Starting phenix.real_space_refine on Sat Mar 7 08:02:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d59_30578/03_2026/7d59_30578.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d59_30578/03_2026/7d59_30578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d59_30578/03_2026/7d59_30578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d59_30578/03_2026/7d59_30578.map" model { file = "/net/cci-nas-00/data/ceres_data/7d59_30578/03_2026/7d59_30578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d59_30578/03_2026/7d59_30578.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 S 275 5.16 5 C 25230 2.51 5 N 6906 2.21 5 O 7476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 385 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39898 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 10881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1386, 10881 Classifications: {'peptide': 1386} Link IDs: {'PTRANS': 65, 'TRANS': 1320} Chain: "B" Number of atoms: 8668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8668 Classifications: {'peptide': 1095} Link IDs: {'PTRANS': 49, 'TRANS': 1045} Chain breaks: 2 Chain: "C" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2752 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 17, 'TRANS': 327} Chain: "D" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1013 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1723 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 198} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1470 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain breaks: 2 Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 857 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 397 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "M" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1797 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 13, 'TRANS': 208} Chain breaks: 3 Chain: "N" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1038 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3913 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 16, 'TRANS': 473} Chain breaks: 2 Chain: "P" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain breaks: 1 Chain: "Q" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1049 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 12, 'TRANS': 108} Chain breaks: 2 Chain: "A" 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: "B" 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} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 550 SG CYS A 69 54.653 108.165 92.906 1.00155.88 S ATOM 620 SG CYS A 79 58.931 108.579 92.852 1.00133.57 S ATOM 883 SG CYS A 112 68.677 80.410 132.900 1.00158.01 S ATOM 19127 SG CYS B1080 62.971 113.987 110.709 1.00123.98 S ATOM 19146 SG CYS B1083 62.708 109.790 111.897 1.00126.17 S ATOM 19212 SG CYS B1092 60.235 110.521 108.514 1.00127.53 S ATOM 28381 SG CYS I 5 118.169 35.651 107.873 1.00162.49 S ATOM 28398 SG CYS I 8 114.768 36.865 107.068 1.00162.55 S ATOM 28529 SG CYS I 25 115.414 37.842 111.809 1.00167.43 S ATOM 28550 SG CYS I 28 115.075 34.333 109.593 1.00164.81 S ATOM 29111 SG CYS I 98 137.804 109.699 94.458 1.00231.72 S ATOM 29252 SG CYS J 7 106.870 111.937 39.723 1.00 76.18 S ATOM 29276 SG CYS J 10 108.124 115.266 37.879 1.00 80.33 S ATOM 30653 SG CYS L 19 71.825 84.885 38.622 1.00113.18 S ATOM 30672 SG CYS L 22 71.018 84.086 34.555 1.00119.05 S ATOM 30789 SG CYS L 36 67.977 83.884 36.821 1.00126.01 S ATOM 30815 SG CYS L 39 70.993 81.549 37.334 1.00130.06 S ATOM 38624 SG CYS P 290 44.561 89.676 119.081 1.00178.43 S ATOM 38671 SG CYS P 296 48.300 94.393 120.566 1.00160.77 S ATOM 38748 SG CYS P 307 41.782 94.335 120.100 1.00175.10 S ATOM 38606 SG CYS P 287 45.381 91.660 125.530 1.00183.21 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN I 202 " occ=0.75 Time building chain proxies: 8.09, per 1000 atoms: 0.20 Number of scatterers: 39898 At special positions: 0 Unit cell: (168.95, 173.31, 185.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 275 16.00 O 7476 8.00 N 6906 7.00 C 25230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 400 " pdb="FE2 SF4 P 400 " - pdb=" SG CYS P 296 " pdb="FE3 SF4 P 400 " - pdb=" SG CYS P 307 " pdb="FE4 SF4 P 400 " - pdb=" SG CYS P 287 " pdb="FE1 SF4 P 400 " - pdb=" SG CYS P 290 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 69 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 79 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 112 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1080 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1083 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1092 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 98 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 12 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9434 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 54 sheets defined 37.8% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.706A pdb=" N GLN A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.565A pdb=" N LYS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.506A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 203 removed outlier: 4.253A pdb=" N HIS A 203 " --> pdb=" O ALA A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 203' Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.631A pdb=" N ARG A 213 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.613A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 277 through 300 removed outlier: 3.534A pdb=" N PHE A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.709A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 removed outlier: 3.885A pdb=" N GLN A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.764A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 522 removed outlier: 3.705A pdb=" N ALA A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 569 through 572 removed outlier: 3.962A pdb=" N LEU A 572 " --> pdb=" O ALA A 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 569 through 572' Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 682 through 695 Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 706 through 734 removed outlier: 4.363A pdb=" N LYS A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 728 " --> pdb=" O CYS A 724 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 Processing helix chain 'A' and resid 754 through 771 removed outlier: 3.802A pdb=" N ILE A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 760 " --> pdb=" O LEU A 756 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 784 Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 827 through 832 removed outlier: 3.523A pdb=" N GLY A 832 " --> pdb=" O PRO A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 863 removed outlier: 3.600A pdb=" N ALA A 853 " --> pdb=" O PHE A 849 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 861 " --> pdb=" O GLY A 857 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 863 " --> pdb=" O VAL A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 877 removed outlier: 3.836A pdb=" N GLU A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 932 removed outlier: 3.569A pdb=" N VAL A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 930 " --> pdb=" O ASP A 926 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 954 removed outlier: 3.787A pdb=" N LEU A 947 " --> pdb=" O ASN A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 988 removed outlier: 3.542A pdb=" N SER A 977 " --> pdb=" O ILE A 973 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 979 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 987 " --> pdb=" O THR A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1003 removed outlier: 3.917A pdb=" N LEU A1003 " --> pdb=" O LEU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1025 removed outlier: 3.787A pdb=" N GLU A1012 " --> pdb=" O PRO A1008 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A1014 " --> pdb=" O GLN A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1039 removed outlier: 3.542A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1047 removed outlier: 3.521A pdb=" N GLN A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1094 through 1105 removed outlier: 3.875A pdb=" N ALA A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A1103 " --> pdb=" O ARG A1099 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A1104 " --> pdb=" O LEU A1100 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A1105 " --> pdb=" O VAL A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1133 through 1141 removed outlier: 3.629A pdb=" N ILE A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1155 Processing helix chain 'A' and resid 1184 through 1194 removed outlier: 3.758A pdb=" N VAL A1188 " --> pdb=" O SER A1184 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1237 removed outlier: 3.795A pdb=" N VAL A1235 " --> pdb=" O ASN A1231 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A1237 " --> pdb=" O ARG A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 Processing helix chain 'A' and resid 1262 through 1276 removed outlier: 3.756A pdb=" N THR A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A1268 " --> pdb=" O ARG A1264 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A1271 " --> pdb=" O ILE A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1294 removed outlier: 3.768A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1290 " --> pdb=" O HIS A1286 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET A1294 " --> pdb=" O LEU A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 removed outlier: 3.652A pdb=" N ALA A1309 " --> pdb=" O ARG A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1322 removed outlier: 3.677A pdb=" N LEU A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A1320 " --> pdb=" O LEU A1316 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A1321 " --> pdb=" O MET A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1335 removed outlier: 3.568A pdb=" N ALA A1332 " --> pdb=" O LEU A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1350 Processing helix chain 'A' and resid 1381 through 1386 removed outlier: 3.638A pdb=" N ILE A1386 " --> pdb=" O ASN A1382 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.666A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 37 " --> pdb=" O PHE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 removed outlier: 3.989A pdb=" N ILE B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 235 through 244 removed outlier: 3.554A pdb=" N GLY B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.731A pdb=" N ILE B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 264 removed outlier: 3.568A pdb=" N ALA B 264 " --> pdb=" O HIS B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 Processing helix chain 'B' and resid 279 through 291 Processing helix chain 'B' and resid 304 through 315 removed outlier: 4.042A pdb=" N SER B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 364 through 388 removed outlier: 4.254A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 removed outlier: 4.153A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 removed outlier: 3.507A pdb=" N LEU B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.554A pdb=" N GLY B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 566 Processing helix chain 'B' and resid 607 through 617 removed outlier: 3.678A pdb=" N GLU B 613 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 614 " --> pdb=" O HIS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.562A pdb=" N CYS B 641 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.760A pdb=" N THR B 663 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 660 through 665' Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.985A pdb=" N LEU B 671 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 672 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 691 removed outlier: 4.221A pdb=" N LYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 729 Processing helix chain 'B' and resid 730 through 733 Processing helix chain 'B' and resid 759 through 765 Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 940 through 956 removed outlier: 3.509A pdb=" N ILE B 944 " --> pdb=" O VAL B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 980 removed outlier: 3.549A pdb=" N CYS B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B 975 " --> pdb=" O ASP B 971 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 977 " --> pdb=" O CYS B 973 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS B 979 " --> pdb=" O ASP B 975 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 980 " --> pdb=" O LEU B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1059 removed outlier: 4.099A pdb=" N CYS B1054 " --> pdb=" O MET B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1067 Processing helix chain 'B' and resid 1107 through 1117 Processing helix chain 'B' and resid 1118 through 1121 removed outlier: 3.743A pdb=" N ASN B1121 " --> pdb=" O GLN B1118 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1118 through 1121' Processing helix chain 'C' and resid 3 through 12 removed outlier: 3.691A pdb=" N ARG C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.596A pdb=" N ALA C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.523A pdb=" N LEU C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 158 through 162' Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.763A pdb=" N ARG C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 346 removed outlier: 3.602A pdb=" N LEU C 321 " --> pdb=" O PRO C 317 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 326 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP C 346 " --> pdb=" O ALA C 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 22 removed outlier: 3.935A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 31 removed outlier: 3.683A pdb=" N GLN D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 56 removed outlier: 3.723A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 79 through 88 removed outlier: 4.141A pdb=" N LEU D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 removed outlier: 3.865A pdb=" N ILE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 122 removed outlier: 3.572A pdb=" N LEU D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 25 removed outlier: 4.050A pdb=" N GLY E 25 " --> pdb=" O CYS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 removed outlier: 3.678A pdb=" N GLN E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 96 removed outlier: 3.618A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.999A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.822A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 74 Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.811A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'J' and resid 17 through 25 Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.810A pdb=" N GLY J 39 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 51 Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.864A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 62 removed outlier: 3.653A pdb=" N GLY K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN K 62 " --> pdb=" O MET K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 130 removed outlier: 4.042A pdb=" N PHE K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN K 97 " --> pdb=" O VAL K 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 83 Processing helix chain 'M' and resid 140 through 155 removed outlier: 3.914A pdb=" N LYS M 144 " --> pdb=" O SER M 140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA M 145 " --> pdb=" O TYR M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 203 removed outlier: 3.616A pdb=" N LEU M 196 " --> pdb=" O SER M 192 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU M 203 " --> pdb=" O LYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 227 Processing helix chain 'M' and resid 241 through 250 removed outlier: 3.708A pdb=" N MET M 247 " --> pdb=" O SER M 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 261 removed outlier: 3.503A pdb=" N THR N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 398 removed outlier: 3.693A pdb=" N LEU N 392 " --> pdb=" O ASP N 388 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 16 Processing helix chain 'O' and resid 18 through 31 removed outlier: 3.883A pdb=" N ARG O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR O 31 " --> pdb=" O HIS O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 44 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.586A pdb=" N HIS O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 83 removed outlier: 3.584A pdb=" N VAL O 82 " --> pdb=" O GLN O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 99 removed outlier: 4.428A pdb=" N LEU O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 109 removed outlier: 3.787A pdb=" N GLU O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 114 Processing helix chain 'O' and resid 117 through 133 removed outlier: 3.618A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 154 removed outlier: 3.764A pdb=" N THR O 147 " --> pdb=" O GLU O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 259 removed outlier: 3.728A pdb=" N PHE O 242 " --> pdb=" O ASN O 238 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET O 259 " --> pdb=" O VAL O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 273 removed outlier: 3.514A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET O 273 " --> pdb=" O THR O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 278 removed outlier: 4.217A pdb=" N THR O 277 " --> pdb=" O MET O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 296 Processing helix chain 'O' and resid 304 through 317 removed outlier: 3.670A pdb=" N ASP O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 358 removed outlier: 3.671A pdb=" N SER O 344 " --> pdb=" O LYS O 340 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 372 removed outlier: 3.683A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 379 through 384 Processing helix chain 'O' and resid 387 through 401 Processing helix chain 'O' and resid 427 through 455 removed outlier: 3.691A pdb=" N HIS O 437 " --> pdb=" O ARG O 433 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR O 440 " --> pdb=" O LEU O 436 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS O 441 " --> pdb=" O HIS O 437 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU O 453 " --> pdb=" O ARG O 449 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR O 454 " --> pdb=" O ARG O 450 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS O 455 " --> pdb=" O GLN O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 478 removed outlier: 3.564A pdb=" N VAL O 467 " --> pdb=" O LYS O 463 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU O 468 " --> pdb=" O SER O 464 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE O 470 " --> pdb=" O ARG O 466 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET O 474 " --> pdb=" O ILE O 470 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA O 476 " --> pdb=" O ALA O 472 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR O 477 " --> pdb=" O SER O 473 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 491 removed outlier: 3.516A pdb=" N ILE O 491 " --> pdb=" O ILE O 487 " (cutoff:3.500A) Processing helix chain 'O' and resid 492 through 531 removed outlier: 3.602A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU O 500 " --> pdb=" O ARG O 496 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG O 504 " --> pdb=" O GLU O 500 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN O 515 " --> pdb=" O ALA O 511 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE O 520 " --> pdb=" O VAL O 516 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE O 527 " --> pdb=" O LEU O 523 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU O 528 " --> pdb=" O GLU O 524 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS O 529 " --> pdb=" O SER O 525 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR O 530 " --> pdb=" O TYR O 526 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 199 removed outlier: 3.620A pdb=" N LYS P 199 " --> pdb=" O ALA P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 208 Processing helix chain 'P' and resid 213 through 224 removed outlier: 3.578A pdb=" N LYS P 218 " --> pdb=" O HIS P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 230 through 246 Processing helix chain 'P' and resid 285 through 290 removed outlier: 4.134A pdb=" N LEU P 289 " --> pdb=" O ALA P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 307 through 316 Processing helix chain 'Q' and resid 51 through 70 removed outlier: 3.549A pdb=" N ALA Q 59 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 93 removed outlier: 3.618A pdb=" N MET Q 92 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 1337 through 1339 removed outlier: 6.775A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 92 removed outlier: 6.859A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 169 removed outlier: 4.135A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 216 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA5, first strand: chain 'B' and resid 1020 through 1023 removed outlier: 3.925A pdb=" N HIS B1021 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 366 " --> pdb=" O HIS B1021 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 364 " --> pdb=" O ARG B1023 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 487 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 488 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.992A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA8, first strand: chain 'A' and resid 616 through 620 removed outlier: 3.783A pdb=" N SER A 647 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN A 641 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 800 through 801 removed outlier: 4.000A pdb=" N GLY A 800 " --> pdb=" O VAL A 834 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.864A pdb=" N CYS A 883 " --> pdb=" O ARG A 891 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1209 through 1216 removed outlier: 4.171A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N THR A1086 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N THR A1244 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN A1088 " --> pdb=" O LYS A1242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 3.557A pdb=" N GLN A1202 " --> pdb=" O THR A1108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1165 through 1167 removed outlier: 7.032A pdb=" N PHE A1127 " --> pdb=" O GLU A1119 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLU A1119 " --> pdb=" O PHE A1127 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A1129 " --> pdb=" O ILE A1117 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE A1117 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A1131 " --> pdb=" O GLU A1115 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A1117 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A1119 " --> pdb=" O ASN I 40 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN I 40 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1361 through 1364 Processing sheet with id=AB6, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.658A pdb=" N VAL B 65 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR B 74 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 120 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL B 82 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 111 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG B 135 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE B 113 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 133 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 117 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN B 129 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B 119 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE B 127 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 121 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.842A pdb=" N VAL B 87 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG B 95 " --> pdb=" O VAL B 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'B' and resid 361 through 363 removed outlier: 6.132A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 188 through 193 removed outlier: 4.038A pdb=" N ARG B 188 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 203 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALA B 198 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 218 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AC3, first strand: chain 'B' and resid 501 through 502 removed outlier: 3.746A pdb=" N ARG B 594 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 633 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC5, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.585A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE B 537 " --> pdb=" O VAL B 548 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 712 removed outlier: 4.026A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR B 888 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N SER B 864 " --> pdb=" O THR B 888 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 712 removed outlier: 4.026A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR B 888 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N SER B 864 " --> pdb=" O THR B 888 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS L 46 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 871 " --> pdb=" O MET L 44 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 986 through 987 removed outlier: 3.724A pdb=" N ASP B 987 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B1002 " --> pdb=" O ASP B 987 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 755 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE B 910 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 757 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL B 756 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 928 " --> pdb=" O VAL B 756 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ILE B 927 " --> pdb=" O ASN B 738 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR B 740 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N MET B 929 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 742 " --> pdb=" O MET B 929 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 794 through 796 Processing sheet with id=AD1, first strand: chain 'B' and resid 825 through 826 removed outlier: 4.099A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 831 through 833 Processing sheet with id=AD3, first strand: chain 'B' and resid 1028 through 1029 removed outlier: 3.655A pdb=" N ARG B1028 " --> pdb=" O TYR Q 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1075 through 1079 Processing sheet with id=AD5, first strand: chain 'C' and resid 13 through 16 removed outlier: 4.779A pdb=" N LEU C 299 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 56 removed outlier: 6.976A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 232 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 138 through 145 removed outlier: 5.707A pdb=" N GLU C 207 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN C 96 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASP C 209 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL C 94 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 115 through 116 removed outlier: 3.788A pdb=" N ARG C 191 " --> pdb=" O HIS C 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.907A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 167 through 168 removed outlier: 3.877A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 262 through 267 removed outlier: 3.503A pdb=" N LYS C 270 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 2 through 3 removed outlier: 3.757A pdb=" N GLU D 2 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 8 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL G 3 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP G 9 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 70 " --> pdb=" O ASP G 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 12.666A pdb=" N HIS G 67 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N LEU G 54 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 12.311A pdb=" N LYS G 69 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N THR G 52 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N HIS G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP G 50 " --> pdb=" O HIS G 71 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG G 73 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.703A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA E 102 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 147 through 150 removed outlier: 4.411A pdb=" N GLN E 189 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 107 through 109 removed outlier: 6.372A pdb=" N SER G 100 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE G 89 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG G 149 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG G 151 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER G 189 " --> pdb=" O ARG G 151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL G 187 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU G 155 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR G 185 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 15 removed outlier: 5.530A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP H 38 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP H 42 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 13 through 16 Processing sheet with id=AF1, first strand: chain 'I' and resid 65 through 66 removed outlier: 3.940A pdb=" N ALA I 77 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE I 94 " --> pdb=" O ASP I 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP I 108 " --> pdb=" O PHE I 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 27 through 31 removed outlier: 3.818A pdb=" N PHE K 67 " --> pdb=" O GLN K 85 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 13 through 17 removed outlier: 4.674A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY N 327 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL M 15 " --> pdb=" O GLY N 327 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE M 13 " --> pdb=" O LEU N 329 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 106 through 107 removed outlier: 3.943A pdb=" N THR M 107 " --> pdb=" O ILE M 132 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE M 132 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY N 371 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET N 373 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL N 375 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 63 through 68 Processing sheet with id=AF6, first strand: chain 'O' and resid 157 through 159 Processing sheet with id=AF7, first strand: chain 'O' and resid 323 through 327 Processing sheet with id=AF8, first strand: chain 'O' and resid 375 through 376 Processing sheet with id=AF9, first strand: chain 'P' and resid 211 through 212 removed outlier: 3.660A pdb=" N ALA P 211 " --> pdb=" O TYR P 270 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR P 270 " --> pdb=" O ALA P 211 " (cutoff:3.500A) 1511 hydrogen bonds defined for protein. 4326 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: 10.37 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.45: 16809 1.45 - 1.67: 23391 1.67 - 1.89: 427 1.89 - 2.11: 0 2.11 - 2.33: 12 Bond restraints: 40639 Sorted by residual: bond pdb=" C ARG N 30 " pdb=" N PRO N 31 " ideal model delta sigma weight residual 1.333 1.357 -0.023 1.01e-02 9.80e+03 5.31e+00 bond pdb=" N GLU B 752 " pdb=" CA GLU B 752 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.23e-02 6.61e+03 5.01e+00 bond pdb=" C GLU A 996 " pdb=" N PRO A 997 " ideal model delta sigma weight residual 1.333 1.354 -0.020 1.01e-02 9.80e+03 4.09e+00 bond pdb=" CA GLU G 95 " pdb=" CB GLU G 95 " ideal model delta sigma weight residual 1.527 1.572 -0.045 2.48e-02 1.63e+03 3.30e+00 bond pdb=" C ILE B 392 " pdb=" N PRO B 393 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.30e-02 5.92e+03 3.16e+00 ... (remaining 40634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 53834 1.86 - 3.72: 878 3.72 - 5.57: 127 5.57 - 7.43: 15 7.43 - 9.29: 1 Bond angle restraints: 54855 Sorted by residual: angle pdb=" C GLY A 914 " pdb=" N LYS A 915 " pdb=" CA LYS A 915 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.37e+01 angle pdb=" N ASN A1180 " pdb=" CA ASN A1180 " pdb=" C ASN A1180 " ideal model delta sigma weight residual 108.52 115.32 -6.80 1.52e+00 4.33e-01 2.00e+01 angle pdb=" N VAL B 391 " pdb=" CA VAL B 391 " pdb=" C VAL B 391 " ideal model delta sigma weight residual 113.53 109.23 4.30 9.80e-01 1.04e+00 1.93e+01 angle pdb=" N VAL A 37 " pdb=" CA VAL A 37 " pdb=" C VAL A 37 " ideal model delta sigma weight residual 113.71 109.60 4.11 9.50e-01 1.11e+00 1.88e+01 angle pdb=" N LEU A 529 " pdb=" CA LEU A 529 " pdb=" C LEU A 529 " ideal model delta sigma weight residual 114.56 109.30 5.26 1.27e+00 6.20e-01 1.72e+01 ... (remaining 54850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 22515 17.95 - 35.89: 2001 35.89 - 53.84: 354 53.84 - 71.78: 81 71.78 - 89.73: 45 Dihedral angle restraints: 24996 sinusoidal: 10404 harmonic: 14592 Sorted by residual: dihedral pdb=" CA LYS D 77 " pdb=" C LYS D 77 " pdb=" N LEU D 78 " pdb=" CA LEU D 78 " ideal model delta harmonic sigma weight residual -180.00 -128.52 -51.48 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA HIS O 68 " pdb=" C HIS O 68 " pdb=" N LYS O 69 " pdb=" CA LYS O 69 " ideal model delta harmonic sigma weight residual -180.00 -135.43 -44.57 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA LYS A 915 " pdb=" C LYS A 915 " pdb=" N ASP A 916 " pdb=" CA ASP A 916 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 24993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.276: 6143 4.276 - 8.552: 0 8.552 - 12.828: 0 12.828 - 17.105: 0 17.105 - 21.381: 4 Chirality restraints: 6147 Sorted by residual: chirality pdb="FE4 SF4 P 400 " pdb=" S1 SF4 P 400 " pdb=" S2 SF4 P 400 " pdb=" S3 SF4 P 400 " both_signs ideal model delta sigma weight residual False 10.55 -10.83 21.38 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 P 400 " pdb=" S1 SF4 P 400 " pdb=" S2 SF4 P 400 " pdb=" S4 SF4 P 400 " both_signs ideal model delta sigma weight residual False -10.55 10.76 -21.32 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE2 SF4 P 400 " pdb=" S1 SF4 P 400 " pdb=" S3 SF4 P 400 " pdb=" S4 SF4 P 400 " both_signs ideal model delta sigma weight residual False 10.55 -10.72 21.28 2.00e-01 2.50e+01 1.13e+04 ... (remaining 6144 not shown) Planarity restraints: 7080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS O 68 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C HIS O 68 " -0.047 2.00e-02 2.50e+03 pdb=" O HIS O 68 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS O 69 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU Q 27 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO Q 28 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO Q 28 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO Q 28 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 110 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO G 111 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " -0.024 5.00e-02 4.00e+02 ... (remaining 7077 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2451 2.74 - 3.28: 38358 3.28 - 3.82: 62182 3.82 - 4.36: 71428 4.36 - 4.90: 124377 Nonbonded interactions: 298796 Sorted by model distance: nonbonded pdb=" OG SER I 86 " pdb=" O GLU I 89 " model vdw 2.196 3.040 nonbonded pdb=" OG SER O 289 " pdb=" OD1 ASN O 291 " model vdw 2.216 3.040 nonbonded pdb=" O ALA D 72 " pdb=" OG SER D 75 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLU E 78 " pdb=" OH TYR E 90 " model vdw 2.273 3.040 nonbonded pdb=" NH2 ARG O 241 " pdb=" OE1 GLU O 275 " model vdw 2.285 3.120 ... (remaining 298791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 45.630 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.009 0.646 40661 Z= 0.310 Angle : 0.735 38.644 54879 Z= 0.376 Chirality : 0.543 21.381 6147 Planarity : 0.003 0.045 7080 Dihedral : 14.302 89.729 15562 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.52 (0.10), residues: 4948 helix: -1.83 (0.11), residues: 1724 sheet: -1.05 (0.18), residues: 721 loop : -3.19 (0.09), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.014 0.001 TYR B 983 PHE 0.010 0.001 PHE M 139 TRP 0.006 0.001 TRP C 40 HIS 0.004 0.000 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00226 (40639) covalent geometry : angle 0.60909 (54855) hydrogen bonds : bond 0.19405 ( 1488) hydrogen bonds : angle 6.68284 ( 4326) metal coordination : bond 0.36123 ( 22) metal coordination : angle 19.65220 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 951 time to evaluate : 1.585 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.6727 (ttp80) cc_final: 0.6243 (ttp80) REVERT: A 107 MET cc_start: 0.8064 (mmp) cc_final: 0.6858 (mtt) REVERT: A 228 LYS cc_start: 0.9070 (mttt) cc_final: 0.8759 (mtmm) REVERT: A 324 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7263 (mm-30) REVERT: A 353 ARG cc_start: 0.6494 (ptt90) cc_final: 0.6107 (ptt90) REVERT: A 440 MET cc_start: 0.8345 (mmp) cc_final: 0.7821 (mtt) REVERT: A 635 ASP cc_start: 0.7733 (t70) cc_final: 0.7388 (t0) REVERT: A 646 MET cc_start: 0.8038 (mmm) cc_final: 0.7714 (mmm) REVERT: A 678 ASP cc_start: 0.7945 (t0) cc_final: 0.7612 (t0) REVERT: A 759 ILE cc_start: 0.7974 (pt) cc_final: 0.7716 (pt) REVERT: A 963 ASP cc_start: 0.7927 (t0) cc_final: 0.7686 (t0) REVERT: A 968 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8118 (tm-30) REVERT: A 1118 GLU cc_start: 0.7498 (pt0) cc_final: 0.6305 (pt0) REVERT: A 1191 PHE cc_start: 0.8504 (t80) cc_final: 0.8227 (t80) REVERT: A 1193 LYS cc_start: 0.9482 (pptt) cc_final: 0.9135 (pttt) REVERT: A 1250 ASN cc_start: 0.8221 (t0) cc_final: 0.6758 (t0) REVERT: A 1252 TYR cc_start: 0.7675 (t80) cc_final: 0.7256 (t80) REVERT: A 1255 GLU cc_start: 0.8753 (pp20) cc_final: 0.8535 (pp20) REVERT: A 1318 LEU cc_start: 0.8980 (mt) cc_final: 0.8615 (tt) REVERT: A 1330 ASP cc_start: 0.8075 (m-30) cc_final: 0.7819 (m-30) REVERT: B 54 GLU cc_start: 0.8310 (tp30) cc_final: 0.7793 (mp0) REVERT: B 106 ASP cc_start: 0.7149 (m-30) cc_final: 0.6850 (m-30) REVERT: B 192 GLU cc_start: 0.7348 (mm-30) cc_final: 0.5529 (mm-30) REVERT: B 239 ILE cc_start: 0.9244 (mm) cc_final: 0.8962 (mm) REVERT: B 354 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7548 (mpt-90) REVERT: B 1121 ASN cc_start: 0.6967 (t0) cc_final: 0.6576 (t0) REVERT: C 180 ASN cc_start: 0.8436 (t0) cc_final: 0.8223 (p0) REVERT: D 100 MET cc_start: 0.6205 (mmt) cc_final: 0.5905 (mmm) REVERT: E 73 PHE cc_start: 0.8465 (t80) cc_final: 0.7709 (t80) REVERT: F 88 ASP cc_start: 0.7491 (t70) cc_final: 0.7151 (t70) REVERT: F 91 LEU cc_start: 0.9090 (tp) cc_final: 0.8883 (tp) REVERT: G 82 ASP cc_start: 0.7273 (p0) cc_final: 0.6915 (p0) REVERT: G 108 LEU cc_start: 0.9034 (pp) cc_final: 0.8828 (tt) REVERT: G 185 THR cc_start: 0.9030 (m) cc_final: 0.8771 (p) REVERT: I 13 ILE cc_start: 0.8260 (pt) cc_final: 0.7876 (pt) REVERT: I 15 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7167 (mm-30) REVERT: K 28 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7502 (mp0) REVERT: K 60 MET cc_start: 0.9149 (mmt) cc_final: 0.8906 (mmt) REVERT: K 64 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7655 (tp30) REVERT: M 60 MET cc_start: 0.8293 (ptm) cc_final: 0.7989 (ppp) REVERT: M 220 HIS cc_start: 0.8835 (m-70) cc_final: 0.8589 (m90) REVERT: N 382 LYS cc_start: 0.9292 (ttpt) cc_final: 0.8792 (tttm) REVERT: O 513 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8610 (mt-10) REVERT: P 185 PHE cc_start: 0.9235 (t80) cc_final: 0.8995 (t80) REVERT: P 245 ASP cc_start: 0.8558 (t70) cc_final: 0.8157 (t70) REVERT: P 247 LYS cc_start: 0.8343 (mtmm) cc_final: 0.7665 (pttm) REVERT: P 250 MET cc_start: 0.7776 (ttt) cc_final: 0.7311 (tpt) REVERT: P 295 ASP cc_start: 0.8353 (t70) cc_final: 0.7515 (t0) REVERT: Q 43 TYR cc_start: 0.6231 (m-80) cc_final: 0.5782 (m-80) REVERT: Q 61 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8628 (ptmt) outliers start: 0 outliers final: 0 residues processed: 951 average time/residue: 0.3030 time to fit residues: 438.5797 Evaluate side-chains 583 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 157 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 436 ASN A 469 HIS A 534 ASN A 599 GLN A 616 ASN A 737 GLN A 794 GLN A 815 ASN A 872 GLN A 927 ASN A1010 GLN A1039 GLN A1168 HIS A1213 HIS A1231 ASN A1286 HIS B 92 ASN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS B 260 HIS B 280 GLN B 282 GLN B 349 ASN B 410 GLN B 413 ASN B 678 ASN B 683 ASN B 692 GLN B 758 ASN B 806 HIS B 932 HIS B1034 GLN B1121 ASN C 32 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS C 305 HIS C 344 GLN D 33 ASN D 76 HIS E 98 ASN E 129 GLN E 168 ASN G 17 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 83 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN M 130 HIS ** M 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 338 GLN N 358 GLN ** N 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS O 377 GLN O 415 HIS O 515 GLN P 181 ASN ** P 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.115659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.079977 restraints weight = 105720.927| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.83 r_work: 0.3259 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.273 40661 Z= 0.206 Angle : 1.106 51.425 54879 Z= 0.612 Chirality : 0.161 6.398 6147 Planarity : 0.005 0.111 7080 Dihedral : 3.714 49.818 5451 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 1.85 % Allowed : 12.69 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.44 (0.11), residues: 4948 helix: -0.65 (0.12), residues: 1759 sheet: -0.45 (0.19), residues: 708 loop : -2.79 (0.10), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 419 TYR 0.016 0.001 TYR B1009 PHE 0.019 0.002 PHE P 210 TRP 0.022 0.002 TRP M 700 HIS 0.016 0.001 HIS N 397 Details of bonding type rmsd covalent geometry : bond 0.00545 (40639) covalent geometry : angle 1.00401 (54855) hydrogen bonds : bond 0.04234 ( 1488) hydrogen bonds : angle 4.91486 ( 4326) metal coordination : bond 0.01608 ( 22) metal coordination : angle 22.16814 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 597 time to evaluate : 1.521 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: 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: 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 107 MET cc_start: 0.8163 (mmp) cc_final: 0.7863 (mmp) REVERT: A 168 LYS cc_start: 0.8864 (pttt) cc_final: 0.8484 (tttm) REVERT: A 228 LYS cc_start: 0.9153 (mttt) cc_final: 0.8912 (mtmm) REVERT: A 428 MET cc_start: 0.8107 (tpp) cc_final: 0.7345 (ppp) REVERT: A 429 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7861 (mtpp) REVERT: A 440 MET cc_start: 0.8812 (mmp) cc_final: 0.8039 (mtt) REVERT: A 474 MET cc_start: 0.8364 (mtt) cc_final: 0.8135 (mtt) REVERT: A 678 ASP cc_start: 0.8800 (t0) cc_final: 0.8476 (t0) REVERT: A 968 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8481 (tm-30) REVERT: A 1061 MET cc_start: 0.6992 (mpp) cc_final: 0.6593 (mpp) REVERT: A 1096 ASP cc_start: 0.8683 (m-30) cc_final: 0.8449 (t0) REVERT: A 1185 MET cc_start: 0.8571 (ppp) cc_final: 0.8017 (mtm) REVERT: A 1193 LYS cc_start: 0.9567 (pptt) cc_final: 0.9329 (pttt) REVERT: A 1318 LEU cc_start: 0.8894 (mt) cc_final: 0.8565 (tt) REVERT: A 1330 ASP cc_start: 0.8490 (m-30) cc_final: 0.8274 (m-30) REVERT: B 54 GLU cc_start: 0.8619 (tp30) cc_final: 0.7851 (mp0) REVERT: B 536 VAL cc_start: 0.9142 (t) cc_final: 0.8844 (p) REVERT: C 43 ASP cc_start: 0.8858 (p0) cc_final: 0.8656 (p0) REVERT: C 87 MET cc_start: 0.9249 (mmm) cc_final: 0.8927 (mmt) REVERT: C 124 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7377 (t80) REVERT: C 180 ASN cc_start: 0.8875 (t0) cc_final: 0.8451 (p0) REVERT: E 29 THR cc_start: 0.6747 (OUTLIER) cc_final: 0.6336 (t) REVERT: E 72 MET cc_start: 0.8416 (tpt) cc_final: 0.8167 (tpt) REVERT: E 73 PHE cc_start: 0.8594 (t80) cc_final: 0.8010 (t80) REVERT: F 50 LYS cc_start: 0.8433 (tptp) cc_final: 0.8193 (tptp) REVERT: F 88 ASP cc_start: 0.7829 (t70) cc_final: 0.7240 (t0) REVERT: F 91 LEU cc_start: 0.9215 (tp) cc_final: 0.8911 (mt) REVERT: G 7 MET cc_start: 0.7974 (mmm) cc_final: 0.7726 (mmm) REVERT: G 82 ASP cc_start: 0.7586 (p0) cc_final: 0.7298 (p0) REVERT: G 90 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8601 (mtmm) REVERT: G 142 MET cc_start: 0.4944 (pmm) cc_final: 0.3753 (mmt) REVERT: G 185 THR cc_start: 0.9126 (m) cc_final: 0.8863 (p) REVERT: H 13 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8257 (mppt) REVERT: I 42 LYS cc_start: 0.8189 (tptm) cc_final: 0.7966 (tptm) REVERT: I 47 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7887 (ttmt) REVERT: I 91 MET cc_start: 0.2386 (tpt) cc_final: 0.1611 (tmm) REVERT: K 28 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7819 (mp0) REVERT: K 64 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8450 (tp30) REVERT: L 32 ASP cc_start: 0.7870 (p0) cc_final: 0.7627 (p0) REVERT: M 37 MET cc_start: 0.8791 (mpp) cc_final: 0.8466 (ptp) REVERT: M 60 MET cc_start: 0.8664 (ptm) cc_final: 0.8286 (ppp) REVERT: N 29 ARG cc_start: 0.7764 (mtp180) cc_final: 0.7379 (tpt90) REVERT: N 273 ASP cc_start: 0.8785 (t70) cc_final: 0.8542 (t0) REVERT: N 373 MET cc_start: 0.8071 (tmm) cc_final: 0.7779 (tmm) REVERT: N 380 LYS cc_start: 0.8508 (tptp) cc_final: 0.8193 (tptp) REVERT: O 133 MET cc_start: 0.7301 (mtm) cc_final: 0.6946 (ptt) REVERT: O 398 MET cc_start: 0.9199 (mmt) cc_final: 0.8923 (mmt) REVERT: O 419 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7922 (ppt90) REVERT: O 490 MET cc_start: 0.3419 (tmm) cc_final: 0.3083 (ppp) REVERT: P 203 MET cc_start: 0.8700 (pmm) cc_final: 0.8496 (tpt) REVERT: P 245 ASP cc_start: 0.8792 (t70) cc_final: 0.8505 (t70) REVERT: P 250 MET cc_start: 0.7722 (ttt) cc_final: 0.7367 (tpt) REVERT: P 295 ASP cc_start: 0.8348 (t70) cc_final: 0.7902 (t0) REVERT: Q 61 LYS cc_start: 0.9153 (ttpt) cc_final: 0.8539 (ptmt) REVERT: Q 92 MET cc_start: 0.2674 (mmt) cc_final: 0.2296 (mpp) REVERT: Q 103 TRP cc_start: 0.8624 (m-90) cc_final: 0.8385 (m100) outliers start: 82 outliers final: 46 residues processed: 650 average time/residue: 0.2649 time to fit residues: 275.4351 Evaluate side-chains 570 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 519 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 706 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 55 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 444 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 396 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 245 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 409 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A1010 GLN A1168 HIS A1239 HIS B 346 GLN B 405 HIS B 501 HIS B 823 ASN C 25 HIS E 168 ASN G 36 ASN G 98 HIS ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 HIS M 149 HIS N 325 GLN N 358 GLN N 378 HIS N 395 HIS ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.111215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.074265 restraints weight = 104104.288| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.73 r_work: 0.3120 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 40661 Z= 0.219 Angle : 1.092 50.588 54879 Z= 0.606 Chirality : 0.166 6.330 6147 Planarity : 0.004 0.081 7080 Dihedral : 3.824 48.407 5451 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 2.73 % Allowed : 15.16 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.11), residues: 4948 helix: -0.05 (0.12), residues: 1766 sheet: -0.21 (0.19), residues: 737 loop : -2.56 (0.10), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 128 TYR 0.017 0.001 TYR B1009 PHE 0.027 0.002 PHE P 176 TRP 0.023 0.002 TRP B 27 HIS 0.014 0.001 HIS N 397 Details of bonding type rmsd covalent geometry : bond 0.00574 (40639) covalent geometry : angle 0.99097 (54855) hydrogen bonds : bond 0.04229 ( 1488) hydrogen bonds : angle 4.68708 ( 4326) metal coordination : bond 0.00994 ( 22) metal coordination : angle 21.90807 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 566 time to evaluate : 1.565 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: 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: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8163 (mmp) cc_final: 0.7214 (mtt) REVERT: A 168 LYS cc_start: 0.8893 (pttt) cc_final: 0.8507 (tttm) REVERT: A 228 LYS cc_start: 0.9251 (mttt) cc_final: 0.9035 (mtmm) REVERT: A 353 ARG cc_start: 0.7488 (ptt90) cc_final: 0.7254 (ptt90) REVERT: A 429 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8081 (mtpp) REVERT: A 440 MET cc_start: 0.8787 (mmp) cc_final: 0.8120 (mtt) REVERT: A 465 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7601 (tp-100) REVERT: A 572 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8911 (pp) REVERT: A 968 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8413 (tm-30) REVERT: A 1004 ASP cc_start: 0.7030 (p0) cc_final: 0.6748 (p0) REVERT: A 1061 MET cc_start: 0.6888 (mpp) cc_final: 0.6639 (mpp) REVERT: A 1096 ASP cc_start: 0.8708 (m-30) cc_final: 0.8410 (t0) REVERT: A 1193 LYS cc_start: 0.9570 (pptt) cc_final: 0.9217 (pttt) REVERT: A 1322 GLU cc_start: 0.6971 (tp30) cc_final: 0.6764 (tp30) REVERT: A 1349 MET cc_start: 0.9018 (mmm) cc_final: 0.8735 (mmm) REVERT: B 114 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8124 (t) REVERT: B 870 MET cc_start: 0.8440 (tmm) cc_final: 0.8216 (tmm) REVERT: B 1037 GLU cc_start: 0.8476 (tp30) cc_final: 0.8140 (tp30) REVERT: C 124 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7430 (t80) REVERT: C 180 ASN cc_start: 0.8986 (t0) cc_final: 0.8591 (p0) REVERT: E 72 MET cc_start: 0.8449 (tpt) cc_final: 0.8136 (tpt) REVERT: E 73 PHE cc_start: 0.8692 (t80) cc_final: 0.8094 (t80) REVERT: E 110 MET cc_start: 0.6785 (tpp) cc_final: 0.6150 (tpt) REVERT: F 50 LYS cc_start: 0.8529 (tptp) cc_final: 0.8277 (tptp) REVERT: F 88 ASP cc_start: 0.8047 (t70) cc_final: 0.7484 (t0) REVERT: F 91 LEU cc_start: 0.9251 (tp) cc_final: 0.8970 (mt) REVERT: F 100 ARG cc_start: 0.8727 (mtp85) cc_final: 0.8508 (mtp180) REVERT: G 82 ASP cc_start: 0.7658 (p0) cc_final: 0.7384 (p0) REVERT: G 142 MET cc_start: 0.5090 (pmm) cc_final: 0.3999 (mmt) REVERT: G 185 THR cc_start: 0.9170 (m) cc_final: 0.8908 (p) REVERT: H 13 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8290 (mppt) REVERT: I 24 SER cc_start: 0.8466 (t) cc_final: 0.8235 (p) REVERT: I 36 ARG cc_start: 0.9174 (ppt170) cc_final: 0.8902 (ppt170) REVERT: I 37 LYS cc_start: 0.6784 (tppt) cc_final: 0.6519 (tppt) REVERT: I 42 LYS cc_start: 0.8247 (tptm) cc_final: 0.8014 (tptm) REVERT: I 47 LYS cc_start: 0.8237 (ttmt) cc_final: 0.8014 (ttmt) REVERT: I 91 MET cc_start: 0.2668 (tpt) cc_final: 0.1886 (tmm) REVERT: K 24 LYS cc_start: 0.6695 (tmtt) cc_final: 0.6131 (tmtt) REVERT: K 28 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7672 (mp0) REVERT: K 64 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8553 (tp30) REVERT: K 123 ASP cc_start: 0.8947 (m-30) cc_final: 0.8647 (m-30) REVERT: M 37 MET cc_start: 0.8769 (mpp) cc_final: 0.8549 (ptp) REVERT: M 60 MET cc_start: 0.8753 (ptm) cc_final: 0.8247 (ppp) REVERT: N 273 ASP cc_start: 0.8856 (t70) cc_final: 0.8635 (t0) REVERT: N 373 MET cc_start: 0.8105 (tmm) cc_final: 0.7889 (tmm) REVERT: N 380 LYS cc_start: 0.8446 (tptp) cc_final: 0.8242 (tptp) REVERT: N 388 ASP cc_start: 0.9087 (p0) cc_final: 0.8708 (p0) REVERT: O 85 MET cc_start: 0.9036 (ttm) cc_final: 0.8360 (ttm) REVERT: O 259 MET cc_start: 0.7892 (ppp) cc_final: 0.7512 (ppp) REVERT: P 183 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8967 (mt0) REVERT: P 203 MET cc_start: 0.8778 (pmm) cc_final: 0.8457 (tpt) REVERT: P 245 ASP cc_start: 0.8877 (t70) cc_final: 0.8505 (t0) REVERT: P 250 MET cc_start: 0.7676 (ttt) cc_final: 0.7352 (tpt) REVERT: P 295 ASP cc_start: 0.8425 (t70) cc_final: 0.7857 (t0) REVERT: Q 61 LYS cc_start: 0.9247 (ttpt) cc_final: 0.8928 (ptmt) REVERT: Q 198 ASP cc_start: 0.7576 (m-30) cc_final: 0.7238 (m-30) outliers start: 121 outliers final: 63 residues processed: 648 average time/residue: 0.2574 time to fit residues: 268.2685 Evaluate side-chains 572 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 504 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 325 GLN Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 43 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 12 optimal weight: 9.9990 chunk 361 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 393 optimal weight: 3.9990 chunk 387 optimal weight: 1.9990 chunk 281 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 465 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 79 ASN B 524 ASN B 678 ASN B 829 ASN D 41 ASN E 71 GLN E 129 GLN E 168 ASN G 98 HIS H 126 GLN I 18 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS K 38 HIS M 707 GLN N 358 GLN ** P 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.106514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.068203 restraints weight = 102685.544| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.95 r_work: 0.2973 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.236 40661 Z= 0.304 Angle : 1.147 50.633 54879 Z= 0.633 Chirality : 0.167 6.325 6147 Planarity : 0.005 0.062 7080 Dihedral : 4.268 47.585 5451 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 3.73 % Allowed : 17.10 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.11), residues: 4948 helix: 0.19 (0.12), residues: 1769 sheet: -0.26 (0.18), residues: 761 loop : -2.39 (0.11), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 428 TYR 0.044 0.002 TYR E 90 PHE 0.027 0.002 PHE P 176 TRP 0.023 0.002 TRP Q 103 HIS 0.011 0.001 HIS B 676 Details of bonding type rmsd covalent geometry : bond 0.00761 (40639) covalent geometry : angle 1.05116 (54855) hydrogen bonds : bond 0.04942 ( 1488) hydrogen bonds : angle 4.77086 ( 4326) metal coordination : bond 0.00804 ( 22) metal coordination : angle 22.03034 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 534 time to evaluate : 1.517 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: 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 107 MET cc_start: 0.8130 (mmp) cc_final: 0.7301 (mtt) REVERT: A 197 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7271 (m-80) REVERT: A 228 LYS cc_start: 0.9298 (mttt) cc_final: 0.9091 (mtmm) REVERT: A 324 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7643 (mm-30) REVERT: A 353 ARG cc_start: 0.7808 (ptt90) cc_final: 0.7464 (ptt90) REVERT: A 428 MET cc_start: 0.8425 (tpp) cc_final: 0.7579 (ppp) REVERT: A 440 MET cc_start: 0.8787 (mmp) cc_final: 0.8216 (mtt) REVERT: A 460 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8738 (m) REVERT: A 572 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8801 (pp) REVERT: A 588 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8701 (pt) REVERT: A 678 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8721 (t0) REVERT: A 968 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 1004 ASP cc_start: 0.7048 (p0) cc_final: 0.6744 (p0) REVERT: A 1048 MET cc_start: 0.7944 (mtt) cc_final: 0.7663 (mtp) REVERT: A 1061 MET cc_start: 0.7128 (mpp) cc_final: 0.6873 (mpp) REVERT: A 1096 ASP cc_start: 0.8913 (m-30) cc_final: 0.8620 (t0) REVERT: A 1193 LYS cc_start: 0.9602 (pptt) cc_final: 0.9322 (pttm) REVERT: A 1322 GLU cc_start: 0.6987 (tp30) cc_final: 0.6784 (tp30) REVERT: A 1349 MET cc_start: 0.9092 (mmm) cc_final: 0.8755 (mmm) REVERT: B 43 HIS cc_start: 0.8682 (OUTLIER) cc_final: 0.7823 (t70) REVERT: B 114 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8628 (t) REVERT: B 192 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 292 ARG cc_start: 0.8910 (ptt90) cc_final: 0.8328 (pmt-80) REVERT: B 354 ARG cc_start: 0.8437 (mtm110) cc_final: 0.8055 (mtm110) REVERT: B 499 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8673 (mtm) REVERT: B 508 ASP cc_start: 0.9075 (p0) cc_final: 0.8696 (m-30) REVERT: C 180 ASN cc_start: 0.9049 (t0) cc_final: 0.8711 (p0) REVERT: D 2 GLU cc_start: 0.6570 (tm-30) cc_final: 0.6322 (tm-30) REVERT: E 29 THR cc_start: 0.7166 (OUTLIER) cc_final: 0.6725 (t) REVERT: E 72 MET cc_start: 0.8321 (tpt) cc_final: 0.7994 (tpt) REVERT: E 73 PHE cc_start: 0.8715 (t80) cc_final: 0.8105 (t80) REVERT: E 110 MET cc_start: 0.7248 (tpp) cc_final: 0.6373 (tpt) REVERT: F 50 LYS cc_start: 0.8626 (tptp) cc_final: 0.8376 (tptp) REVERT: F 82 GLU cc_start: 0.8590 (pm20) cc_final: 0.8292 (pm20) REVERT: F 84 GLU cc_start: 0.8034 (pm20) cc_final: 0.7750 (mp0) REVERT: F 88 ASP cc_start: 0.8434 (t70) cc_final: 0.7853 (t0) REVERT: F 91 LEU cc_start: 0.9388 (tp) cc_final: 0.9091 (mt) REVERT: F 100 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8533 (mtp180) REVERT: G 1 MET cc_start: 0.8919 (pmm) cc_final: 0.8557 (pmm) REVERT: G 7 MET cc_start: 0.8013 (mmm) cc_final: 0.7459 (mmm) REVERT: G 90 LYS cc_start: 0.8835 (mmmt) cc_final: 0.8626 (mtmm) REVERT: G 151 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8206 (mtp85) REVERT: H 13 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8307 (mppt) REVERT: H 15 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8561 (mt) REVERT: H 92 MET cc_start: 0.8788 (mmm) cc_final: 0.8437 (mmm) REVERT: I 24 SER cc_start: 0.8590 (t) cc_final: 0.8287 (p) REVERT: I 91 MET cc_start: 0.2828 (tpt) cc_final: 0.2281 (tmm) REVERT: I 104 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.7237 (m90) REVERT: K 28 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7658 (mp0) REVERT: K 64 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8603 (tp30) REVERT: K 112 ASP cc_start: 0.8616 (m-30) cc_final: 0.8371 (m-30) REVERT: M 60 MET cc_start: 0.8794 (ptm) cc_final: 0.8223 (ppp) REVERT: M 220 HIS cc_start: 0.8916 (m-70) cc_final: 0.8703 (m90) REVERT: M 707 GLN cc_start: 0.4354 (OUTLIER) cc_final: 0.3631 (mm-40) REVERT: N 262 LYS cc_start: 0.9064 (tppt) cc_final: 0.8740 (tppt) REVERT: N 265 GLU cc_start: 0.8009 (tp30) cc_final: 0.7802 (tp30) REVERT: N 373 MET cc_start: 0.8087 (tmm) cc_final: 0.7852 (tmm) REVERT: N 380 LYS cc_start: 0.8406 (tptp) cc_final: 0.8028 (tptp) REVERT: N 388 ASP cc_start: 0.9181 (p0) cc_final: 0.8962 (p0) REVERT: O 85 MET cc_start: 0.9137 (ttm) cc_final: 0.8519 (ttm) REVERT: O 193 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7457 (mm) REVERT: O 259 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7316 (ppp) REVERT: O 398 MET cc_start: 0.9204 (mmt) cc_final: 0.8977 (mmt) REVERT: O 490 MET cc_start: 0.3321 (ppp) cc_final: 0.2923 (ppp) REVERT: P 203 MET cc_start: 0.8906 (pmm) cc_final: 0.8431 (tpt) REVERT: P 210 PHE cc_start: 0.7327 (p90) cc_final: 0.7080 (p90) REVERT: P 245 ASP cc_start: 0.8767 (t70) cc_final: 0.8553 (t70) REVERT: P 247 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7345 (pttm) REVERT: P 250 MET cc_start: 0.7768 (ttt) cc_final: 0.7425 (tpt) REVERT: Q 103 TRP cc_start: 0.8957 (m-90) cc_final: 0.8678 (m-90) outliers start: 165 outliers final: 85 residues processed: 649 average time/residue: 0.2541 time to fit residues: 267.5277 Evaluate side-chains 588 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 488 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 707 GLN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 43 TYR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 197 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 210 optimal weight: 0.0270 chunk 22 optimal weight: 0.9980 chunk 421 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 430 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 149 optimal weight: 0.4980 chunk 93 optimal weight: 0.1980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 423 ASN B 524 ASN B 678 ASN C 213 HIS ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS I 18 GLN I 104 HIS K 81 ASN ** P 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.109702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.071824 restraints weight = 102745.197| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.02 r_work: 0.3047 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 40661 Z= 0.175 Angle : 1.090 50.500 54879 Z= 0.602 Chirality : 0.166 6.307 6147 Planarity : 0.004 0.062 7080 Dihedral : 4.047 49.126 5451 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.01 % Favored : 94.97 % Rotamer: Outliers : 2.80 % Allowed : 18.43 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.11), residues: 4948 helix: 0.48 (0.13), residues: 1764 sheet: -0.14 (0.19), residues: 750 loop : -2.23 (0.11), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 189 TYR 0.040 0.001 TYR E 90 PHE 0.031 0.001 PHE M 195 TRP 0.019 0.001 TRP B 73 HIS 0.024 0.001 HIS I 104 Details of bonding type rmsd covalent geometry : bond 0.00478 (40639) covalent geometry : angle 0.99017 (54855) hydrogen bonds : bond 0.03573 ( 1488) hydrogen bonds : angle 4.45179 ( 4326) metal coordination : bond 0.00563 ( 22) metal coordination : angle 21.83684 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 530 time to evaluate : 1.656 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8090 (mmp) cc_final: 0.7277 (mtt) REVERT: A 144 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8552 (tppt) REVERT: A 168 LYS cc_start: 0.8930 (pttt) cc_final: 0.8518 (tttm) REVERT: A 197 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: A 353 ARG cc_start: 0.7778 (ptt90) cc_final: 0.7427 (ptt90) REVERT: A 428 MET cc_start: 0.8421 (tpp) cc_final: 0.7483 (ppp) REVERT: A 440 MET cc_start: 0.8780 (mmp) cc_final: 0.8238 (mtt) REVERT: A 460 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8643 (m) REVERT: A 572 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8731 (pp) REVERT: A 588 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8696 (pt) REVERT: A 678 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8586 (t0) REVERT: A 968 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 1004 ASP cc_start: 0.6945 (p0) cc_final: 0.6707 (p0) REVERT: A 1048 MET cc_start: 0.7818 (mtt) cc_final: 0.7549 (mtp) REVERT: A 1193 LYS cc_start: 0.9623 (pptt) cc_final: 0.9334 (pttt) REVERT: B 114 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8538 (t) REVERT: B 292 ARG cc_start: 0.8923 (ptt90) cc_final: 0.8376 (pmt-80) REVERT: B 354 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8236 (mtm-85) REVERT: B 427 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.7336 (pptt) REVERT: B 508 ASP cc_start: 0.8992 (p0) cc_final: 0.8785 (m-30) REVERT: C 180 ASN cc_start: 0.9058 (t0) cc_final: 0.8688 (p0) REVERT: D 100 MET cc_start: 0.6297 (mmt) cc_final: 0.5975 (mmm) REVERT: E 29 THR cc_start: 0.7251 (OUTLIER) cc_final: 0.6818 (t) REVERT: E 72 MET cc_start: 0.8422 (tpt) cc_final: 0.8016 (tpt) REVERT: E 73 PHE cc_start: 0.8736 (t80) cc_final: 0.8083 (t80) REVERT: E 110 MET cc_start: 0.7132 (tpp) cc_final: 0.6272 (tpt) REVERT: F 82 GLU cc_start: 0.8539 (pm20) cc_final: 0.8192 (pm20) REVERT: F 84 GLU cc_start: 0.7897 (pm20) cc_final: 0.7676 (mp0) REVERT: F 86 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: F 88 ASP cc_start: 0.8320 (t70) cc_final: 0.7713 (t0) REVERT: F 91 LEU cc_start: 0.9339 (tp) cc_final: 0.9078 (mt) REVERT: F 100 ARG cc_start: 0.8806 (mtp85) cc_final: 0.8514 (mtp180) REVERT: G 1 MET cc_start: 0.8797 (pmm) cc_final: 0.8421 (pmm) REVERT: G 7 MET cc_start: 0.8060 (mmm) cc_final: 0.7427 (mmm) REVERT: G 32 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8468 (ttmm) REVERT: G 90 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8701 (mtmm) REVERT: G 185 THR cc_start: 0.9190 (m) cc_final: 0.8926 (p) REVERT: H 13 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8308 (mppt) REVERT: H 92 MET cc_start: 0.8565 (mmm) cc_final: 0.8292 (mmm) REVERT: I 42 LYS cc_start: 0.8388 (tptp) cc_final: 0.8125 (tptp) REVERT: I 91 MET cc_start: 0.2868 (tpt) cc_final: 0.2565 (tmm) REVERT: I 104 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.7211 (m90) REVERT: J 33 ASP cc_start: 0.8644 (t0) cc_final: 0.8221 (t0) REVERT: J 36 ASP cc_start: 0.9179 (t0) cc_final: 0.8974 (p0) REVERT: K 28 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7491 (mp0) REVERT: K 47 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8831 (mm-30) REVERT: K 64 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8616 (tp30) REVERT: K 66 GLU cc_start: 0.8850 (tt0) cc_final: 0.8318 (tm-30) REVERT: K 124 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7424 (tm-30) REVERT: K 128 ARG cc_start: 0.7235 (ttp80) cc_final: 0.6544 (ttm110) REVERT: L 25 GLU cc_start: 0.8619 (pm20) cc_final: 0.8351 (pm20) REVERT: L 37 ARG cc_start: 0.8563 (ptt90) cc_final: 0.8312 (ptt90) REVERT: M 37 MET cc_start: 0.8681 (ptp) cc_final: 0.8109 (ptp) REVERT: M 60 MET cc_start: 0.8753 (ptm) cc_final: 0.8088 (ppp) REVERT: M 220 HIS cc_start: 0.8982 (m-70) cc_final: 0.8678 (m90) REVERT: M 248 MET cc_start: 0.8635 (ptp) cc_final: 0.8183 (ptp) REVERT: N 247 LYS cc_start: 0.8781 (tppt) cc_final: 0.8263 (tptp) REVERT: N 262 LYS cc_start: 0.9008 (tppt) cc_final: 0.8684 (tppt) REVERT: N 265 GLU cc_start: 0.8064 (tp30) cc_final: 0.7838 (tp30) REVERT: N 358 GLN cc_start: 0.8715 (mt0) cc_final: 0.8448 (mm-40) REVERT: N 373 MET cc_start: 0.8092 (tmm) cc_final: 0.7851 (tmm) REVERT: N 380 LYS cc_start: 0.8282 (tptp) cc_final: 0.7876 (tptp) REVERT: O 85 MET cc_start: 0.9097 (ttm) cc_final: 0.8511 (ttm) REVERT: O 133 MET cc_start: 0.7208 (ptp) cc_final: 0.6992 (ptp) REVERT: O 259 MET cc_start: 0.7804 (ppp) cc_final: 0.7263 (ppp) REVERT: O 385 MET cc_start: 0.8171 (ttm) cc_final: 0.7936 (ttm) REVERT: O 490 MET cc_start: 0.3211 (ppp) cc_final: 0.2718 (ppp) REVERT: P 203 MET cc_start: 0.8882 (pmm) cc_final: 0.8425 (tpt) REVERT: P 245 ASP cc_start: 0.8738 (t70) cc_final: 0.8514 (t70) REVERT: P 247 LYS cc_start: 0.8060 (mtmm) cc_final: 0.7354 (pttm) REVERT: P 250 MET cc_start: 0.7695 (ttt) cc_final: 0.7392 (tpt) REVERT: Q 57 MET cc_start: 0.9002 (mtt) cc_final: 0.8801 (mmm) outliers start: 124 outliers final: 69 residues processed: 611 average time/residue: 0.2465 time to fit residues: 246.2476 Evaluate side-chains 562 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 481 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 197 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 128 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 283 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 chunk 12 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 389 optimal weight: 0.9980 chunk 361 optimal weight: 5.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 58 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN B 423 ASN B 678 ASN C 213 HIS ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS K 129 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.108089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.069941 restraints weight = 103646.951| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 4.00 r_work: 0.3002 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 40661 Z= 0.204 Angle : 1.100 50.524 54879 Z= 0.606 Chirality : 0.166 6.305 6147 Planarity : 0.004 0.100 7080 Dihedral : 4.038 48.093 5451 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.91 % Allowed : 19.67 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.11), residues: 4948 helix: 0.59 (0.13), residues: 1770 sheet: -0.11 (0.19), residues: 736 loop : -2.18 (0.11), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 256 TYR 0.039 0.001 TYR E 90 PHE 0.029 0.001 PHE P 185 TRP 0.031 0.002 TRP P 217 HIS 0.012 0.001 HIS I 104 Details of bonding type rmsd covalent geometry : bond 0.00546 (40639) covalent geometry : angle 0.99745 (54855) hydrogen bonds : bond 0.03819 ( 1488) hydrogen bonds : angle 4.40807 ( 4326) metal coordination : bond 0.00568 ( 22) metal coordination : angle 22.24794 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 500 time to evaluate : 1.600 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: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9076 (tt) cc_final: 0.8620 (mp) REVERT: A 107 MET cc_start: 0.8137 (mmp) cc_final: 0.7286 (mtt) REVERT: A 144 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8594 (tppt) REVERT: A 197 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: A 353 ARG cc_start: 0.7878 (ptt90) cc_final: 0.7503 (ptt90) REVERT: A 428 MET cc_start: 0.8491 (tpp) cc_final: 0.7631 (ppp) REVERT: A 440 MET cc_start: 0.8797 (mmp) cc_final: 0.8277 (mtt) REVERT: A 460 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8702 (m) REVERT: A 572 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8779 (pp) REVERT: A 678 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8592 (t0) REVERT: A 736 LEU cc_start: 0.9152 (mp) cc_final: 0.8944 (pp) REVERT: A 814 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8018 (mt-10) REVERT: A 968 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 1004 ASP cc_start: 0.6918 (p0) cc_final: 0.6617 (p0) REVERT: A 1048 MET cc_start: 0.7891 (mtt) cc_final: 0.7661 (mtp) REVERT: A 1096 ASP cc_start: 0.8879 (m-30) cc_final: 0.8557 (t0) REVERT: A 1193 LYS cc_start: 0.9638 (pptt) cc_final: 0.9351 (pttt) REVERT: B 43 HIS cc_start: 0.8460 (OUTLIER) cc_final: 0.7188 (t-90) REVERT: B 114 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8564 (t) REVERT: B 292 ARG cc_start: 0.8941 (ptt90) cc_final: 0.8391 (pmt-80) REVERT: B 324 LYS cc_start: 0.8953 (pptt) cc_final: 0.8633 (pptt) REVERT: B 354 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8183 (mtm-85) REVERT: B 406 MET cc_start: 0.8269 (mtt) cc_final: 0.7871 (mtm) REVERT: B 429 PHE cc_start: 0.8644 (m-80) cc_final: 0.8388 (m-80) REVERT: B 508 ASP cc_start: 0.9035 (p0) cc_final: 0.8813 (m-30) REVERT: B 536 VAL cc_start: 0.9119 (t) cc_final: 0.8793 (p) REVERT: B 791 MET cc_start: 0.8819 (mmt) cc_final: 0.8568 (mmt) REVERT: C 180 ASN cc_start: 0.9025 (t0) cc_final: 0.8675 (p0) REVERT: D 1 MET cc_start: 0.8640 (ttm) cc_final: 0.8299 (ttm) REVERT: D 2 GLU cc_start: 0.8085 (mp0) cc_final: 0.7529 (tm-30) REVERT: D 100 MET cc_start: 0.6306 (mmt) cc_final: 0.5954 (mmm) REVERT: E 29 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.6878 (t) REVERT: E 72 MET cc_start: 0.8273 (tpt) cc_final: 0.7937 (tpt) REVERT: E 73 PHE cc_start: 0.8775 (t80) cc_final: 0.8130 (t80) REVERT: E 110 MET cc_start: 0.7233 (tpp) cc_final: 0.6365 (tpt) REVERT: F 50 LYS cc_start: 0.8533 (tptp) cc_final: 0.8332 (tptp) REVERT: F 82 GLU cc_start: 0.8530 (pm20) cc_final: 0.7780 (pm20) REVERT: F 88 ASP cc_start: 0.8369 (t70) cc_final: 0.7753 (t0) REVERT: F 91 LEU cc_start: 0.9397 (tp) cc_final: 0.9101 (mt) REVERT: F 100 ARG cc_start: 0.8826 (mtp85) cc_final: 0.8558 (mtp180) REVERT: G 1 MET cc_start: 0.8825 (pmm) cc_final: 0.8395 (pmm) REVERT: G 41 ASN cc_start: 0.8762 (p0) cc_final: 0.8539 (p0) REVERT: G 151 ARG cc_start: 0.8577 (mtp180) cc_final: 0.8134 (mtp85) REVERT: G 185 THR cc_start: 0.9210 (m) cc_final: 0.8938 (p) REVERT: H 13 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8330 (mppt) REVERT: H 15 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8491 (mt) REVERT: I 36 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8708 (ppt170) REVERT: I 41 ARG cc_start: 0.8906 (ttm170) cc_final: 0.8597 (tpp80) REVERT: I 91 MET cc_start: 0.3031 (tpt) cc_final: 0.2785 (tmm) REVERT: I 104 HIS cc_start: 0.7225 (OUTLIER) cc_final: 0.6994 (m170) REVERT: J 33 ASP cc_start: 0.8724 (t0) cc_final: 0.8299 (t0) REVERT: J 36 ASP cc_start: 0.9184 (t0) cc_final: 0.8930 (p0) REVERT: K 28 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7516 (mp0) REVERT: K 64 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8643 (tp30) REVERT: K 66 GLU cc_start: 0.8896 (tt0) cc_final: 0.8377 (tm-30) REVERT: K 112 ASP cc_start: 0.8508 (m-30) cc_final: 0.8224 (m-30) REVERT: K 124 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7717 (tm-30) REVERT: K 128 ARG cc_start: 0.6859 (ttp80) cc_final: 0.6590 (ttp80) REVERT: L 37 ARG cc_start: 0.8624 (ptt90) cc_final: 0.8388 (ptt90) REVERT: M 37 MET cc_start: 0.8745 (ptp) cc_final: 0.8151 (ptp) REVERT: M 60 MET cc_start: 0.8769 (ptm) cc_final: 0.8113 (ppp) REVERT: M 220 HIS cc_start: 0.8982 (m-70) cc_final: 0.8749 (m-70) REVERT: N 262 LYS cc_start: 0.9045 (tppt) cc_final: 0.8729 (tppt) REVERT: N 265 GLU cc_start: 0.8098 (tp30) cc_final: 0.7865 (tp30) REVERT: N 373 MET cc_start: 0.8104 (tmm) cc_final: 0.7867 (tmm) REVERT: N 380 LYS cc_start: 0.8322 (tptp) cc_final: 0.7913 (tptp) REVERT: O 85 MET cc_start: 0.9123 (ttm) cc_final: 0.8563 (ttm) REVERT: O 259 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.6269 (pmm) REVERT: O 385 MET cc_start: 0.8214 (ttm) cc_final: 0.7928 (ttm) REVERT: O 398 MET cc_start: 0.9161 (mmt) cc_final: 0.8941 (mmt) REVERT: O 490 MET cc_start: 0.3273 (ppp) cc_final: 0.2816 (ppp) REVERT: P 203 MET cc_start: 0.8938 (pmm) cc_final: 0.8421 (tpt) REVERT: P 210 PHE cc_start: 0.7387 (p90) cc_final: 0.7111 (p90) REVERT: P 232 MET cc_start: 0.4831 (mmp) cc_final: 0.3507 (tmm) REVERT: P 245 ASP cc_start: 0.8735 (t70) cc_final: 0.8526 (t0) REVERT: P 247 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7311 (pttm) REVERT: P 250 MET cc_start: 0.7664 (ttt) cc_final: 0.7431 (ttt) REVERT: P 270 TYR cc_start: 0.5579 (m-80) cc_final: 0.4467 (m-80) REVERT: Q 27 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6218 (mt) REVERT: Q 57 MET cc_start: 0.9065 (mtt) cc_final: 0.8635 (mmt) outliers start: 129 outliers final: 87 residues processed: 587 average time/residue: 0.2488 time to fit residues: 239.9599 Evaluate side-chains 577 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 476 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 197 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 47 optimal weight: 1.9990 chunk 202 optimal weight: 0.1980 chunk 100 optimal weight: 0.9990 chunk 93 optimal weight: 0.1980 chunk 156 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 286 optimal weight: 20.0000 chunk 104 optimal weight: 0.6980 chunk 371 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN B 423 ASN B1100 HIS C 213 HIS ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.109480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071051 restraints weight = 103748.167| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.81 r_work: 0.3045 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.245 40661 Z= 0.173 Angle : 1.091 50.511 54879 Z= 0.600 Chirality : 0.166 6.301 6147 Planarity : 0.004 0.067 7080 Dihedral : 3.967 47.871 5451 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.03 % Favored : 94.95 % Rotamer: Outliers : 2.82 % Allowed : 20.37 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.12), residues: 4948 helix: 0.67 (0.13), residues: 1778 sheet: -0.02 (0.19), residues: 744 loop : -2.10 (0.11), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 206 TYR 0.037 0.001 TYR E 90 PHE 0.025 0.001 PHE P 185 TRP 0.030 0.001 TRP P 217 HIS 0.017 0.001 HIS I 104 Details of bonding type rmsd covalent geometry : bond 0.00477 (40639) covalent geometry : angle 0.98796 (54855) hydrogen bonds : bond 0.03322 ( 1488) hydrogen bonds : angle 4.27637 ( 4326) metal coordination : bond 0.00487 ( 22) metal coordination : angle 22.13593 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 510 time to evaluate : 1.586 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: A 56 LEU cc_start: 0.9073 (tt) cc_final: 0.8609 (mp) REVERT: A 107 MET cc_start: 0.8285 (mmp) cc_final: 0.7549 (mtt) REVERT: A 144 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8498 (tppt) REVERT: A 148 ASP cc_start: 0.8524 (p0) cc_final: 0.8300 (m-30) REVERT: A 197 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: A 353 ARG cc_start: 0.7827 (ptt90) cc_final: 0.7481 (ptt90) REVERT: A 428 MET cc_start: 0.8454 (tpp) cc_final: 0.7645 (ppp) REVERT: A 440 MET cc_start: 0.8781 (mmp) cc_final: 0.8275 (mtt) REVERT: A 572 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8695 (pp) REVERT: A 678 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8533 (t0) REVERT: A 814 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8010 (mt-10) REVERT: A 912 MET cc_start: 0.8472 (mtm) cc_final: 0.8254 (mtt) REVERT: A 968 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 1004 ASP cc_start: 0.6899 (p0) cc_final: 0.6651 (p0) REVERT: A 1048 MET cc_start: 0.7734 (mtt) cc_final: 0.7522 (mtp) REVERT: A 1084 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8733 (mt) REVERT: A 1096 ASP cc_start: 0.8842 (m-30) cc_final: 0.8507 (t0) REVERT: A 1193 LYS cc_start: 0.9643 (pptt) cc_final: 0.9318 (pttm) REVERT: A 1330 ASP cc_start: 0.8596 (m-30) cc_final: 0.8291 (p0) REVERT: B 43 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.7168 (t-90) REVERT: B 73 TRP cc_start: 0.7778 (t60) cc_final: 0.7522 (t60) REVERT: B 292 ARG cc_start: 0.8866 (ptt90) cc_final: 0.8342 (pmt-80) REVERT: B 324 LYS cc_start: 0.8911 (pptt) cc_final: 0.8580 (pptt) REVERT: B 354 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8183 (mtm-85) REVERT: B 536 VAL cc_start: 0.9157 (t) cc_final: 0.8857 (p) REVERT: C 55 HIS cc_start: 0.8450 (t-90) cc_final: 0.8125 (t70) REVERT: C 180 ASN cc_start: 0.9025 (t0) cc_final: 0.8690 (p0) REVERT: D 100 MET cc_start: 0.6288 (mmt) cc_final: 0.5948 (mmm) REVERT: E 29 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7173 (t) REVERT: E 72 MET cc_start: 0.8238 (tpt) cc_final: 0.7907 (tpt) REVERT: E 73 PHE cc_start: 0.8813 (t80) cc_final: 0.8169 (t80) REVERT: E 110 MET cc_start: 0.7303 (tpp) cc_final: 0.6438 (tpt) REVERT: F 50 LYS cc_start: 0.8522 (tptp) cc_final: 0.8280 (tptp) REVERT: F 82 GLU cc_start: 0.8515 (pm20) cc_final: 0.7987 (pm20) REVERT: F 84 GLU cc_start: 0.7754 (mp0) cc_final: 0.7197 (pp20) REVERT: F 88 ASP cc_start: 0.8305 (t70) cc_final: 0.7673 (t0) REVERT: F 91 LEU cc_start: 0.9377 (tp) cc_final: 0.9080 (mt) REVERT: F 100 ARG cc_start: 0.8786 (mtp85) cc_final: 0.8558 (mtp180) REVERT: G 1 MET cc_start: 0.8794 (pmm) cc_final: 0.8375 (pmm) REVERT: G 7 MET cc_start: 0.8183 (mmm) cc_final: 0.7527 (mmm) REVERT: G 41 ASN cc_start: 0.8753 (p0) cc_final: 0.8480 (p0) REVERT: G 90 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8369 (ptpp) REVERT: G 151 ARG cc_start: 0.8613 (mtp180) cc_final: 0.8160 (mtp85) REVERT: G 185 THR cc_start: 0.9190 (m) cc_final: 0.8930 (p) REVERT: H 13 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8341 (mppt) REVERT: I 36 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8761 (ppt170) REVERT: I 41 ARG cc_start: 0.8935 (ttm170) cc_final: 0.8594 (tpp80) REVERT: I 42 LYS cc_start: 0.8209 (tptp) cc_final: 0.7869 (tptp) REVERT: I 91 MET cc_start: 0.3088 (tpt) cc_final: 0.2876 (tmm) REVERT: I 104 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.7015 (m170) REVERT: J 33 ASP cc_start: 0.8685 (t0) cc_final: 0.8221 (t0) REVERT: J 36 ASP cc_start: 0.9152 (t0) cc_final: 0.8943 (p0) REVERT: K 28 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7487 (mp0) REVERT: K 47 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8824 (mm-30) REVERT: K 64 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8628 (tp30) REVERT: K 66 GLU cc_start: 0.8827 (tt0) cc_final: 0.8328 (tm-30) REVERT: K 112 ASP cc_start: 0.8432 (m-30) cc_final: 0.8164 (m-30) REVERT: K 128 ARG cc_start: 0.6792 (ttp80) cc_final: 0.6394 (ttp80) REVERT: L 37 ARG cc_start: 0.8641 (ptt90) cc_final: 0.8418 (ptt90) REVERT: M 37 MET cc_start: 0.8733 (ptp) cc_final: 0.8071 (ptp) REVERT: M 60 MET cc_start: 0.8742 (ptm) cc_final: 0.8098 (ppp) REVERT: M 248 MET cc_start: 0.8590 (ptp) cc_final: 0.8111 (ptp) REVERT: N 247 LYS cc_start: 0.8845 (tppt) cc_final: 0.8407 (tptp) REVERT: N 262 LYS cc_start: 0.9016 (tppt) cc_final: 0.8719 (tppt) REVERT: N 265 GLU cc_start: 0.8081 (tp30) cc_final: 0.7819 (tp30) REVERT: N 347 ASP cc_start: 0.8492 (p0) cc_final: 0.8145 (t0) REVERT: N 358 GLN cc_start: 0.9175 (mt0) cc_final: 0.8862 (mt0) REVERT: N 373 MET cc_start: 0.8103 (tmm) cc_final: 0.7862 (tmm) REVERT: N 380 LYS cc_start: 0.8358 (tptp) cc_final: 0.7961 (tptp) REVERT: O 85 MET cc_start: 0.9095 (ttm) cc_final: 0.8517 (ttm) REVERT: O 259 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7396 (ppp) REVERT: O 385 MET cc_start: 0.8068 (ttm) cc_final: 0.7766 (ttm) REVERT: O 490 MET cc_start: 0.3259 (ppp) cc_final: 0.2811 (ppp) REVERT: P 210 PHE cc_start: 0.7278 (p90) cc_final: 0.7018 (p90) REVERT: P 218 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8335 (mmtt) REVERT: P 232 MET cc_start: 0.4525 (mmp) cc_final: 0.4120 (tmm) REVERT: P 247 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7331 (pttm) REVERT: P 250 MET cc_start: 0.7671 (ttt) cc_final: 0.7442 (ttt) REVERT: P 270 TYR cc_start: 0.5469 (m-80) cc_final: 0.4257 (m-80) REVERT: Q 27 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5360 (mm) REVERT: Q 57 MET cc_start: 0.9098 (mtt) cc_final: 0.8717 (mmt) REVERT: Q 92 MET cc_start: 0.3603 (mpp) cc_final: 0.3173 (mpp) outliers start: 125 outliers final: 87 residues processed: 598 average time/residue: 0.2460 time to fit residues: 240.8519 Evaluate side-chains 572 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 473 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 197 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 268 optimal weight: 3.9990 chunk 470 optimal weight: 0.6980 chunk 479 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 383 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 348 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN B 423 ASN C 213 HIS D 40 GLN D 89 HIS ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS N 278 GLN O 507 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.107899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069301 restraints weight = 103512.235| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.77 r_work: 0.2995 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 40661 Z= 0.208 Angle : 1.104 50.504 54879 Z= 0.608 Chirality : 0.166 6.316 6147 Planarity : 0.004 0.054 7080 Dihedral : 4.016 47.034 5451 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.89 % Allowed : 20.60 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.12), residues: 4948 helix: 0.72 (0.13), residues: 1770 sheet: -0.01 (0.18), residues: 780 loop : -2.07 (0.11), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 99 TYR 0.036 0.001 TYR E 90 PHE 0.029 0.001 PHE P 185 TRP 0.022 0.001 TRP P 217 HIS 0.016 0.001 HIS I 104 Details of bonding type rmsd covalent geometry : bond 0.00554 (40639) covalent geometry : angle 1.00339 (54855) hydrogen bonds : bond 0.03759 ( 1488) hydrogen bonds : angle 4.30685 ( 4326) metal coordination : bond 0.00555 ( 22) metal coordination : angle 22.08289 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 481 time to evaluate : 1.615 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7812 (pttp) REVERT: A 56 LEU cc_start: 0.9095 (tt) cc_final: 0.8624 (mp) REVERT: A 107 MET cc_start: 0.8235 (mmp) cc_final: 0.7521 (mtt) REVERT: A 144 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8729 (tppt) REVERT: A 197 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: A 353 ARG cc_start: 0.7894 (ptt90) cc_final: 0.7507 (ptt90) REVERT: A 428 MET cc_start: 0.8515 (tpp) cc_final: 0.7627 (ppp) REVERT: A 440 MET cc_start: 0.8790 (mmp) cc_final: 0.8301 (mtt) REVERT: A 572 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8743 (pp) REVERT: A 678 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8646 (t0) REVERT: A 736 LEU cc_start: 0.9105 (mp) cc_final: 0.8895 (pp) REVERT: A 912 MET cc_start: 0.8445 (mtm) cc_final: 0.8196 (mtp) REVERT: A 968 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 1004 ASP cc_start: 0.6802 (p0) cc_final: 0.6476 (p0) REVERT: A 1048 MET cc_start: 0.7887 (mtt) cc_final: 0.7668 (mtp) REVERT: A 1193 LYS cc_start: 0.9646 (pptt) cc_final: 0.9389 (pttm) REVERT: B 43 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.7054 (t-90) REVERT: B 114 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8547 (t) REVERT: B 292 ARG cc_start: 0.8834 (ptt90) cc_final: 0.8286 (pmt-80) REVERT: B 324 LYS cc_start: 0.8939 (pptt) cc_final: 0.8616 (pptt) REVERT: B 354 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8189 (mtm-85) REVERT: B 611 MET cc_start: 0.8780 (mmt) cc_final: 0.8504 (mmt) REVERT: C 55 HIS cc_start: 0.8548 (t-90) cc_final: 0.8251 (t70) REVERT: C 180 ASN cc_start: 0.8974 (t0) cc_final: 0.8665 (p0) REVERT: D 100 MET cc_start: 0.6471 (mmt) cc_final: 0.6088 (mmm) REVERT: E 29 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7206 (t) REVERT: E 72 MET cc_start: 0.8164 (tpt) cc_final: 0.7881 (tpt) REVERT: E 110 MET cc_start: 0.7353 (tpp) cc_final: 0.6529 (tpt) REVERT: F 50 LYS cc_start: 0.8531 (tptp) cc_final: 0.8137 (tptt) REVERT: F 82 GLU cc_start: 0.8468 (pm20) cc_final: 0.7715 (pm20) REVERT: F 88 ASP cc_start: 0.8367 (t70) cc_final: 0.7742 (t0) REVERT: F 91 LEU cc_start: 0.9399 (tp) cc_final: 0.9101 (mt) REVERT: F 100 ARG cc_start: 0.8825 (mtp85) cc_final: 0.8594 (mtp180) REVERT: G 1 MET cc_start: 0.8883 (pmm) cc_final: 0.8108 (pmm) REVERT: G 41 ASN cc_start: 0.8756 (p0) cc_final: 0.8504 (p0) REVERT: G 90 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8652 (ptpp) REVERT: G 185 THR cc_start: 0.9215 (m) cc_final: 0.8925 (p) REVERT: H 13 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8356 (mppt) REVERT: I 36 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8777 (ppt170) REVERT: I 41 ARG cc_start: 0.8975 (ttm170) cc_final: 0.8771 (tpp80) REVERT: I 42 LYS cc_start: 0.8137 (tptp) cc_final: 0.7928 (tptp) REVERT: I 91 MET cc_start: 0.3068 (tpt) cc_final: 0.2864 (tmm) REVERT: J 33 ASP cc_start: 0.8784 (t0) cc_final: 0.8298 (t0) REVERT: K 28 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7504 (mp0) REVERT: K 47 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8820 (mm-30) REVERT: K 64 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8622 (tp30) REVERT: K 66 GLU cc_start: 0.8877 (tt0) cc_final: 0.8409 (tm-30) REVERT: K 112 ASP cc_start: 0.8470 (m-30) cc_final: 0.8238 (m-30) REVERT: L 37 ARG cc_start: 0.8678 (ptt90) cc_final: 0.8444 (ptt90) REVERT: M 37 MET cc_start: 0.8776 (ptp) cc_final: 0.8178 (ptp) REVERT: M 60 MET cc_start: 0.8676 (ptm) cc_final: 0.7954 (ppp) REVERT: M 248 MET cc_start: 0.8593 (ptp) cc_final: 0.8111 (ptp) REVERT: N 30 ARG cc_start: 0.8734 (mmp80) cc_final: 0.8505 (mmp80) REVERT: N 247 LYS cc_start: 0.8814 (tppt) cc_final: 0.8376 (tptp) REVERT: N 262 LYS cc_start: 0.9030 (tppt) cc_final: 0.8761 (tppt) REVERT: N 347 ASP cc_start: 0.8475 (p0) cc_final: 0.8084 (t0) REVERT: N 373 MET cc_start: 0.8124 (tmm) cc_final: 0.7882 (tmm) REVERT: N 380 LYS cc_start: 0.8306 (tptp) cc_final: 0.7974 (tptp) REVERT: O 85 MET cc_start: 0.9120 (ttm) cc_final: 0.8584 (ttm) REVERT: O 259 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7269 (pmm) REVERT: O 385 MET cc_start: 0.8083 (ttm) cc_final: 0.7774 (ttm) REVERT: O 398 MET cc_start: 0.9196 (mmt) cc_final: 0.8791 (mmt) REVERT: O 490 MET cc_start: 0.3299 (ppp) cc_final: 0.2839 (ppp) REVERT: P 203 MET cc_start: 0.8885 (pmm) cc_final: 0.8419 (tpt) REVERT: P 210 PHE cc_start: 0.7442 (p90) cc_final: 0.7154 (p90) REVERT: P 232 MET cc_start: 0.5071 (mmp) cc_final: 0.4226 (tmm) REVERT: P 247 LYS cc_start: 0.8124 (mtmm) cc_final: 0.7628 (pttm) REVERT: P 250 MET cc_start: 0.7687 (ttt) cc_final: 0.7474 (ttt) REVERT: P 270 TYR cc_start: 0.5548 (m-80) cc_final: 0.4352 (m-80) REVERT: Q 27 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5191 (mm) REVERT: Q 57 MET cc_start: 0.9135 (mtt) cc_final: 0.8706 (mmt) REVERT: Q 92 MET cc_start: 0.3612 (mpp) cc_final: 0.3163 (mpp) outliers start: 128 outliers final: 96 residues processed: 571 average time/residue: 0.2443 time to fit residues: 230.2208 Evaluate side-chains 578 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 471 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 197 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 193 optimal weight: 0.8980 chunk 458 optimal weight: 6.9990 chunk 333 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 478 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 483 optimal weight: 8.9990 chunk 486 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B 524 ASN C 213 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 358 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.106435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.068027 restraints weight = 103762.707| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 4.03 r_work: 0.2956 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 40661 Z= 0.233 Angle : 1.124 50.535 54879 Z= 0.618 Chirality : 0.166 6.308 6147 Planarity : 0.004 0.050 7080 Dihedral : 4.204 46.221 5451 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.00 % Favored : 93.98 % Rotamer: Outliers : 2.91 % Allowed : 20.76 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 4948 helix: 0.73 (0.13), residues: 1758 sheet: -0.05 (0.18), residues: 785 loop : -2.03 (0.11), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 256 TYR 0.038 0.001 TYR E 90 PHE 0.026 0.001 PHE P 185 TRP 0.024 0.002 TRP P 217 HIS 0.006 0.001 HIS B 676 Details of bonding type rmsd covalent geometry : bond 0.00609 (40639) covalent geometry : angle 1.02506 (54855) hydrogen bonds : bond 0.04129 ( 1488) hydrogen bonds : angle 4.39172 ( 4326) metal coordination : bond 0.00673 ( 22) metal coordination : angle 22.07928 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 470 time to evaluate : 1.524 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 14 LYS cc_start: 0.8169 (ptpt) cc_final: 0.7836 (pttp) REVERT: A 56 LEU cc_start: 0.9118 (tt) cc_final: 0.8542 (mp) REVERT: A 107 MET cc_start: 0.8163 (mmp) cc_final: 0.7397 (mtt) REVERT: A 197 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: A 353 ARG cc_start: 0.7907 (ptt90) cc_final: 0.7465 (ptt90) REVERT: A 428 MET cc_start: 0.8599 (tpp) cc_final: 0.7616 (ppp) REVERT: A 440 MET cc_start: 0.8767 (mmp) cc_final: 0.8304 (mtt) REVERT: A 572 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8671 (pp) REVERT: A 678 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8706 (t0) REVERT: A 736 LEU cc_start: 0.9124 (mp) cc_final: 0.8890 (pp) REVERT: A 912 MET cc_start: 0.8344 (mtm) cc_final: 0.8136 (mtp) REVERT: A 1004 ASP cc_start: 0.6894 (p0) cc_final: 0.6508 (p0) REVERT: A 1048 MET cc_start: 0.8235 (mtt) cc_final: 0.7919 (mtp) REVERT: A 1193 LYS cc_start: 0.9636 (pptt) cc_final: 0.9378 (pttm) REVERT: A 1330 ASP cc_start: 0.8622 (m-30) cc_final: 0.8301 (p0) REVERT: A 1349 MET cc_start: 0.8942 (mmm) cc_final: 0.8730 (mmm) REVERT: B 43 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.7037 (t-90) REVERT: B 114 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8587 (t) REVERT: B 292 ARG cc_start: 0.8864 (ptt90) cc_final: 0.8225 (pmt-80) REVERT: B 324 LYS cc_start: 0.8930 (pptt) cc_final: 0.8639 (pptt) REVERT: B 352 ASP cc_start: 0.8335 (m-30) cc_final: 0.7907 (t0) REVERT: B 354 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8181 (mtm-85) REVERT: B 611 MET cc_start: 0.8741 (mmt) cc_final: 0.8480 (mmt) REVERT: C 180 ASN cc_start: 0.9046 (t0) cc_final: 0.8732 (p0) REVERT: D 100 MET cc_start: 0.6438 (mmt) cc_final: 0.6025 (mmm) REVERT: E 29 THR cc_start: 0.7677 (OUTLIER) cc_final: 0.7217 (t) REVERT: E 110 MET cc_start: 0.7461 (tpp) cc_final: 0.6669 (tpt) REVERT: F 82 GLU cc_start: 0.8497 (pm20) cc_final: 0.7842 (pm20) REVERT: F 88 ASP cc_start: 0.8526 (t70) cc_final: 0.8046 (t0) REVERT: F 100 ARG cc_start: 0.8821 (mtp85) cc_final: 0.8545 (mtp180) REVERT: G 1 MET cc_start: 0.8879 (pmm) cc_final: 0.8056 (pmm) REVERT: G 90 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8652 (ptpp) REVERT: G 151 ARG cc_start: 0.8620 (mtp180) cc_final: 0.8197 (mtp85) REVERT: H 13 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8389 (mppt) REVERT: H 15 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8461 (mt) REVERT: I 36 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8786 (ppt170) REVERT: I 41 ARG cc_start: 0.8992 (ttm170) cc_final: 0.8754 (ttm-80) REVERT: I 91 MET cc_start: 0.3135 (tpt) cc_final: 0.2926 (tmm) REVERT: I 92 THR cc_start: 0.7149 (OUTLIER) cc_final: 0.6857 (t) REVERT: K 28 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7535 (mp0) REVERT: K 64 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8670 (tp30) REVERT: K 66 GLU cc_start: 0.8992 (tt0) cc_final: 0.8488 (tm-30) REVERT: K 112 ASP cc_start: 0.8559 (m-30) cc_final: 0.8329 (m-30) REVERT: K 124 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8172 (tm-30) REVERT: M 37 MET cc_start: 0.8792 (ptp) cc_final: 0.8133 (ptp) REVERT: M 60 MET cc_start: 0.8658 (ptm) cc_final: 0.7796 (ppp) REVERT: M 248 MET cc_start: 0.8622 (ptp) cc_final: 0.8162 (ptp) REVERT: N 30 ARG cc_start: 0.8762 (mmp80) cc_final: 0.8506 (mmp80) REVERT: N 247 LYS cc_start: 0.8922 (tppt) cc_final: 0.8516 (tptp) REVERT: N 262 LYS cc_start: 0.9067 (tppt) cc_final: 0.8808 (tppt) REVERT: N 347 ASP cc_start: 0.8498 (p0) cc_final: 0.8089 (t0) REVERT: N 373 MET cc_start: 0.8150 (tmm) cc_final: 0.7900 (tmm) REVERT: N 380 LYS cc_start: 0.8385 (tptp) cc_final: 0.8070 (tptp) REVERT: O 85 MET cc_start: 0.9165 (ttm) cc_final: 0.8687 (ttm) REVERT: O 259 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7304 (pmm) REVERT: O 385 MET cc_start: 0.8137 (ttm) cc_final: 0.7840 (ttm) REVERT: O 490 MET cc_start: 0.3247 (ppp) cc_final: 0.2841 (ppp) REVERT: P 203 MET cc_start: 0.8871 (pmm) cc_final: 0.8348 (tpt) REVERT: P 210 PHE cc_start: 0.7606 (p90) cc_final: 0.7315 (p90) REVERT: P 232 MET cc_start: 0.5507 (mmp) cc_final: 0.4622 (tmm) REVERT: P 247 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7605 (pttm) REVERT: Q 57 MET cc_start: 0.9144 (mtt) cc_final: 0.8821 (mmm) REVERT: Q 92 MET cc_start: 0.4015 (mpp) cc_final: 0.3549 (mpp) REVERT: Q 204 PHE cc_start: 0.8211 (t80) cc_final: 0.7925 (t80) outliers start: 129 outliers final: 101 residues processed: 560 average time/residue: 0.2437 time to fit residues: 224.9501 Evaluate side-chains 567 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 454 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 348 VAL Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 197 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 150 optimal weight: 0.3980 chunk 190 optimal weight: 0.3980 chunk 235 optimal weight: 0.6980 chunk 374 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 445 optimal weight: 20.0000 chunk 318 optimal weight: 3.9990 chunk 302 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 319 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN C 213 HIS D 40 GLN ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.107046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.068780 restraints weight = 103170.205| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 4.05 r_work: 0.2962 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 40661 Z= 0.198 Angle : 1.121 50.465 54879 Z= 0.615 Chirality : 0.166 6.318 6147 Planarity : 0.004 0.057 7080 Dihedral : 4.175 46.167 5451 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.56 % Favored : 94.42 % Rotamer: Outliers : 2.67 % Allowed : 21.30 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 4948 helix: 0.77 (0.13), residues: 1761 sheet: 0.04 (0.18), residues: 762 loop : -2.00 (0.11), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG P 206 TYR 0.037 0.001 TYR E 90 PHE 0.026 0.001 PHE P 185 TRP 0.025 0.002 TRP P 217 HIS 0.009 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00534 (40639) covalent geometry : angle 1.02251 (54855) hydrogen bonds : bond 0.03797 ( 1488) hydrogen bonds : angle 4.34234 ( 4326) metal coordination : bond 0.00589 ( 22) metal coordination : angle 21.97143 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 461 time to evaluate : 1.635 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: symmetry clash REVERT: A 14 LYS cc_start: 0.8157 (ptpt) cc_final: 0.7820 (pttp) REVERT: A 15 ILE cc_start: 0.8877 (pt) cc_final: 0.8675 (mt) REVERT: A 56 LEU cc_start: 0.8974 (tt) cc_final: 0.8416 (mp) REVERT: A 107 MET cc_start: 0.8199 (mmp) cc_final: 0.7490 (mtt) REVERT: A 197 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7243 (m-80) REVERT: A 353 ARG cc_start: 0.7908 (ptt90) cc_final: 0.7470 (ptt90) REVERT: A 428 MET cc_start: 0.8574 (tpp) cc_final: 0.7615 (ppp) REVERT: A 440 MET cc_start: 0.8749 (mmp) cc_final: 0.8314 (mtt) REVERT: A 572 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8614 (pp) REVERT: A 678 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8687 (t0) REVERT: A 736 LEU cc_start: 0.9118 (mp) cc_final: 0.8889 (pp) REVERT: A 1004 ASP cc_start: 0.6918 (p0) cc_final: 0.6641 (p0) REVERT: A 1048 MET cc_start: 0.7961 (mtt) cc_final: 0.7704 (mtp) REVERT: A 1193 LYS cc_start: 0.9637 (pptt) cc_final: 0.9328 (pttm) REVERT: A 1330 ASP cc_start: 0.8623 (m-30) cc_final: 0.8305 (p0) REVERT: A 1349 MET cc_start: 0.8957 (mmm) cc_final: 0.8733 (mmm) REVERT: B 43 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.6969 (t-90) REVERT: B 114 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8569 (t) REVERT: B 292 ARG cc_start: 0.8833 (ptt90) cc_final: 0.8192 (pmt-80) REVERT: B 324 LYS cc_start: 0.8909 (pptt) cc_final: 0.8633 (pptt) REVERT: B 352 ASP cc_start: 0.8354 (m-30) cc_final: 0.7929 (t0) REVERT: B 354 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8194 (mtm-85) REVERT: B 611 MET cc_start: 0.8746 (mmt) cc_final: 0.8506 (mmt) REVERT: B 832 MET cc_start: 0.7893 (ttp) cc_final: 0.7595 (ttp) REVERT: B 1052 ARG cc_start: 0.8657 (tmm160) cc_final: 0.8391 (ttt-90) REVERT: D 100 MET cc_start: 0.6484 (mmt) cc_final: 0.6137 (mmm) REVERT: E 29 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7310 (t) REVERT: E 110 MET cc_start: 0.7475 (tpp) cc_final: 0.6709 (tpt) REVERT: F 50 LYS cc_start: 0.8592 (tptp) cc_final: 0.8305 (tptp) REVERT: F 82 GLU cc_start: 0.8457 (pm20) cc_final: 0.7803 (pm20) REVERT: F 88 ASP cc_start: 0.8494 (t70) cc_final: 0.8046 (t0) REVERT: F 100 ARG cc_start: 0.8777 (mtp85) cc_final: 0.8502 (mtp180) REVERT: G 1 MET cc_start: 0.8881 (pmm) cc_final: 0.8241 (pmm) REVERT: G 41 ASN cc_start: 0.8616 (p0) cc_final: 0.8332 (p0) REVERT: H 13 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8374 (mppt) REVERT: H 15 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8430 (mt) REVERT: I 36 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8673 (ppt170) REVERT: I 41 ARG cc_start: 0.9023 (ttm170) cc_final: 0.8793 (tpp80) REVERT: I 92 THR cc_start: 0.7290 (OUTLIER) cc_final: 0.7035 (t) REVERT: K 28 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7494 (mp0) REVERT: K 64 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8723 (tp30) REVERT: K 66 GLU cc_start: 0.9014 (tt0) cc_final: 0.8472 (tm-30) REVERT: K 102 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8662 (mm-30) REVERT: K 112 ASP cc_start: 0.8522 (m-30) cc_final: 0.8286 (m-30) REVERT: K 124 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7860 (tm-30) REVERT: K 128 ARG cc_start: 0.6898 (ttm110) cc_final: 0.6489 (ttp-110) REVERT: L 13 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8364 (tm-30) REVERT: M 37 MET cc_start: 0.8873 (ptp) cc_final: 0.8204 (ptp) REVERT: M 60 MET cc_start: 0.8655 (ptm) cc_final: 0.7793 (ppp) REVERT: M 248 MET cc_start: 0.8613 (ptp) cc_final: 0.8156 (ptp) REVERT: N 30 ARG cc_start: 0.8776 (mmp80) cc_final: 0.8550 (mmp80) REVERT: N 247 LYS cc_start: 0.8915 (tppt) cc_final: 0.8513 (tptp) REVERT: N 262 LYS cc_start: 0.9056 (tppt) cc_final: 0.8800 (tppt) REVERT: N 347 ASP cc_start: 0.8476 (p0) cc_final: 0.8078 (t0) REVERT: N 358 GLN cc_start: 0.8959 (mt0) cc_final: 0.8473 (mt0) REVERT: N 373 MET cc_start: 0.8158 (tmm) cc_final: 0.7905 (tmm) REVERT: N 380 LYS cc_start: 0.8373 (tptp) cc_final: 0.8053 (tptp) REVERT: N 396 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8313 (ttmm) REVERT: O 1 MET cc_start: 0.8108 (mtm) cc_final: 0.7269 (mmt) REVERT: O 85 MET cc_start: 0.9165 (ttm) cc_final: 0.8692 (ttm) REVERT: O 133 MET cc_start: 0.7015 (ptp) cc_final: 0.5903 (ppp) REVERT: O 259 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7286 (pmm) REVERT: O 385 MET cc_start: 0.8155 (ttm) cc_final: 0.7861 (ttm) REVERT: O 490 MET cc_start: 0.3160 (ppp) cc_final: 0.2782 (ppp) REVERT: P 203 MET cc_start: 0.8946 (pmm) cc_final: 0.8331 (tpt) REVERT: P 210 PHE cc_start: 0.7600 (p90) cc_final: 0.7313 (p90) REVERT: P 232 MET cc_start: 0.5575 (mmp) cc_final: 0.4657 (tmm) REVERT: P 247 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7660 (pttm) REVERT: P 250 MET cc_start: 0.8000 (ttt) cc_final: 0.7722 (tpt) REVERT: Q 57 MET cc_start: 0.9130 (mtt) cc_final: 0.8807 (mmm) REVERT: Q 92 MET cc_start: 0.4034 (mpp) cc_final: 0.3567 (mpp) REVERT: Q 204 PHE cc_start: 0.8210 (t80) cc_final: 0.7932 (t80) outliers start: 118 outliers final: 97 residues processed: 548 average time/residue: 0.2436 time to fit residues: 219.6412 Evaluate side-chains 561 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 452 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 348 VAL Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 197 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 289 optimal weight: 20.0000 chunk 413 optimal weight: 0.3980 chunk 386 optimal weight: 2.9990 chunk 479 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 371 optimal weight: 5.9990 chunk 366 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B1093 HIS C 213 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 ASN P 207 ASN Q 197 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.105355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.066829 restraints weight = 103986.361| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 4.03 r_work: 0.2930 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 40661 Z= 0.251 Angle : 1.143 50.536 54879 Z= 0.626 Chirality : 0.166 6.320 6147 Planarity : 0.005 0.074 7080 Dihedral : 4.361 45.325 5451 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.35 % Favored : 93.61 % Rotamer: Outliers : 2.73 % Allowed : 21.44 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4948 helix: 0.72 (0.13), residues: 1773 sheet: -0.01 (0.18), residues: 770 loop : -1.98 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG P 206 TYR 0.035 0.002 TYR E 90 PHE 0.023 0.002 PHE P 185 TRP 0.026 0.002 TRP P 217 HIS 0.010 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00647 (40639) covalent geometry : angle 1.04656 (54855) hydrogen bonds : bond 0.04434 ( 1488) hydrogen bonds : angle 4.48662 ( 4326) metal coordination : bond 0.00668 ( 22) metal coordination : angle 21.96580 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13455.49 seconds wall clock time: 230 minutes 24.23 seconds (13824.23 seconds total)