 Evaluate side-chains 468 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 388 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 HIS Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 312 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 317 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 273 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 552 ASN B 731 GLN B 817 GLN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN H 130 ASN I 41 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120497 restraints weight = 42549.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119867 restraints weight = 49367.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121138 restraints weight = 41607.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121440 restraints weight = 29439.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.121585 restraints weight = 27310.074| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27212 Z= 0.181 Angle : 0.655 12.213 36761 Z= 0.337 Chirality : 0.047 0.218 4148 Planarity : 0.005 0.054 4742 Dihedral : 5.667 47.725 3645 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.16 % Allowed : 12.29 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.14), residues: 3240 helix: -2.51 (0.14), residues: 985 sheet: -1.97 (0.23), residues: 488 loop : -2.09 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 483 TYR 0.016 0.001 TYR J 43 PHE 0.023 0.002 PHE B 320 TRP 0.021 0.002 TRP B 236 HIS 0.007 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00429 (27194) covalent geometry : angle 0.64898 (36743) hydrogen bonds : bond 0.03916 ( 634) hydrogen bonds : angle 5.60847 ( 1782) metal coordination : bond 0.00831 ( 18) metal coordination : angle 4.12317 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 423 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 MET cc_start: 0.4578 (OUTLIER) cc_final: 0.4022 (mtt) REVERT: A 565 MET cc_start: 0.8419 (tpp) cc_final: 0.7972 (tpp) REVERT: A 634 GLU cc_start: 0.8294 (tt0) cc_final: 0.7378 (mt-10) REVERT: A 645 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8384 (tt) REVERT: A 853 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6956 (tttt) REVERT: A 1199 MET cc_start: 0.7807 (ppp) cc_final: 0.7160 (ppp) REVERT: A 1202 PHE cc_start: 0.6878 (m-80) cc_final: 0.6666 (m-80) REVERT: A 1228 MET cc_start: 0.7596 (mtm) cc_final: 0.7269 (mtm) REVERT: A 1257 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8491 (tp) REVERT: A 1384 HIS cc_start: 0.7658 (t70) cc_final: 0.7379 (t-170) REVERT: B 119 THR cc_start: 0.8911 (m) cc_final: 0.8547 (p) REVERT: B 296 GLU cc_start: 0.7885 (mp0) cc_final: 0.7598 (mp0) REVERT: B 446 TYR cc_start: 0.7324 (t80) cc_final: 0.7050 (t80) REVERT: B 448 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8282 (tt) REVERT: B 508 MET cc_start: 0.8118 (mmt) cc_final: 0.7720 (mmm) REVERT: B 621 ILE cc_start: 0.8754 (tt) cc_final: 0.8509 (tt) REVERT: B 668 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.7904 (tt) REVERT: B 674 MET cc_start: 0.8839 (tpt) cc_final: 0.8301 (tpt) REVERT: B 692 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7741 (t) REVERT: B 764 MET cc_start: 0.8669 (mmt) cc_final: 0.8096 (mmt) REVERT: B 796 MET cc_start: 0.8135 (mtp) cc_final: 0.7845 (mmm) REVERT: B 802 ASP cc_start: 0.8354 (m-30) cc_final: 0.8106 (m-30) REVERT: B 870 THR cc_start: 0.8663 (p) cc_final: 0.8457 (t) REVERT: B 908 MET cc_start: 0.7496 (tmm) cc_final: 0.7110 (tmm) REVERT: C 179 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9081 (t) REVERT: C 258 ASP cc_start: 0.7444 (t0) cc_final: 0.7170 (t0) REVERT: D 39 MET cc_start: 0.7038 (tmm) cc_final: 0.6648 (tmm) REVERT: F 59 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8261 (mtmm) REVERT: F 94 MET cc_start: 0.7978 (mpp) cc_final: 0.7307 (mpp) REVERT: G 117 MET cc_start: 0.2521 (mmm) cc_final: 0.1853 (tpp) REVERT: H 10 PHE cc_start: 0.8507 (m-80) cc_final: 0.8164 (m-80) REVERT: I 43 ASP cc_start: 0.7640 (m-30) cc_final: 0.6969 (t0) REVERT: I 57 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7732 (mttt) REVERT: I 64 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7663 (mm-30) REVERT: J 1 MET cc_start: 0.8119 (mpp) cc_final: 0.7012 (mpp) REVERT: J 55 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8097 (tt) REVERT: L 46 LYS cc_start: 0.8410 (tptp) cc_final: 0.8109 (tptp) outliers start: 122 outliers final: 87 residues processed: 503 average time/residue: 0.1784 time to fit residues: 145.5644 Evaluate side-chains 480 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 384 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 HIS Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 312 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 304 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 chunk 210 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 195 optimal weight: 1.9990 chunk 318 optimal weight: 0.8980 chunk 206 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN A 599 HIS A 671 ASN A 677 ASN A 721 HIS ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 HIS A1230 GLN ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS H 46 GLN I 41 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.152023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124241 restraints weight = 42014.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.123714 restraints weight = 44101.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124907 restraints weight = 38128.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125324 restraints weight = 27214.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125453 restraints weight = 25433.507| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27212 Z= 0.110 Angle : 0.593 13.271 36761 Z= 0.303 Chirality : 0.045 0.173 4148 Planarity : 0.004 0.044 4742 Dihedral : 5.153 48.348 3643 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.48 % Allowed : 14.10 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.14), residues: 3240 helix: -2.15 (0.15), residues: 1003 sheet: -1.78 (0.22), residues: 529 loop : -1.89 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 111 TYR 0.011 0.001 TYR B 651 PHE 0.019 0.001 PHE B 320 TRP 0.016 0.001 TRP B 236 HIS 0.016 0.001 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00253 (27194) covalent geometry : angle 0.58922 (36743) hydrogen bonds : bond 0.03364 ( 634) hydrogen bonds : angle 5.20827 ( 1782) metal coordination : bond 0.00538 ( 18) metal coordination : angle 2.92142 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 451 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5430 (tpt) REVERT: A 634 GLU cc_start: 0.8390 (tt0) cc_final: 0.7438 (mt-10) REVERT: A 677 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7971 (t0) REVERT: A 1199 MET cc_start: 0.7917 (ppp) cc_final: 0.6630 (ppp) REVERT: A 1202 PHE cc_start: 0.6945 (m-80) cc_final: 0.6686 (m-80) REVERT: A 1228 MET cc_start: 0.7861 (mtm) cc_final: 0.7536 (mtm) REVERT: A 1229 GLU cc_start: 0.7550 (mp0) cc_final: 0.7338 (mp0) REVERT: A 1384 HIS cc_start: 0.7536 (t70) cc_final: 0.7305 (t-170) REVERT: B 119 THR cc_start: 0.8833 (m) cc_final: 0.8490 (p) REVERT: B 296 GLU cc_start: 0.7934 (mp0) cc_final: 0.7637 (pm20) REVERT: B 446 TYR cc_start: 0.7105 (t80) cc_final: 0.6779 (t80) REVERT: B 508 MET cc_start: 0.8023 (mmt) cc_final: 0.7721 (mmm) REVERT: B 668 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.7817 (tt) REVERT: B 674 MET cc_start: 0.8874 (tpt) cc_final: 0.8342 (tpt) REVERT: B 677 MET cc_start: 0.8089 (mmm) cc_final: 0.7011 (mtm) REVERT: B 692 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7770 (t) REVERT: B 697 GLU cc_start: 0.7745 (pt0) cc_final: 0.7543 (pt0) REVERT: B 802 ASP cc_start: 0.8211 (m-30) cc_final: 0.7998 (m-30) REVERT: B 908 MET cc_start: 0.7496 (tmm) cc_final: 0.7083 (tmm) REVERT: B 976 MET cc_start: 0.3677 (mmm) cc_final: 0.3452 (mmm) REVERT: B 1026 GLU cc_start: 0.6090 (tp30) cc_final: 0.5871 (mm-30) REVERT: C 258 ASP cc_start: 0.7666 (t0) cc_final: 0.7385 (t0) REVERT: C 260 GLN cc_start: 0.7645 (pp30) cc_final: 0.6901 (pp30) REVERT: D 39 MET cc_start: 0.6850 (tmm) cc_final: 0.6588 (tmm) REVERT: F 94 MET cc_start: 0.8021 (mpp) cc_final: 0.7236 (mpp) REVERT: F 107 ARG cc_start: 0.7749 (tpp80) cc_final: 0.6975 (tpp80) REVERT: G 117 MET cc_start: 0.2406 (mmm) cc_final: 0.1800 (tpp) REVERT: H 10 PHE cc_start: 0.8538 (m-80) cc_final: 0.8154 (m-80) REVERT: H 142 TYR cc_start: 0.8481 (m-80) cc_final: 0.8122 (m-80) REVERT: H 147 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8210 (mmtt) REVERT: I 43 ASP cc_start: 0.7411 (m-30) cc_final: 0.6915 (t0) REVERT: I 57 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7675 (mttt) REVERT: I 64 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7575 (mm-30) REVERT: J 1 MET cc_start: 0.8002 (mpp) cc_final: 0.7202 (mpp) REVERT: J 55 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8492 (tt) REVERT: K 24 ASP cc_start: 0.7289 (t0) cc_final: 0.6809 (t0) outliers start: 102 outliers final: 59 residues processed: 521 average time/residue: 0.1764 time to fit residues: 148.9066 Evaluate side-chains 463 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 399 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 312 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 319 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 258 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 309 optimal weight: 0.2980 chunk 235 optimal weight: 20.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS I 84 HIS K 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.143862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115117 restraints weight = 43343.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114522 restraints weight = 41112.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115847 restraints weight = 39756.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115981 restraints weight = 27099.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116217 restraints weight = 25253.007| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 27212 Z= 0.332 Angle : 0.796 13.821 36761 Z= 0.406 Chirality : 0.052 0.264 4148 Planarity : 0.006 0.067 4742 Dihedral : 5.742 48.226 3642 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 4.68 % Allowed : 14.98 % Favored : 80.34 % 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: -3.18 (0.14), residues: 3240 helix: -2.21 (0.15), residues: 989 sheet: -2.01 (0.23), residues: 479 loop : -2.06 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 40 TYR 0.029 0.002 TYR J 43 PHE 0.032 0.002 PHE A 592 TRP 0.026 0.002 TRP F 118 HIS 0.018 0.002 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00786 (27194) covalent geometry : angle 0.78895 (36743) hydrogen bonds : bond 0.04297 ( 634) hydrogen bonds : angle 5.66377 ( 1782) metal coordination : bond 0.01192 ( 18) metal coordination : angle 4.79236 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 409 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 524 MET cc_start: 0.4711 (OUTLIER) cc_final: 0.4303 (mtt) REVERT: A 634 GLU cc_start: 0.8275 (tt0) cc_final: 0.7465 (mt-10) REVERT: A 868 MET cc_start: 0.6945 (mtt) cc_final: 0.6672 (mtt) REVERT: A 959 MET cc_start: 0.7957 (mmm) cc_final: 0.7745 (mmm) REVERT: A 1199 MET cc_start: 0.7860 (ppp) cc_final: 0.7472 (ppp) REVERT: A 1202 PHE cc_start: 0.6910 (m-80) cc_final: 0.6667 (m-80) REVERT: A 1384 HIS cc_start: 0.7671 (t70) cc_final: 0.7456 (t-170) REVERT: B 43 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7744 (mp10) REVERT: B 119 THR cc_start: 0.8886 (m) cc_final: 0.8483 (p) REVERT: B 336 ILE cc_start: 0.8455 (mt) cc_final: 0.8212 (mm) REVERT: B 508 MET cc_start: 0.8028 (mmt) cc_final: 0.7773 (mmm) REVERT: B 668 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.7816 (tt) REVERT: B 674 MET cc_start: 0.8944 (tpt) cc_final: 0.8260 (tpt) REVERT: B 724 TYR cc_start: 0.8251 (t80) cc_final: 0.7697 (t80) REVERT: B 764 MET cc_start: 0.8625 (mmt) cc_final: 0.8092 (mmt) REVERT: B 908 MET cc_start: 0.7462 (tmm) cc_final: 0.7029 (tmm) REVERT: B 1026 GLU cc_start: 0.6171 (tp30) cc_final: 0.5934 (mm-30) REVERT: C 258 ASP cc_start: 0.7587 (t0) cc_final: 0.7362 (t70) REVERT: C 260 GLN cc_start: 0.7958 (pp30) cc_final: 0.7296 (pp30) REVERT: D 39 MET cc_start: 0.7122 (tmm) cc_final: 0.6871 (tmm) REVERT: E 13 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8897 (tp) REVERT: F 59 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8226 (mtmm) REVERT: F 64 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7274 (ttt90) REVERT: F 94 MET cc_start: 0.8031 (mpp) cc_final: 0.7216 (mpp) REVERT: H 10 PHE cc_start: 0.8573 (m-80) cc_final: 0.8204 (m-80) REVERT: H 147 LYS cc_start: 0.8744 (mmmm) cc_final: 0.8273 (mmtt) REVERT: I 40 ARG cc_start: 0.6535 (tmm160) cc_final: 0.6237 (tmm160) REVERT: I 43 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7004 (t0) REVERT: I 54 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7403 (p90) REVERT: I 64 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7713 (mm-30) REVERT: J 1 MET cc_start: 0.8538 (mpp) cc_final: 0.7706 (mpp) REVERT: J 12 LYS cc_start: 0.7838 (ttmt) cc_final: 0.7615 (tptt) REVERT: J 55 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8224 (tt) REVERT: K 24 ASP cc_start: 0.7355 (t0) cc_final: 0.7040 (t70) outliers start: 137 outliers final: 99 residues processed: 498 average time/residue: 0.1781 time to fit residues: 143.5337 Evaluate side-chains 481 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 374 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 HIS Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 299 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 321 optimal weight: 0.3980 chunk 287 optimal weight: 2.9990 chunk 292 optimal weight: 0.0070 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 599 HIS A 671 ASN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120897 restraints weight = 42466.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120416 restraints weight = 45219.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121508 restraints weight = 40167.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.121974 restraints weight = 28575.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.122129 restraints weight = 26039.644| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27212 Z= 0.141 Angle : 0.639 14.944 36761 Z= 0.329 Chirality : 0.046 0.224 4148 Planarity : 0.004 0.047 4742 Dihedral : 5.290 48.751 3642 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 3.55 % Allowed : 16.66 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.14), residues: 3240 helix: -1.93 (0.15), residues: 1009 sheet: -1.81 (0.23), residues: 502 loop : -1.88 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 202 TYR 0.020 0.001 TYR I 44 PHE 0.030 0.001 PHE B 309 TRP 0.017 0.002 TRP B 99 HIS 0.017 0.001 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00333 (27194) covalent geometry : angle 0.63565 (36743) hydrogen bonds : bond 0.03449 ( 634) hydrogen bonds : angle 5.27148 ( 1782) metal coordination : bond 0.00523 ( 18) metal coordination : angle 3.13485 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 410 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 520 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.5317 (tpt) REVERT: A 524 MET cc_start: 0.4628 (OUTLIER) cc_final: 0.4275 (mtt) REVERT: A 634 GLU cc_start: 0.8162 (tt0) cc_final: 0.7403 (mt-10) REVERT: A 766 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8597 (m-10) REVERT: A 925 THR cc_start: 0.7000 (OUTLIER) cc_final: 0.6794 (p) REVERT: A 1199 MET cc_start: 0.7540 (ppp) cc_final: 0.7163 (ppp) REVERT: A 1202 PHE cc_start: 0.6834 (m-80) cc_final: 0.6603 (m-80) REVERT: A 1384 HIS cc_start: 0.7587 (t70) cc_final: 0.7363 (t-170) REVERT: B 119 THR cc_start: 0.8736 (m) cc_final: 0.8401 (p) REVERT: B 446 TYR cc_start: 0.7198 (t80) cc_final: 0.6789 (t80) REVERT: B 508 MET cc_start: 0.8070 (mmt) cc_final: 0.7754 (mmm) REVERT: B 668 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8044 (tt) REVERT: B 674 MET cc_start: 0.8840 (tpt) cc_final: 0.8331 (tpt) REVERT: B 908 MET cc_start: 0.7392 (tmm) cc_final: 0.6894 (tmm) REVERT: D 39 MET cc_start: 0.7048 (tmm) cc_final: 0.6812 (tmm) REVERT: E 13 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8847 (tp) REVERT: E 100 THR cc_start: 0.7889 (m) cc_final: 0.7347 (p) REVERT: F 94 MET cc_start: 0.8005 (mpp) cc_final: 0.7600 (mpp) REVERT: H 10 PHE cc_start: 0.8429 (m-80) cc_final: 0.8076 (m-80) REVERT: H 147 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8132 (mmtt) REVERT: I 43 ASP cc_start: 0.7262 (m-30) cc_final: 0.6874 (t0) REVERT: I 54 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7546 (p90) REVERT: I 56 ASN cc_start: 0.7981 (t0) cc_final: 0.7366 (p0) REVERT: I 57 LYS cc_start: 0.8251 (mtpp) cc_final: 0.7767 (mttt) REVERT: J 55 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8250 (tt) REVERT: K 24 ASP cc_start: 0.7492 (t0) cc_final: 0.7227 (t70) outliers start: 104 outliers final: 71 residues processed: 483 average time/residue: 0.1839 time to fit residues: 144.2723 Evaluate side-chains 464 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 385 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1405 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 HIS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 312 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 146 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 234 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 268 optimal weight: 9.9990 chunk 310 optimal weight: 6.9990 chunk 124 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN A 677 ASN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 410 ASN B 941 GLN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.151356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123740 restraints weight = 42656.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123531 restraints weight = 46407.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124623 restraints weight = 38495.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125060 restraints weight = 27483.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.125216 restraints weight = 25508.555| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27212 Z= 0.117 Angle : 0.619 15.242 36761 Z= 0.316 Chirality : 0.045 0.201 4148 Planarity : 0.004 0.050 4742 Dihedral : 4.984 49.283 3642 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.21 % Allowed : 17.58 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.14), residues: 3240 helix: -1.67 (0.15), residues: 999 sheet: -1.63 (0.23), residues: 512 loop : -1.69 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 924 TYR 0.013 0.001 TYR H 118 PHE 0.026 0.001 PHE B 309 TRP 0.016 0.001 TRP B 99 HIS 0.017 0.001 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00272 (27194) covalent geometry : angle 0.61535 (36743) hydrogen bonds : bond 0.03171 ( 634) hydrogen bonds : angle 5.07769 ( 1782) metal coordination : bond 0.00397 ( 18) metal coordination : angle 2.89497 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 434 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 634 GLU cc_start: 0.8156 (tt0) cc_final: 0.7361 (mt-10) REVERT: A 677 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8078 (t0) REVERT: A 766 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8589 (m-10) REVERT: A 1199 MET cc_start: 0.7505 (ppp) cc_final: 0.7119 (ppp) REVERT: A 1213 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7290 (tmm-80) REVERT: A 1384 HIS cc_start: 0.7544 (t70) cc_final: 0.7324 (t-170) REVERT: B 119 THR cc_start: 0.8735 (m) cc_final: 0.8358 (p) REVERT: B 210 LYS cc_start: 0.7930 (mmmm) cc_final: 0.7612 (mmtt) REVERT: B 264 LYS cc_start: 0.8614 (pttp) cc_final: 0.8375 (pttm) REVERT: B 407 MET cc_start: 0.7631 (tpp) cc_final: 0.6926 (mmt) REVERT: B 410 ASN cc_start: 0.7782 (m-40) cc_final: 0.7530 (m-40) REVERT: B 446 TYR cc_start: 0.6946 (t80) cc_final: 0.6541 (t80) REVERT: B 508 MET cc_start: 0.8021 (mmt) cc_final: 0.7690 (mmm) REVERT: B 668 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.7985 (tt) REVERT: B 908 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6808 (tmm) REVERT: E 13 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8762 (tp) REVERT: F 94 MET cc_start: 0.7929 (mpp) cc_final: 0.7678 (mpp) REVERT: H 10 PHE cc_start: 0.8394 (m-80) cc_final: 0.8154 (m-80) REVERT: H 142 TYR cc_start: 0.8540 (m-80) cc_final: 0.8163 (m-80) REVERT: H 147 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8049 (mmtt) REVERT: I 40 ARG cc_start: 0.6149 (tmm-80) cc_final: 0.5948 (tmm-80) REVERT: I 43 ASP cc_start: 0.7353 (m-30) cc_final: 0.6882 (t0) REVERT: I 54 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7456 (p90) REVERT: I 56 ASN cc_start: 0.8073 (t0) cc_final: 0.7485 (p0) REVERT: I 57 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7779 (mttt) REVERT: J 1 MET cc_start: 0.7977 (mpp) cc_final: 0.7742 (mpp) REVERT: J 55 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8478 (tt) REVERT: L 15 MET cc_start: 0.7047 (ptp) cc_final: 0.6309 (ttt) outliers start: 94 outliers final: 65 residues processed: 499 average time/residue: 0.1799 time to fit residues: 145.6327 Evaluate side-chains 471 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 398 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1213 ARG Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 83 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 239 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 265 optimal weight: 20.0000 chunk 211 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN K 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.147478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119812 restraints weight = 43186.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119174 restraints weight = 43244.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.120451 restraints weight = 42953.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120617 restraints weight = 29749.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120843 restraints weight = 27820.598| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 27212 Z= 0.211 Angle : 0.707 15.774 36761 Z= 0.360 Chirality : 0.048 0.301 4148 Planarity : 0.005 0.055 4742 Dihedral : 5.192 49.237 3642 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 3.52 % Allowed : 17.27 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.14), residues: 3240 helix: -1.70 (0.15), residues: 1014 sheet: -1.73 (0.23), residues: 506 loop : -1.81 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 109 TYR 0.025 0.002 TYR H 118 PHE 0.025 0.002 PHE B 309 TRP 0.016 0.002 TRP F 118 HIS 0.018 0.001 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00505 (27194) covalent geometry : angle 0.70300 (36743) hydrogen bonds : bond 0.03537 ( 634) hydrogen bonds : angle 5.21515 ( 1782) metal coordination : bond 0.00766 ( 18) metal coordination : angle 3.44441 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 406 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 524 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.4233 (mtt) REVERT: A 579 ILE cc_start: 0.8115 (mm) cc_final: 0.7831 (mm) REVERT: A 634 GLU cc_start: 0.8206 (tt0) cc_final: 0.7435 (mt-10) REVERT: A 766 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8644 (m-10) REVERT: A 1199 MET cc_start: 0.7335 (ppp) cc_final: 0.6949 (ppp) REVERT: A 1213 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7293 (tmm-80) REVERT: A 1384 HIS cc_start: 0.7596 (t70) cc_final: 0.7367 (t-170) REVERT: B 119 THR cc_start: 0.8786 (m) cc_final: 0.8428 (p) REVERT: B 210 LYS cc_start: 0.8070 (mmmm) cc_final: 0.7731 (mmtt) REVERT: B 407 MET cc_start: 0.7741 (tpp) cc_final: 0.7022 (mmt) REVERT: B 508 MET cc_start: 0.8029 (mmt) cc_final: 0.7698 (mmm) REVERT: B 668 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.7783 (tt) REVERT: B 743 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8346 (mtp-110) REVERT: B 764 MET cc_start: 0.8554 (mmt) cc_final: 0.8135 (mmt) REVERT: B 908 MET cc_start: 0.7447 (tmm) cc_final: 0.7104 (tmm) REVERT: E 13 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8847 (tp) REVERT: F 94 MET cc_start: 0.7960 (mpp) cc_final: 0.7579 (mpp) REVERT: F 107 ARG cc_start: 0.7571 (tpp80) cc_final: 0.7350 (tpp80) REVERT: G 117 MET cc_start: 0.0885 (tpp) cc_final: 0.0672 (tpp) REVERT: H 10 PHE cc_start: 0.8497 (m-80) cc_final: 0.8104 (m-80) REVERT: H 147 LYS cc_start: 0.8594 (mmmm) cc_final: 0.8111 (mmtt) REVERT: I 43 ASP cc_start: 0.7476 (m-30) cc_final: 0.7007 (t0) REVERT: I 54 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7447 (p90) REVERT: I 56 ASN cc_start: 0.8050 (t0) cc_final: 0.7334 (p0) REVERT: I 57 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7771 (mttt) REVERT: J 55 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8322 (tt) REVERT: L 15 MET cc_start: 0.7033 (ptp) cc_final: 0.6077 (ttt) outliers start: 103 outliers final: 79 residues processed: 474 average time/residue: 0.1759 time to fit residues: 136.4154 Evaluate side-chains 475 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 388 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 669 TYR Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1213 ARG Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1405 MET Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 743 ARG Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 227 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 273 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN K 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.148594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120055 restraints weight = 42700.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119375 restraints weight = 41398.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120587 restraints weight = 37972.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120972 restraints weight = 26921.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121115 restraints weight = 24446.717| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27212 Z= 0.176 Angle : 0.694 19.009 36761 Z= 0.352 Chirality : 0.047 0.247 4148 Planarity : 0.004 0.052 4742 Dihedral : 5.179 49.117 3642 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.58 % Favored : 91.39 % Rotamer: Outliers : 3.17 % Allowed : 17.99 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.14), residues: 3240 helix: -1.64 (0.15), residues: 1012 sheet: -1.72 (0.23), residues: 493 loop : -1.82 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 109 TYR 0.022 0.001 TYR H 118 PHE 0.023 0.002 PHE B 309 TRP 0.015 0.002 TRP B 99 HIS 0.019 0.001 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00421 (27194) covalent geometry : angle 0.69103 (36743) hydrogen bonds : bond 0.03485 ( 634) hydrogen bonds : angle 5.17602 ( 1782) metal coordination : bond 0.00646 ( 18) metal coordination : angle 3.18707 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 394 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 524 MET cc_start: 0.4597 (OUTLIER) cc_final: 0.4217 (mtt) REVERT: A 579 ILE cc_start: 0.8061 (mm) cc_final: 0.7803 (mm) REVERT: A 634 GLU cc_start: 0.8218 (tt0) cc_final: 0.7437 (mt-10) REVERT: A 766 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8607 (m-10) REVERT: A 1199 MET cc_start: 0.7364 (ppp) cc_final: 0.7091 (ppp) REVERT: A 1384 HIS cc_start: 0.7574 (t70) cc_final: 0.7344 (t-170) REVERT: B 119 THR cc_start: 0.8759 (m) cc_final: 0.8401 (p) REVERT: B 210 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7652 (mmtt) REVERT: B 381 GLU cc_start: 0.7852 (tp30) cc_final: 0.7581 (tp30) REVERT: B 407 MET cc_start: 0.7592 (tpp) cc_final: 0.6952 (mmt) REVERT: B 508 MET cc_start: 0.8044 (mmt) cc_final: 0.7733 (mmm) REVERT: B 668 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8071 (tt) REVERT: B 764 MET cc_start: 0.8552 (mmt) cc_final: 0.8120 (mmt) REVERT: B 908 MET cc_start: 0.7370 (tmm) cc_final: 0.7042 (tmm) REVERT: E 13 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8829 (tp) REVERT: E 121 MET cc_start: 0.4409 (tpp) cc_final: 0.4199 (ppp) REVERT: F 94 MET cc_start: 0.7970 (mpp) cc_final: 0.7583 (mpp) REVERT: F 107 ARG cc_start: 0.7581 (tpp80) cc_final: 0.7372 (tpp80) REVERT: G 24 ASN cc_start: 0.6949 (OUTLIER) cc_final: 0.6660 (m-40) REVERT: G 117 MET cc_start: 0.0943 (tpp) cc_final: 0.0693 (tpp) REVERT: H 10 PHE cc_start: 0.8406 (m-80) cc_final: 0.8169 (m-80) REVERT: H 147 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8097 (mmtt) REVERT: I 43 ASP cc_start: 0.7515 (m-30) cc_final: 0.7005 (t0) REVERT: I 54 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7428 (p90) REVERT: I 57 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7793 (mttt) REVERT: J 55 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8273 (tt) REVERT: L 15 MET cc_start: 0.7105 (ptp) cc_final: 0.6208 (ttt) outliers start: 93 outliers final: 79 residues processed: 454 average time/residue: 0.1693 time to fit residues: 126.7406 Evaluate side-chains 473 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 387 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 669 TYR Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1405 MET Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 297 optimal weight: 0.0770 chunk 301 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 0.5980 chunk 303 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.151581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.124070 restraints weight = 42357.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123330 restraints weight = 43784.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124563 restraints weight = 38598.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125005 restraints weight = 27343.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125151 restraints weight = 25112.598| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27212 Z= 0.123 Angle : 0.645 16.945 36761 Z= 0.327 Chirality : 0.046 0.198 4148 Planarity : 0.004 0.050 4742 Dihedral : 4.960 49.466 3642 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.98 % Favored : 92.99 % Rotamer: Outliers : 2.83 % Allowed : 18.36 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.14), residues: 3240 helix: -1.47 (0.16), residues: 1016 sheet: -1.62 (0.22), residues: 519 loop : -1.72 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 109 TYR 0.017 0.001 TYR A1392 PHE 0.022 0.001 PHE B 309 TRP 0.016 0.001 TRP B 99 HIS 0.019 0.001 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00290 (27194) covalent geometry : angle 0.64244 (36743) hydrogen bonds : bond 0.03215 ( 634) hydrogen bonds : angle 5.00416 ( 1782) metal coordination : bond 0.00400 ( 18) metal coordination : angle 2.73899 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4271.60 seconds wall clock time: 74 minutes 57.81 seconds (4497.81 seconds total)