Starting phenix.real_space_refine on Sun Jul 28 09:15:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s52_19719/07_2024/8s52_19719_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s52_19719/07_2024/8s52_19719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s52_19719/07_2024/8s52_19719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s52_19719/07_2024/8s52_19719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s52_19719/07_2024/8s52_19719_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s52_19719/07_2024/8s52_19719_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 126 5.49 5 Mg 1 5.21 5 S 250 5.16 5 C 27920 2.51 5 N 7897 2.21 5 O 8671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 425": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 44875 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 11249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11249 Classifications: {'peptide': 1420} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1349} Chain breaks: 4 Chain: "B" Number of atoms: 9031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1130, 9031 Classifications: {'peptide': 1130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1076} Chain breaks: 4 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2221 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 14, 'TRANS': 274} Chain breaks: 1 Chain: "N" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1117 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "P" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1288 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain breaks: 1 Chain: "U" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 70.250 106.839 85.054 1.00 95.01 S ATOM 486 SG CYS A 74 67.194 105.839 86.879 1.00 92.54 S ATOM 533 SG CYS A 81 70.320 104.028 87.496 1.00 88.96 S ATOM 768 SG CYS A 111 71.019 75.564 49.612 1.00120.31 S ATOM 796 SG CYS A 114 67.945 76.386 47.229 1.00124.83 S ATOM 1109 SG CYS A 154 69.093 72.847 48.031 1.00139.35 S ATOM 1132 SG CYS A 184 71.103 75.399 45.820 1.00139.00 S ATOM 19849 SG CYS B1119 56.707 95.678 78.459 1.00 90.28 S ATOM 19871 SG CYS B1122 59.786 93.888 77.191 1.00 92.97 S ATOM 19986 SG CYS B1137 59.778 97.696 77.639 1.00103.53 S ATOM 20007 SG CYS B1140 57.918 95.912 74.771 1.00109.51 S ATOM 20974 SG CYS C 88 86.463 106.841 152.042 1.00 96.92 S ATOM 20987 SG CYS C 90 87.718 108.320 148.808 1.00101.85 S ATOM 21022 SG CYS C 94 89.672 108.629 152.114 1.00 90.64 S ATOM 21044 SG CYS C 97 89.434 105.325 150.104 1.00 86.68 S ATOM 28330 SG CYS I 17 126.819 43.846 54.855 1.00116.29 S ATOM 28354 SG CYS I 20 125.894 47.298 53.818 1.00113.26 S ATOM 28515 SG CYS I 39 123.292 44.612 53.619 1.00114.16 S ATOM 28540 SG CYS I 42 125.884 44.466 51.115 1.00117.14 S ATOM 28892 SG CYS I 86 133.409 28.854 95.520 1.00 89.86 S ATOM 28916 SG CYS I 89 136.846 29.631 96.838 1.00 92.65 S ATOM 29120 SG CYS I 114 134.163 32.205 97.146 1.00 76.60 S ATOM 29155 SG CYS I 119 135.695 31.526 93.781 1.00 89.66 S ATOM 29266 SG CYS J 7 104.360 78.665 142.596 1.00 52.15 S ATOM 29290 SG CYS J 10 102.864 78.437 146.076 1.00 53.51 S ATOM 29554 SG CYS J 44 103.919 75.283 144.338 1.00 58.27 S ATOM 29560 SG CYS J 45 106.422 77.693 145.781 1.00 58.06 S ATOM 30680 SG CYS L 19 118.724 111.113 116.414 1.00 71.68 S ATOM 30699 SG CYS L 22 121.704 112.474 118.556 1.00 77.58 S ATOM 30816 SG CYS L 36 119.416 114.706 116.416 1.00 83.61 S ATOM 30842 SG CYS L 39 121.938 112.327 114.842 1.00 85.50 S ATOM 31024 SG CYS M 15 66.572 115.185 109.238 1.00126.63 S ATOM 31171 SG CYS M 34 69.720 115.291 111.349 1.00112.91 S ATOM 31193 SG CYS M 37 66.415 114.117 112.911 1.00114.72 S ATOM 42924 SG CYS W 129 59.371 129.335 77.307 1.00491.02 S ATOM 43116 SG CYS W 154 59.286 127.232 80.800 1.00364.41 S ATOM 43140 SG CYS W 157 61.723 130.207 80.357 1.00419.65 S Time building chain proxies: 23.03, per 1000 atoms: 0.51 Number of scatterers: 44875 At special positions: 0 Unit cell: (179.55, 175.35, 186.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 250 16.00 P 126 15.00 Mg 1 11.99 O 8671 8.00 N 7897 7.00 C 27920 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 - 3.50 Amino acid : False - 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: 19.71 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" ND1 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " Number of angles added : 48 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9956 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 62 sheets defined 40.7% alpha, 17.7% beta 54 base pairs and 110 stacking pairs defined. Time for finding SS restraints: 17.10 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.683A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.483A pdb=" N VAL A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 150 removed outlier: 4.418A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.530A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.824A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.617A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.568A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.916A pdb=" N ASP A 614 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 662 through 684 removed outlier: 4.141A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.910A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 removed outlier: 3.812A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.029A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 4.099A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.547A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1186 through 1189 Processing helix chain 'A' and resid 1190 through 1197 Processing helix chain 'A' and resid 1218 through 1225 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.551A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1295 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1362 through 1369 Processing helix chain 'A' and resid 1370 through 1387 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.937A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1454 through 1460 Processing helix chain 'A' and resid 1466 through 1469 removed outlier: 3.547A pdb=" N GLY A1469 " --> pdb=" O ALA A1466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1466 through 1469' Processing helix chain 'A' and resid 1476 through 1482 Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 21 through 37 Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.587A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.695A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 removed outlier: 4.438A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 425 removed outlier: 3.672A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.504A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 435' Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.781A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.597A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.543A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.538A pdb=" N GLU B 671 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.515A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 761 through 766 removed outlier: 3.761A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.681A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.578A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.077A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.568A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 90 removed outlier: 4.064A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.693A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.854A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.581A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 34' Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 121 removed outlier: 4.034A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 removed outlier: 3.660A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.586A pdb=" N GLN E 169 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 166 through 170' Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.537A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 113 Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.725A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 54 through 60 removed outlier: 4.236A pdb=" N LYS J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.028A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 89 through 93 Processing helix chain 'M' and resid 108 through 128 removed outlier: 4.066A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.518A pdb=" N VAL M 135 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.737A pdb=" N VAL M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 203 Processing helix chain 'M' and resid 214 through 221 removed outlier: 3.863A pdb=" N PHE M 218 " --> pdb=" O PHE M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 263 Processing helix chain 'M' and resid 270 through 279 removed outlier: 3.544A pdb=" N ILE M 274 " --> pdb=" O THR M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 293 Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.719A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 295 through 300' Processing helix chain 'M' and resid 309 through 313 removed outlier: 3.648A pdb=" N LEU M 313 " --> pdb=" O VAL M 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 187 Processing helix chain 'O' and resid 226 through 243 Processing helix chain 'O' and resid 269 through 277 removed outlier: 3.532A pdb=" N LEU O 273 " --> pdb=" O ARG O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 317 through 334 removed outlier: 3.823A pdb=" N ILE O 321 " --> pdb=" O VAL O 317 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR O 322 " --> pdb=" O ARG O 318 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU O 323 " --> pdb=" O ALA O 319 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA O 324 " --> pdb=" O GLU O 320 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE O 325 " --> pdb=" O ILE O 321 " (cutoff:3.500A) Proline residue: O 330 - end of helix Processing helix chain 'Q' and resid 156 through 164 Processing helix chain 'Q' and resid 172 through 180 removed outlier: 3.583A pdb=" N ILE Q 176 " --> pdb=" O ASN Q 172 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG Q 180 " --> pdb=" O ILE Q 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 15 Processing helix chain 'R' and resid 24 through 34 removed outlier: 3.589A pdb=" N SER R 28 " --> pdb=" O PRO R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'R' and resid 123 through 136 removed outlier: 3.733A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 173 Processing helix chain 'R' and resid 179 through 194 Processing helix chain 'R' and resid 198 through 207 Processing helix chain 'R' and resid 209 through 221 removed outlier: 3.840A pdb=" N GLU R 219 " --> pdb=" O GLU R 215 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 32 removed outlier: 3.792A pdb=" N ARG U 26 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP U 32 " --> pdb=" O ILE U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 51 removed outlier: 3.718A pdb=" N MET U 40 " --> pdb=" O GLU U 36 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU U 41 " --> pdb=" O GLN U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 324 through 330 removed outlier: 4.192A pdb=" N LEU U 328 " --> pdb=" O GLU U 324 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP U 330 " --> pdb=" O GLN U 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 52 removed outlier: 3.972A pdb=" N VAL V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 26 removed outlier: 3.699A pdb=" N LYS W 15 " --> pdb=" O PRO W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 40 Processing helix chain 'W' and resid 46 through 50 removed outlier: 3.913A pdb=" N GLU W 50 " --> pdb=" O ASP W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 70 Processing helix chain 'W' and resid 95 through 124 removed outlier: 3.692A pdb=" N GLU W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 145 Processing helix chain 'W' and resid 163 through 166 removed outlier: 3.964A pdb=" N SER W 166 " --> pdb=" O GLU W 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 163 through 166' Processing helix chain 'W' and resid 167 through 194 removed outlier: 3.950A pdb=" N LYS W 171 " --> pdb=" O ALA W 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG W 179 " --> pdb=" O THR W 175 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU W 185 " --> pdb=" O ASN W 181 " (cutoff:3.500A) Proline residue: W 186 - end of helix removed outlier: 4.144A pdb=" N GLU W 193 " --> pdb=" O ALA W 189 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR W 194 " --> pdb=" O LEU W 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 91 removed outlier: 3.810A pdb=" N LYS X 80 " --> pdb=" O GLY X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 98 through 106 removed outlier: 4.027A pdb=" N GLU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 122 Processing helix chain 'X' and resid 122 through 127 removed outlier: 3.773A pdb=" N ASN X 127 " --> pdb=" O ALA X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 162 Processing helix chain 'X' and resid 168 through 175 Processing helix chain 'X' and resid 178 through 186 Processing helix chain 'X' and resid 213 through 223 removed outlier: 3.537A pdb=" N VAL X 223 " --> pdb=" O LEU X 219 " (cutoff:3.500A) Processing helix chain 'X' and resid 229 through 241 removed outlier: 3.698A pdb=" N ILE X 233 " --> pdb=" O ASP X 229 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU X 234 " --> pdb=" O GLU X 230 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.675A pdb=" N ARG A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 94 removed outlier: 6.873A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.616A pdb=" N GLU A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 214 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1061 Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.565A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG A 426 " --> pdb=" O VAL M 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.130A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS H 146 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.788A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB4, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.903A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB6, first strand: chain 'A' and resid 1335 through 1337 removed outlier: 3.547A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 7.081A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1172 through 1173 Processing sheet with id=AB9, first strand: chain 'A' and resid 1212 through 1213 Processing sheet with id=AC1, first strand: chain 'A' and resid 1321 through 1322 Processing sheet with id=AC2, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.576A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL B 132 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN B 141 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 65 through 68 removed outlier: 9.157A pdb=" N GLN R 143 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE B 91 " --> pdb=" O GLN R 143 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU R 145 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU B 93 " --> pdb=" O LEU R 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC6, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC8, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AC9, first strand: chain 'B' and resid 238 through 239 Processing sheet with id=AD1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD2, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD3, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.106A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.654A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.654A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD7, first strand: chain 'B' and resid 935 through 936 removed outlier: 4.202A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 935 through 936 Processing sheet with id=AD9, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AE1, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.686A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AE3, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE4, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.755A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.769A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE7, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.947A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.947A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.109A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AF2, first strand: chain 'E' and resid 147 through 151 removed outlier: 4.435A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.596A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE G 108 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU G 97 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 117 through 119 removed outlier: 4.459A pdb=" N GLU G 118 " --> pdb=" O LYS G 129 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS G 129 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 24 through 28 Processing sheet with id=AF6, first strand: chain 'I' and resid 94 through 97 Processing sheet with id=AF7, first strand: chain 'K' and resid 19 through 20 Processing sheet with id=AF8, first strand: chain 'M' and resid 24 through 26 Processing sheet with id=AF9, first strand: chain 'O' and resid 190 through 191 removed outlier: 3.609A pdb=" N VAL O 220 " --> pdb=" O LEU O 212 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU O 165 " --> pdb=" O SER O 261 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N SER O 261 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR O 171 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE O 255 " --> pdb=" O THR O 171 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASN O 173 " --> pdb=" O PHE O 253 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE O 253 " --> pdb=" O ASN O 173 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE O 292 " --> pdb=" O SER O 282 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 16 through 17 removed outlier: 3.525A pdb=" N PHE Q 138 " --> pdb=" O ILE Q 126 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE Q 126 " --> pdb=" O PHE Q 138 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR Q 125 " --> pdb=" O VAL R 21 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL R 21 " --> pdb=" O TYR Q 125 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE Q 127 " --> pdb=" O TRP R 19 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TRP R 19 " --> pdb=" O PHE Q 127 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL R 18 " --> pdb=" O GLN R 112 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA R 114 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU R 20 " --> pdb=" O ALA R 114 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N CYS R 116 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS R 22 " --> pdb=" O CYS R 116 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 45 through 49 removed outlier: 3.592A pdb=" N GLU Q 48 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TRP Q 98 " --> pdb=" O GLY Q 112 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY Q 112 " --> pdb=" O TRP Q 98 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS Q 109 " --> pdb=" O LEU Q 149 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU Q 149 " --> pdb=" O LYS Q 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS Q 111 " --> pdb=" O THR Q 147 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Q 113 " --> pdb=" O ASN Q 145 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN Q 145 " --> pdb=" O ILE Q 113 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TYR Q 26 " --> pdb=" O ASN Q 142 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N TYR Q 144 " --> pdb=" O TYR Q 26 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE Q 28 " --> pdb=" O TYR Q 144 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE Q 146 " --> pdb=" O ILE Q 28 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA Q 30 " --> pdb=" O PHE Q 146 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN Q 27 " --> pdb=" O PHE R 96 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE R 96 " --> pdb=" O ASN Q 27 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR R 92 " --> pdb=" O PHE Q 31 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU R 93 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY R 108 " --> pdb=" O VAL R 95 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR R 97 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU R 106 " --> pdb=" O THR R 97 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL R 54 " --> pdb=" O PHE R 83 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU R 85 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR R 52 " --> pdb=" O LEU R 85 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 222 through 224 removed outlier: 3.641A pdb=" N VAL R 222 " --> pdb=" O GLU R 234 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 363 through 367 removed outlier: 3.714A pdb=" N LYS U 341 " --> pdb=" O HIS U 352 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS U 354 " --> pdb=" O TYR U 339 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR U 339 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY U 356 " --> pdb=" O CYS U 337 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS U 337 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N MET U 358 " --> pdb=" O VAL U 335 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL U 335 " --> pdb=" O MET U 358 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU U 360 " --> pdb=" O ASN U 333 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASN U 333 " --> pdb=" O LEU U 360 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN U 333 " --> pdb=" O LYS V 92 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS U 337 " --> pdb=" O VAL V 96 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS V 98 " --> pdb=" O CYS U 337 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA V 97 " --> pdb=" O TRP V 72 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL V 75 " --> pdb=" O ASN V 63 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL V 79 " --> pdb=" O ARG V 59 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG V 59 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE V 81 " --> pdb=" O ASN V 57 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN V 57 " --> pdb=" O PHE V 81 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 42 through 44 removed outlier: 3.593A pdb=" N HIS W 89 " --> pdb=" O ARG W 77 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG W 77 " --> pdb=" O HIS W 89 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 127 through 129 removed outlier: 3.747A pdb=" N PHE W 127 " --> pdb=" O PHE W 136 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS W 129 " --> pdb=" O SER W 134 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER W 134 " --> pdb=" O CYS W 129 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 130 through 133 Processing sheet with id=AG8, first strand: chain 'X' and resid 166 through 167 removed outlier: 3.632A pdb=" N ILE X 166 " --> pdb=" O LEU X 201 " (cutoff:3.500A) 1800 hydrogen bonds defined for protein. 5031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 282 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 30.60 Time building geometry restraints manager: 21.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7478 1.32 - 1.45: 12214 1.45 - 1.57: 25619 1.57 - 1.70: 249 1.70 - 1.82: 394 Bond restraints: 45954 Sorted by residual: bond pdb=" C CYS M 219 " pdb=" N SER M 220 " ideal model delta sigma weight residual 1.335 1.435 -0.100 1.30e-02 5.92e+03 5.87e+01 bond pdb=" C PHE B 713 " pdb=" O PHE B 713 " ideal model delta sigma weight residual 1.233 1.269 -0.036 4.80e-03 4.34e+04 5.69e+01 bond pdb=" CA SER M 216 " pdb=" CB SER M 216 " ideal model delta sigma weight residual 1.528 1.456 0.072 1.56e-02 4.11e+03 2.16e+01 bond pdb=" C SER M 220 " pdb=" O SER M 220 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.18e-02 7.18e+03 1.37e+01 bond pdb=" C ASP B 386 " pdb=" N HIS B 387 " ideal model delta sigma weight residual 1.332 1.381 -0.049 1.40e-02 5.10e+03 1.23e+01 ... (remaining 45949 not shown) Histogram of bond angle deviations from ideal: 95.67 - 103.37: 597 103.37 - 111.06: 17287 111.06 - 118.76: 20081 118.76 - 126.46: 23771 126.46 - 134.16: 842 Bond angle restraints: 62578 Sorted by residual: angle pdb=" N ARG B 385 " pdb=" CA ARG B 385 " pdb=" C ARG B 385 " ideal model delta sigma weight residual 113.18 105.18 8.00 1.21e+00 6.83e-01 4.37e+01 angle pdb=" C ASP L 56 " pdb=" CA ASP L 56 " pdb=" CB ASP L 56 " ideal model delta sigma weight residual 110.72 100.58 10.14 1.69e+00 3.50e-01 3.60e+01 angle pdb=" N HIS B 387 " pdb=" CA HIS B 387 " pdb=" C HIS B 387 " ideal model delta sigma weight residual 110.80 98.41 12.39 2.13e+00 2.20e-01 3.38e+01 angle pdb=" C5' DG N 24 " pdb=" C4' DG N 24 " pdb=" C3' DG N 24 " ideal model delta sigma weight residual 114.90 106.32 8.58 1.50e+00 4.44e-01 3.27e+01 angle pdb=" O3' DG T 51 " pdb=" P DG T 52 " pdb=" O5' DG T 52 " ideal model delta sigma weight residual 104.00 95.67 8.33 1.50e+00 4.44e-01 3.09e+01 ... (remaining 62573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 26849 34.65 - 69.30: 911 69.30 - 103.95: 72 103.95 - 138.61: 0 138.61 - 173.26: 2 Dihedral angle restraints: 27834 sinusoidal: 12463 harmonic: 15371 Sorted by residual: dihedral pdb=" O4' A P 1 " pdb=" C4' A P 1 " pdb=" C3' A P 1 " pdb=" C2' A P 1 " ideal model delta sinusoidal sigma weight residual -35.15 -12.98 -22.17 1 4.00e+00 6.25e-02 4.43e+01 dihedral pdb=" C3' A P 1 " pdb=" C4' A P 1 " pdb=" O4' A P 1 " pdb=" C1' A P 1 " ideal model delta sinusoidal sigma weight residual 19.82 -10.05 29.86 3 5.20e+00 3.70e-02 3.92e+01 dihedral pdb=" CA MET O 295 " pdb=" C MET O 295 " pdb=" N ILE O 296 " pdb=" CA ILE O 296 " ideal model delta harmonic sigma weight residual -180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 27831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 6739 0.131 - 0.262: 185 0.262 - 0.393: 21 0.393 - 0.524: 28 0.524 - 0.656: 17 Chirality restraints: 6990 Sorted by residual: chirality pdb=" P DA N 3 " pdb=" OP1 DA N 3 " pdb=" OP2 DA N 3 " pdb=" O5' DA N 3 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P DG N 54 " pdb=" OP1 DG N 54 " pdb=" OP2 DG N 54 " pdb=" O5' DG N 54 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DG N 76 " pdb=" OP1 DG N 76 " pdb=" OP2 DG N 76 " pdb=" O5' DG N 76 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.41e+00 ... (remaining 6987 not shown) Planarity restraints: 7668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1133 " 0.104 5.00e-02 4.00e+02 1.55e-01 3.86e+01 pdb=" N PRO A1134 " -0.269 5.00e-02 4.00e+02 pdb=" CA PRO A1134 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A1134 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 29 " -0.079 2.00e-02 2.50e+03 3.97e-02 3.55e+01 pdb=" N1 DC T 29 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DC T 29 " 0.021 2.00e-02 2.50e+03 pdb=" O2 DC T 29 " 0.038 2.00e-02 2.50e+03 pdb=" N3 DC T 29 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DC T 29 " -0.000 2.00e-02 2.50e+03 pdb=" N4 DC T 29 " -0.054 2.00e-02 2.50e+03 pdb=" C5 DC T 29 " 0.035 2.00e-02 2.50e+03 pdb=" C6 DC T 29 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS M 219 " -0.024 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" C CYS M 219 " 0.089 2.00e-02 2.50e+03 pdb=" O CYS M 219 " -0.036 2.00e-02 2.50e+03 pdb=" N SER M 220 " -0.029 2.00e-02 2.50e+03 ... (remaining 7665 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 19 2.29 - 2.94: 18301 2.94 - 3.59: 65809 3.59 - 4.25: 104157 4.25 - 4.90: 175026 Nonbonded interactions: 363312 Sorted by model distance: nonbonded pdb=" OP1 C P 10 " pdb="MG MG P 101 " model vdw 1.632 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG P 101 " model vdw 1.985 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG P 101 " model vdw 1.994 2.170 nonbonded pdb=" OH TYR A 763 " pdb=" OD2 ASP H 23 " model vdw 2.124 2.440 nonbonded pdb=" OG1 THR A1100 " pdb=" OE1 GLN A1101 " model vdw 2.135 2.440 ... (remaining 363307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.210 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: 0.050 Extract box with map and model: 1.660 Check model and map are aligned: 0.300 Set scattering table: 0.410 Process input model: 149.660 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 : 0.008 0.102 45954 Z= 0.540 Angle : 0.903 12.388 62578 Z= 0.484 Chirality : 0.073 0.656 6990 Planarity : 0.007 0.155 7668 Dihedral : 16.259 173.257 17878 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 5211 helix: 1.18 (0.12), residues: 1886 sheet: -0.43 (0.18), residues: 803 loop : -0.68 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 453 HIS 0.014 0.002 HIS E 64 PHE 0.027 0.003 PHE O 214 TYR 0.048 0.003 TYR E 26 ARG 0.017 0.001 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 683 time to evaluate : 5.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8294 (tpp) cc_final: 0.8043 (tpt) REVERT: A 1351 ASP cc_start: 0.7823 (t0) cc_final: 0.7486 (t0) REVERT: B 61 ASP cc_start: 0.8054 (t70) cc_final: 0.7849 (t0) REVERT: B 239 MET cc_start: 0.8373 (ttm) cc_final: 0.8093 (ttp) REVERT: B 282 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.7163 (tpp80) REVERT: B 286 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7816 (mm-30) REVERT: B 337 LYS cc_start: 0.7590 (tmtt) cc_final: 0.6841 (tptt) REVERT: B 825 GLN cc_start: 0.8185 (pp30) cc_final: 0.7577 (pp30) REVERT: B 1092 ASP cc_start: 0.7340 (t70) cc_final: 0.7128 (t70) REVERT: B 1109 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7590 (tm-30) REVERT: C 107 CYS cc_start: 0.7932 (t) cc_final: 0.7658 (t) REVERT: E 57 ASP cc_start: 0.8591 (m-30) cc_final: 0.8352 (m-30) REVERT: E 92 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8316 (tp40) REVERT: F 95 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8643 (ttpp) REVERT: H 126 GLN cc_start: 0.8513 (mt0) cc_final: 0.8081 (mt0) REVERT: J 47 ARG cc_start: 0.9039 (tmm-80) cc_final: 0.8739 (tmm-80) REVERT: K 8 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7835 (mt-10) REVERT: M 227 GLN cc_start: 0.8546 (pm20) cc_final: 0.8342 (pm20) REVERT: O 256 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7564 (mm110) REVERT: O 277 HIS cc_start: 0.8933 (m90) cc_final: 0.8685 (m90) REVERT: O 322 TYR cc_start: 0.8329 (m-80) cc_final: 0.7717 (m-80) REVERT: U 51 MET cc_start: 0.5590 (mpp) cc_final: 0.5013 (mpm) outliers start: 3 outliers final: 6 residues processed: 686 average time/residue: 1.5704 time to fit residues: 1330.9611 Evaluate side-chains 569 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 563 time to evaluate : 4.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 223 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 446 optimal weight: 20.0000 chunk 400 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 270 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 414 optimal weight: 10.0000 chunk 160 optimal weight: 0.0970 chunk 252 optimal weight: 0.9990 chunk 308 optimal weight: 1.9990 chunk 480 optimal weight: 40.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 757 GLN A 861 GLN A1005 HIS A1042 ASN A1194 ASN A1417 HIS B 111 ASN B 139 GLN B 143 GLN B 265 GLN B 287 HIS B 319 ASN B 639 HIS B 717 ASN B 980 HIS ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN E 64 HIS E 148 HIS G 4 HIS I 22 ASN I 41 ASN K 2 ASN K 36 ASN K 89 ASN M 133 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 45954 Z= 0.214 Angle : 0.561 10.234 62578 Z= 0.294 Chirality : 0.042 0.205 6990 Planarity : 0.004 0.108 7668 Dihedral : 14.341 173.377 7162 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.29 % Allowed : 8.27 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.12), residues: 5211 helix: 1.48 (0.12), residues: 1913 sheet: -0.31 (0.18), residues: 798 loop : -0.60 (0.13), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 27 HIS 0.005 0.001 HIS E 64 PHE 0.030 0.001 PHE R 191 TYR 0.026 0.001 TYR E 26 ARG 0.008 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 624 time to evaluate : 4.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.7975 (tt0) cc_final: 0.7751 (tm-30) REVERT: A 311 GLN cc_start: 0.8602 (tp40) cc_final: 0.8091 (tp40) REVERT: A 317 MET cc_start: 0.8327 (tpp) cc_final: 0.8057 (tpp) REVERT: A 439 HIS cc_start: 0.8298 (m-70) cc_final: 0.8002 (m-70) REVERT: A 467 MET cc_start: 0.7546 (mpp) cc_final: 0.7342 (mpp) REVERT: A 470 MET cc_start: 0.8715 (mtm) cc_final: 0.8457 (mtm) REVERT: A 743 ARG cc_start: 0.7826 (ttp80) cc_final: 0.7614 (ttm-80) REVERT: A 1296 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8021 (ttm) REVERT: A 1351 ASP cc_start: 0.7734 (t0) cc_final: 0.7390 (t0) REVERT: A 1441 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 1449 ASP cc_start: 0.8228 (t0) cc_final: 0.8024 (t0) REVERT: B 239 MET cc_start: 0.8360 (ttm) cc_final: 0.8118 (ttp) REVERT: B 282 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7313 (tpp80) REVERT: B 286 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7854 (mm-30) REVERT: B 388 TYR cc_start: 0.8712 (t80) cc_final: 0.8505 (t80) REVERT: B 581 GLU cc_start: 0.7561 (tt0) cc_final: 0.7355 (mt-10) REVERT: B 609 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7865 (mm-30) REVERT: B 825 GLN cc_start: 0.8206 (pp30) cc_final: 0.7599 (pp30) REVERT: C 107 CYS cc_start: 0.7876 (t) cc_final: 0.7613 (t) REVERT: E 46 ASP cc_start: 0.7960 (m-30) cc_final: 0.7676 (t0) REVERT: E 57 ASP cc_start: 0.8567 (m-30) cc_final: 0.8337 (m-30) REVERT: E 92 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8167 (tp-100) REVERT: F 95 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8604 (ttpp) REVERT: J 36 ASP cc_start: 0.8476 (m-30) cc_final: 0.8185 (m-30) REVERT: M 219 CYS cc_start: 0.8526 (m) cc_final: 0.8153 (m) REVERT: O 166 GLN cc_start: 0.7671 (mm110) cc_final: 0.7415 (mm110) REVERT: O 201 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8781 (pp) REVERT: O 259 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8984 (p) REVERT: O 277 HIS cc_start: 0.8850 (m90) cc_final: 0.8586 (m90) REVERT: O 322 TYR cc_start: 0.8339 (m-80) cc_final: 0.7690 (m-80) REVERT: Q 29 MET cc_start: 0.2680 (tpt) cc_final: 0.2159 (tpt) REVERT: U 40 MET cc_start: 0.8163 (mpm) cc_final: 0.7927 (pmm) REVERT: U 51 MET cc_start: 0.5627 (mpp) cc_final: 0.5183 (mpm) REVERT: U 358 MET cc_start: 0.5200 (OUTLIER) cc_final: 0.4171 (tpt) outliers start: 60 outliers final: 24 residues processed: 645 average time/residue: 1.5438 time to fit residues: 1236.8067 Evaluate side-chains 600 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 572 time to evaluate : 4.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 223 CYS Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain U residue 314 LEU Chi-restraints excluded: chain U residue 358 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 266 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 399 optimal weight: 0.6980 chunk 327 optimal weight: 50.0000 chunk 132 optimal weight: 1.9990 chunk 481 optimal weight: 6.9990 chunk 519 optimal weight: 50.0000 chunk 428 optimal weight: 2.9990 chunk 477 optimal weight: 50.0000 chunk 164 optimal weight: 0.5980 chunk 386 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN A 757 GLN A 765 ASN A1093 GLN B 143 GLN B 265 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS C 260 GLN H 126 GLN I 41 ASN I 45 GLN I 98 GLN K 89 ASN M 139 ASN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 198 ASN W 30 HIS W 142 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 45954 Z= 0.391 Angle : 0.589 9.404 62578 Z= 0.306 Chirality : 0.044 0.220 6990 Planarity : 0.004 0.076 7668 Dihedral : 14.384 176.638 7155 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.86 % Allowed : 10.33 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.12), residues: 5211 helix: 1.51 (0.12), residues: 1923 sheet: -0.28 (0.18), residues: 811 loop : -0.61 (0.13), residues: 2477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1334 HIS 0.011 0.001 HIS D 43 PHE 0.029 0.001 PHE R 191 TYR 0.032 0.001 TYR E 26 ARG 0.009 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 574 time to evaluate : 5.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8010 (tt0) cc_final: 0.7732 (tm-30) REVERT: A 311 GLN cc_start: 0.8706 (tp40) cc_final: 0.8126 (tp40) REVERT: A 1086 MET cc_start: 0.8970 (mmm) cc_final: 0.8725 (mmm) REVERT: A 1351 ASP cc_start: 0.7712 (t0) cc_final: 0.7393 (t0) REVERT: A 1441 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 1449 ASP cc_start: 0.8297 (t0) cc_final: 0.8065 (t0) REVERT: B 286 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8097 (mm-30) REVERT: B 333 GLU cc_start: 0.8072 (mp0) cc_final: 0.7869 (mm-30) REVERT: B 337 LYS cc_start: 0.7582 (tmtt) cc_final: 0.6870 (tptt) REVERT: B 825 GLN cc_start: 0.8254 (pp30) cc_final: 0.7576 (pp30) REVERT: C 107 CYS cc_start: 0.7990 (t) cc_final: 0.7787 (t) REVERT: D 43 HIS cc_start: 0.7550 (m90) cc_final: 0.5425 (m-70) REVERT: E 57 ASP cc_start: 0.8600 (m-30) cc_final: 0.8377 (m-30) REVERT: E 92 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8206 (tp-100) REVERT: F 80 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8283 (mmm) REVERT: F 95 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8644 (ttpp) REVERT: I 64 GLU cc_start: 0.7785 (mp0) cc_final: 0.7506 (mp0) REVERT: I 67 GLN cc_start: 0.7209 (mp10) cc_final: 0.6960 (mp10) REVERT: M 28 ARG cc_start: 0.7906 (mpt180) cc_final: 0.7698 (mpt180) REVERT: M 120 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8219 (tm-30) REVERT: M 277 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8741 (tt) REVERT: O 277 HIS cc_start: 0.8868 (m90) cc_final: 0.8552 (m90) REVERT: O 322 TYR cc_start: 0.8413 (m-80) cc_final: 0.7687 (m-80) REVERT: Q 29 MET cc_start: 0.2520 (tpt) cc_final: 0.2209 (tpt) REVERT: U 358 MET cc_start: 0.5311 (OUTLIER) cc_final: 0.4492 (tpt) REVERT: W 168 MET cc_start: 0.5942 (ppp) cc_final: 0.5715 (ppp) outliers start: 87 outliers final: 47 residues processed: 619 average time/residue: 1.5507 time to fit residues: 1186.1072 Evaluate side-chains 592 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 542 time to evaluate : 5.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 223 CYS Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 287 GLN Chi-restraints excluded: chain U residue 358 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 475 optimal weight: 50.0000 chunk 361 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 53 optimal weight: 0.0570 chunk 229 optimal weight: 0.9980 chunk 323 optimal weight: 10.0000 chunk 482 optimal weight: 8.9990 chunk 511 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 chunk 457 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN A 387 ASN ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN B 143 GLN B 265 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 260 GLN D 93 HIS I 41 ASN I 45 GLN K 89 ASN M 234 HIS ** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 ASN ** W 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45954 Z= 0.226 Angle : 0.532 9.274 62578 Z= 0.276 Chirality : 0.041 0.198 6990 Planarity : 0.004 0.071 7668 Dihedral : 14.341 174.824 7155 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.69 % Allowed : 12.43 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 5211 helix: 1.69 (0.12), residues: 1910 sheet: -0.19 (0.18), residues: 810 loop : -0.58 (0.13), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1334 HIS 0.006 0.001 HIS A1005 PHE 0.028 0.001 PHE R 191 TYR 0.026 0.001 TYR E 26 ARG 0.008 0.000 ARG I 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 578 time to evaluate : 5.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.9003 (tp) REVERT: A 294 GLU cc_start: 0.8027 (tt0) cc_final: 0.7731 (tm-30) REVERT: A 311 GLN cc_start: 0.8669 (tp40) cc_final: 0.8113 (tp40) REVERT: A 1086 MET cc_start: 0.8947 (mmm) cc_final: 0.8705 (mmm) REVERT: A 1351 ASP cc_start: 0.7667 (t0) cc_final: 0.7348 (t0) REVERT: A 1441 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 1449 ASP cc_start: 0.8215 (t0) cc_final: 0.7967 (t0) REVERT: B 239 MET cc_start: 0.8350 (ttm) cc_final: 0.8140 (ttp) REVERT: B 337 LYS cc_start: 0.7552 (tmtt) cc_final: 0.6845 (tptt) REVERT: B 825 GLN cc_start: 0.8217 (pp30) cc_final: 0.7543 (pp30) REVERT: C 107 CYS cc_start: 0.7881 (t) cc_final: 0.7660 (t) REVERT: D 39 MET cc_start: 0.8029 (tpp) cc_final: 0.7718 (tpp) REVERT: E 57 ASP cc_start: 0.8588 (m-30) cc_final: 0.8361 (m-30) REVERT: E 92 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8143 (tp-100) REVERT: E 177 ASP cc_start: 0.8734 (t0) cc_final: 0.8516 (t0) REVERT: F 95 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8665 (ttpp) REVERT: M 120 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8123 (tm-30) REVERT: M 260 MET cc_start: 0.8555 (tmm) cc_final: 0.8354 (tmm) REVERT: M 277 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8641 (tt) REVERT: O 277 HIS cc_start: 0.8852 (m90) cc_final: 0.8470 (m90) REVERT: O 322 TYR cc_start: 0.8468 (m-80) cc_final: 0.7755 (m-80) REVERT: Q 29 MET cc_start: 0.1818 (tpt) cc_final: 0.1599 (tpt) REVERT: R 182 HIS cc_start: 0.8043 (t-90) cc_final: 0.7633 (t-90) REVERT: R 200 LYS cc_start: 0.7325 (mmpt) cc_final: 0.7022 (mmtt) REVERT: U 358 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.4727 (tpt) outliers start: 79 outliers final: 35 residues processed: 617 average time/residue: 1.5660 time to fit residues: 1199.2459 Evaluate side-chains 577 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 539 time to evaluate : 4.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 287 GLN Chi-restraints excluded: chain U residue 358 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 425 optimal weight: 9.9990 chunk 290 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 380 optimal weight: 1.9990 chunk 210 optimal weight: 0.0980 chunk 436 optimal weight: 0.8980 chunk 353 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 458 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A 926 ASN B 143 GLN B 265 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN I 41 ASN I 45 GLN J 26 GLN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45954 Z= 0.181 Angle : 0.523 9.309 62578 Z= 0.270 Chirality : 0.041 0.224 6990 Planarity : 0.004 0.067 7668 Dihedral : 14.269 173.936 7152 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.76 % Allowed : 13.56 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.12), residues: 5211 helix: 1.80 (0.12), residues: 1910 sheet: -0.12 (0.18), residues: 823 loop : -0.51 (0.13), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 202 HIS 0.009 0.001 HIS A1005 PHE 0.029 0.001 PHE R 191 TYR 0.022 0.001 TYR E 26 ARG 0.010 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 583 time to evaluate : 5.403 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: A 311 GLN cc_start: 0.8646 (tp40) cc_final: 0.8089 (tp40) REVERT: A 1086 MET cc_start: 0.8953 (mmm) cc_final: 0.8725 (mmm) REVERT: A 1351 ASP cc_start: 0.7649 (t0) cc_final: 0.7309 (t0) REVERT: A 1441 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7521 (mm-30) REVERT: A 1449 ASP cc_start: 0.8184 (t0) cc_final: 0.7937 (t0) REVERT: B 298 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.7026 (mmt) REVERT: B 337 LYS cc_start: 0.7477 (tmtt) cc_final: 0.6807 (tptt) REVERT: B 744 MET cc_start: 0.8835 (mmm) cc_final: 0.8542 (mtt) REVERT: B 1109 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7517 (tm-30) REVERT: C 41 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7645 (tm-30) REVERT: C 107 CYS cc_start: 0.7791 (t) cc_final: 0.7562 (t) REVERT: D 39 MET cc_start: 0.8299 (tpp) cc_final: 0.8016 (tpp) REVERT: E 46 ASP cc_start: 0.7966 (t0) cc_final: 0.7757 (t0) REVERT: E 57 ASP cc_start: 0.8563 (m-30) cc_final: 0.8338 (m-30) REVERT: E 92 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8123 (tp-100) REVERT: F 95 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8649 (ttpp) REVERT: J 36 ASP cc_start: 0.8491 (m-30) cc_final: 0.8219 (m-30) REVERT: K 8 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: L 25 GLU cc_start: 0.7847 (mp0) cc_final: 0.7615 (mp0) REVERT: M 120 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7950 (tm-30) REVERT: M 227 GLN cc_start: 0.8474 (mp10) cc_final: 0.8111 (pm20) REVERT: M 277 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8532 (tt) REVERT: O 277 HIS cc_start: 0.8813 (m90) cc_final: 0.8326 (m90) REVERT: O 322 TYR cc_start: 0.8423 (m-80) cc_final: 0.7722 (m-80) REVERT: U 358 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.5118 (tpt) outliers start: 82 outliers final: 39 residues processed: 623 average time/residue: 1.5287 time to fit residues: 1188.0200 Evaluate side-chains 591 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 548 time to evaluate : 4.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 287 GLN Chi-restraints excluded: chain O residue 326 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain U residue 51 MET Chi-restraints excluded: chain U residue 358 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 172 optimal weight: 9.9990 chunk 460 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 511 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A 926 ASN B 143 GLN B 265 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 ASN ** W 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 45954 Z= 0.445 Angle : 0.611 9.958 62578 Z= 0.313 Chirality : 0.044 0.214 6990 Planarity : 0.004 0.070 7668 Dihedral : 14.312 175.435 7152 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.16 % Allowed : 14.14 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.12), residues: 5211 helix: 1.68 (0.12), residues: 1921 sheet: -0.21 (0.18), residues: 795 loop : -0.60 (0.12), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1334 HIS 0.008 0.001 HIS A1005 PHE 0.026 0.002 PHE R 191 TYR 0.048 0.002 TYR E 26 ARG 0.009 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 563 time to evaluate : 4.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6880 (ppt170) REVERT: A 294 GLU cc_start: 0.7987 (tt0) cc_final: 0.7644 (tm-30) REVERT: A 311 GLN cc_start: 0.8697 (tp40) cc_final: 0.8066 (tp40) REVERT: A 524 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7291 (mtp) REVERT: A 743 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7719 (ttm-80) REVERT: A 926 ASN cc_start: 0.8829 (t0) cc_final: 0.8470 (t0) REVERT: A 1052 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7698 (ttm170) REVERT: A 1086 MET cc_start: 0.8906 (mmm) cc_final: 0.8660 (mmm) REVERT: A 1282 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8676 (t0) REVERT: A 1334 TRP cc_start: 0.8763 (m100) cc_final: 0.8483 (m100) REVERT: A 1351 ASP cc_start: 0.7687 (t0) cc_final: 0.7341 (t0) REVERT: A 1441 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 1449 ASP cc_start: 0.8258 (t0) cc_final: 0.8024 (t0) REVERT: B 298 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7130 (mmt) REVERT: B 337 LYS cc_start: 0.7654 (tmtt) cc_final: 0.6975 (tptt) REVERT: B 825 GLN cc_start: 0.8227 (pp30) cc_final: 0.7514 (pp30) REVERT: B 1121 LEU cc_start: 0.9422 (mt) cc_final: 0.9222 (mt) REVERT: D 39 MET cc_start: 0.8348 (tpp) cc_final: 0.8036 (tpp) REVERT: E 46 ASP cc_start: 0.8005 (t0) cc_final: 0.7761 (t0) REVERT: E 57 ASP cc_start: 0.8636 (m-30) cc_final: 0.8377 (m-30) REVERT: E 92 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8172 (tp-100) REVERT: F 95 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8686 (ttpp) REVERT: F 121 ASP cc_start: 0.8538 (p0) cc_final: 0.8319 (p0) REVERT: H 55 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8452 (mtpp) REVERT: I 40 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7154 (tpp-160) REVERT: I 64 GLU cc_start: 0.7863 (mp0) cc_final: 0.7650 (mm-30) REVERT: J 31 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: K 111 ASP cc_start: 0.8318 (t70) cc_final: 0.8000 (t0) REVERT: L 25 GLU cc_start: 0.7922 (mp0) cc_final: 0.7687 (mp0) REVERT: M 120 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8006 (tm-30) REVERT: M 277 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8802 (tt) REVERT: O 166 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7298 (tm130) REVERT: O 277 HIS cc_start: 0.8893 (m90) cc_final: 0.8312 (m90) REVERT: O 322 TYR cc_start: 0.8438 (m-80) cc_final: 0.7917 (m-80) REVERT: R 22 LYS cc_start: 0.6760 (ttmt) cc_final: 0.6550 (mmtm) REVERT: R 200 LYS cc_start: 0.7321 (mmpt) cc_final: 0.7021 (mmtt) REVERT: U 358 MET cc_start: 0.5659 (OUTLIER) cc_final: 0.5363 (tpt) outliers start: 101 outliers final: 46 residues processed: 619 average time/residue: 1.6179 time to fit residues: 1247.8477 Evaluate side-chains 598 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 543 time to evaluate : 4.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 287 GLN Chi-restraints excluded: chain O residue 326 GLU Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain U residue 51 MET Chi-restraints excluded: chain U residue 358 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 493 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 291 optimal weight: 5.9990 chunk 373 optimal weight: 1.9990 chunk 289 optimal weight: 7.9990 chunk 430 optimal weight: 9.9990 chunk 285 optimal weight: 20.0000 chunk 509 optimal weight: 0.4980 chunk 319 optimal weight: 9.9990 chunk 310 optimal weight: 1.9990 chunk 235 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN B 143 GLN B 265 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 142 ASN W 143 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 45954 Z= 0.278 Angle : 0.565 10.868 62578 Z= 0.289 Chirality : 0.042 0.304 6990 Planarity : 0.004 0.071 7668 Dihedral : 14.269 173.832 7152 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.84 % Allowed : 15.36 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 5211 helix: 1.72 (0.12), residues: 1919 sheet: -0.12 (0.18), residues: 792 loop : -0.57 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 202 HIS 0.006 0.001 HIS A1005 PHE 0.028 0.001 PHE R 191 TYR 0.045 0.001 TYR M 259 ARG 0.012 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 569 time to evaluate : 5.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6924 (ppt170) REVERT: A 294 GLU cc_start: 0.8017 (tt0) cc_final: 0.7664 (tm-30) REVERT: A 311 GLN cc_start: 0.8642 (tp40) cc_final: 0.8022 (tp40) REVERT: A 524 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7042 (mtp) REVERT: A 743 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7699 (ttm-80) REVERT: A 926 ASN cc_start: 0.8807 (t0) cc_final: 0.8455 (t0) REVERT: A 1005 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7537 (t-90) REVERT: A 1086 MET cc_start: 0.8898 (mmm) cc_final: 0.8665 (mmm) REVERT: A 1334 TRP cc_start: 0.8676 (m100) cc_final: 0.8394 (m100) REVERT: A 1351 ASP cc_start: 0.7675 (t0) cc_final: 0.7323 (t0) REVERT: A 1441 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 1449 ASP cc_start: 0.8204 (t0) cc_final: 0.7978 (t0) REVERT: B 240 LEU cc_start: 0.8877 (mm) cc_final: 0.8624 (mm) REVERT: B 298 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7119 (mmt) REVERT: B 337 LYS cc_start: 0.7636 (tmtt) cc_final: 0.6960 (tptt) REVERT: B 386 ASP cc_start: 0.8346 (m-30) cc_final: 0.8124 (m-30) REVERT: B 581 GLU cc_start: 0.7842 (tt0) cc_final: 0.7492 (mt-10) REVERT: B 825 GLN cc_start: 0.8240 (pp30) cc_final: 0.7551 (pp30) REVERT: C 41 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7672 (tm-30) REVERT: D 39 MET cc_start: 0.8446 (tpp) cc_final: 0.8132 (tpp) REVERT: E 57 ASP cc_start: 0.8630 (m-30) cc_final: 0.8379 (m-30) REVERT: E 92 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8158 (tp-100) REVERT: F 86 GLU cc_start: 0.7376 (mp0) cc_final: 0.6976 (mp0) REVERT: F 95 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8578 (ttpp) REVERT: F 121 ASP cc_start: 0.8520 (p0) cc_final: 0.8273 (p0) REVERT: H 55 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8418 (mtpp) REVERT: H 140 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.8130 (mtt-85) REVERT: I 40 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7346 (tpp-160) REVERT: I 64 GLU cc_start: 0.7806 (mp0) cc_final: 0.7602 (mm-30) REVERT: L 25 GLU cc_start: 0.7918 (mp0) cc_final: 0.7691 (mp0) REVERT: M 120 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7937 (tm-30) REVERT: M 277 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8733 (tt) REVERT: O 166 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7032 (tm130) REVERT: O 277 HIS cc_start: 0.8885 (m90) cc_final: 0.8465 (m90) REVERT: O 322 TYR cc_start: 0.8397 (m-80) cc_final: 0.7821 (m-80) REVERT: R 22 LYS cc_start: 0.6772 (ttmt) cc_final: 0.6449 (mptt) REVERT: R 200 LYS cc_start: 0.7334 (mmpt) cc_final: 0.7106 (mmtt) REVERT: U 358 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.5516 (tpt) outliers start: 86 outliers final: 46 residues processed: 615 average time/residue: 1.5435 time to fit residues: 1179.8168 Evaluate side-chains 604 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 551 time to evaluate : 4.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 287 GLN Chi-restraints excluded: chain O residue 326 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain U residue 51 MET Chi-restraints excluded: chain U residue 358 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 315 optimal weight: 0.1980 chunk 203 optimal weight: 1.9990 chunk 304 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 324 optimal weight: 0.9990 chunk 347 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 47 optimal weight: 0.0570 chunk 400 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN B 143 GLN B 265 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN I 67 GLN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45954 Z= 0.188 Angle : 0.549 10.984 62578 Z= 0.280 Chirality : 0.041 0.251 6990 Planarity : 0.004 0.072 7668 Dihedral : 14.199 173.078 7152 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.65 % Allowed : 15.96 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.12), residues: 5211 helix: 1.81 (0.12), residues: 1917 sheet: -0.08 (0.18), residues: 819 loop : -0.51 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1334 HIS 0.006 0.001 HIS A1005 PHE 0.026 0.001 PHE R 191 TYR 0.031 0.001 TYR E 26 ARG 0.013 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 588 time to evaluate : 5.161 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: A 192 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7158 (ppt170) REVERT: A 227 ARG cc_start: 0.9057 (tpp80) cc_final: 0.8853 (ttm-80) REVERT: A 311 GLN cc_start: 0.8655 (tp40) cc_final: 0.8052 (tp40) REVERT: A 313 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8578 (m170) REVERT: A 317 MET cc_start: 0.8329 (tpp) cc_final: 0.7934 (tpt) REVERT: A 926 ASN cc_start: 0.8800 (t0) cc_final: 0.8434 (t0) REVERT: A 1295 ASP cc_start: 0.8141 (t70) cc_final: 0.7637 (t0) REVERT: A 1351 ASP cc_start: 0.7664 (t0) cc_final: 0.7298 (t0) REVERT: A 1441 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 1449 ASP cc_start: 0.8235 (t0) cc_final: 0.8005 (t0) REVERT: B 36 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8090 (tm-30) REVERT: B 240 LEU cc_start: 0.8901 (mm) cc_final: 0.8658 (mm) REVERT: B 298 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.7037 (mmt) REVERT: B 337 LYS cc_start: 0.7618 (tmtt) cc_final: 0.6940 (tptt) REVERT: B 581 GLU cc_start: 0.7828 (tt0) cc_final: 0.7515 (mt-10) REVERT: B 825 GLN cc_start: 0.8214 (pp30) cc_final: 0.7529 (pp30) REVERT: D 39 MET cc_start: 0.8482 (tpp) cc_final: 0.8166 (tpp) REVERT: E 46 ASP cc_start: 0.7946 (t0) cc_final: 0.7717 (t0) REVERT: E 57 ASP cc_start: 0.8639 (m-30) cc_final: 0.8383 (m-30) REVERT: E 92 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8128 (tp-100) REVERT: F 86 GLU cc_start: 0.7405 (mp0) cc_final: 0.7030 (mp0) REVERT: F 95 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8576 (ttpp) REVERT: H 140 ARG cc_start: 0.8534 (mtt-85) cc_final: 0.8210 (mtt-85) REVERT: I 40 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7329 (tpt-90) REVERT: I 64 GLU cc_start: 0.7804 (mp0) cc_final: 0.7588 (mm-30) REVERT: J 36 ASP cc_start: 0.8492 (m-30) cc_final: 0.8209 (m-30) REVERT: K 8 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: L 25 GLU cc_start: 0.7877 (mp0) cc_final: 0.7632 (mp0) REVERT: M 229 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7652 (tp40) REVERT: M 277 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8626 (tt) REVERT: O 166 GLN cc_start: 0.7430 (tm-30) cc_final: 0.6935 (tm130) REVERT: O 277 HIS cc_start: 0.8906 (m90) cc_final: 0.8379 (m90) REVERT: O 322 TYR cc_start: 0.8399 (m-80) cc_final: 0.7775 (m-80) REVERT: R 22 LYS cc_start: 0.6721 (ttmt) cc_final: 0.6430 (mptt) REVERT: R 200 LYS cc_start: 0.7451 (mmpt) cc_final: 0.7236 (mmtt) outliers start: 77 outliers final: 39 residues processed: 622 average time/residue: 1.4945 time to fit residues: 1154.8928 Evaluate side-chains 613 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 568 time to evaluate : 5.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 287 GLN Chi-restraints excluded: chain O residue 312 LEU Chi-restraints excluded: chain O residue 326 GLU Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain U residue 51 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 463 optimal weight: 7.9990 chunk 488 optimal weight: 10.0000 chunk 445 optimal weight: 0.8980 chunk 475 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 206 optimal weight: 0.5980 chunk 373 optimal weight: 0.2980 chunk 145 optimal weight: 0.9990 chunk 429 optimal weight: 0.8980 chunk 449 optimal weight: 50.0000 chunk 473 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN B 143 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN E 65 ASN I 67 GLN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45954 Z= 0.202 Angle : 0.565 12.243 62578 Z= 0.287 Chirality : 0.041 0.208 6990 Planarity : 0.004 0.071 7668 Dihedral : 14.159 172.483 7152 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.37 % Allowed : 16.86 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.12), residues: 5211 helix: 1.85 (0.12), residues: 1913 sheet: -0.07 (0.18), residues: 816 loop : -0.48 (0.13), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 202 HIS 0.005 0.001 HIS A1005 PHE 0.027 0.001 PHE R 191 TYR 0.054 0.001 TYR E 90 ARG 0.015 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 573 time to evaluate : 5.048 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: A 311 GLN cc_start: 0.8663 (tp40) cc_final: 0.8060 (tp40) REVERT: A 313 HIS cc_start: 0.8896 (OUTLIER) cc_final: 0.8579 (m170) REVERT: A 317 MET cc_start: 0.8291 (tpp) cc_final: 0.7930 (tpt) REVERT: A 926 ASN cc_start: 0.8786 (t0) cc_final: 0.8401 (t0) REVERT: A 1295 ASP cc_start: 0.8146 (t70) cc_final: 0.7649 (t0) REVERT: A 1351 ASP cc_start: 0.7647 (t0) cc_final: 0.7300 (t0) REVERT: A 1441 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 1449 ASP cc_start: 0.8208 (t0) cc_final: 0.7964 (t0) REVERT: B 36 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8113 (tm-30) REVERT: B 240 LEU cc_start: 0.8878 (mm) cc_final: 0.8615 (mm) REVERT: B 298 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7064 (mmt) REVERT: B 337 LYS cc_start: 0.7639 (tmtt) cc_final: 0.6946 (tptt) REVERT: B 581 GLU cc_start: 0.7864 (tt0) cc_final: 0.7561 (mt-10) REVERT: B 825 GLN cc_start: 0.8205 (pp30) cc_final: 0.7516 (pp30) REVERT: D 39 MET cc_start: 0.8489 (tpp) cc_final: 0.8164 (tpp) REVERT: E 57 ASP cc_start: 0.8642 (m-30) cc_final: 0.8386 (m-30) REVERT: E 92 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8156 (tp-100) REVERT: F 86 GLU cc_start: 0.7400 (mp0) cc_final: 0.7030 (mp0) REVERT: F 95 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8585 (ttpp) REVERT: H 55 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8511 (mttp) REVERT: H 140 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.8162 (mtt-85) REVERT: I 40 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7203 (tpp80) REVERT: I 64 GLU cc_start: 0.7735 (mp0) cc_final: 0.7522 (mm-30) REVERT: J 36 ASP cc_start: 0.8498 (m-30) cc_final: 0.8215 (m-30) REVERT: K 8 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: L 25 GLU cc_start: 0.7875 (mp0) cc_final: 0.7645 (mp0) REVERT: M 227 GLN cc_start: 0.8506 (mp10) cc_final: 0.8135 (pm20) REVERT: M 229 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7702 (tp40) REVERT: M 277 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8638 (tt) REVERT: M 283 VAL cc_start: 0.8871 (m) cc_final: 0.8611 (p) REVERT: O 277 HIS cc_start: 0.8909 (m90) cc_final: 0.8319 (m90) REVERT: O 322 TYR cc_start: 0.8381 (m-80) cc_final: 0.7769 (m-80) REVERT: R 22 LYS cc_start: 0.6767 (ttmt) cc_final: 0.6467 (mptt) outliers start: 64 outliers final: 44 residues processed: 601 average time/residue: 1.5355 time to fit residues: 1147.7752 Evaluate side-chains 608 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 559 time to evaluate : 5.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 287 GLN Chi-restraints excluded: chain O residue 326 GLU Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain U residue 51 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 312 optimal weight: 0.0270 chunk 502 optimal weight: 7.9990 chunk 306 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 349 optimal weight: 0.0980 chunk 527 optimal weight: 30.0000 chunk 485 optimal weight: 40.0000 chunk 419 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 324 optimal weight: 0.9990 chunk 257 optimal weight: 0.0770 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A1032 GLN B 143 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN C 5 ASN E 71 GLN I 67 GLN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45954 Z= 0.170 Angle : 0.565 12.469 62578 Z= 0.285 Chirality : 0.041 0.210 6990 Planarity : 0.004 0.070 7668 Dihedral : 14.130 171.865 7152 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.09 % Allowed : 17.31 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.12), residues: 5211 helix: 1.90 (0.12), residues: 1908 sheet: -0.05 (0.18), residues: 832 loop : -0.45 (0.13), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 202 HIS 0.005 0.001 HIS A1005 PHE 0.032 0.001 PHE A 397 TYR 0.036 0.001 TYR E 90 ARG 0.015 0.000 ARG A 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10422 Ramachandran restraints generated. 5211 Oldfield, 0 Emsley, 5211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 594 time to evaluate : 5.049 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: A 311 GLN cc_start: 0.8675 (tp40) cc_final: 0.8118 (tp40) REVERT: A 313 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8576 (m170) REVERT: A 317 MET cc_start: 0.8223 (tpp) cc_final: 0.7876 (tpt) REVERT: A 926 ASN cc_start: 0.8725 (t0) cc_final: 0.8338 (t0) REVERT: A 1295 ASP cc_start: 0.8118 (t70) cc_final: 0.7702 (t0) REVERT: A 1351 ASP cc_start: 0.7652 (t0) cc_final: 0.7299 (t0) REVERT: A 1441 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 1449 ASP cc_start: 0.8172 (t0) cc_final: 0.7941 (t0) REVERT: B 240 LEU cc_start: 0.8850 (mm) cc_final: 0.8595 (mm) REVERT: B 298 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.7059 (mmt) REVERT: B 337 LYS cc_start: 0.7571 (tmtt) cc_final: 0.6900 (tptt) REVERT: B 581 GLU cc_start: 0.7851 (tt0) cc_final: 0.7553 (mt-10) REVERT: B 825 GLN cc_start: 0.8190 (pp30) cc_final: 0.7539 (pp30) REVERT: D 39 MET cc_start: 0.8471 (tpp) cc_final: 0.8135 (tpp) REVERT: E 46 ASP cc_start: 0.7887 (t0) cc_final: 0.7681 (t0) REVERT: E 57 ASP cc_start: 0.8624 (m-30) cc_final: 0.8367 (m-30) REVERT: E 92 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8091 (tp-100) REVERT: F 86 GLU cc_start: 0.7392 (mp0) cc_final: 0.7039 (mp0) REVERT: F 95 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8582 (ttpp) REVERT: H 55 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8507 (mttp) REVERT: I 40 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7175 (tpp80) REVERT: J 36 ASP cc_start: 0.8508 (m-30) cc_final: 0.8238 (m-30) REVERT: K 8 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: L 25 GLU cc_start: 0.7822 (mp0) cc_final: 0.7604 (mp0) REVERT: M 115 MET cc_start: 0.7252 (tmt) cc_final: 0.7005 (tmt) REVERT: M 227 GLN cc_start: 0.8468 (mp10) cc_final: 0.8119 (pm20) REVERT: M 229 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7713 (tp40) REVERT: M 249 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8817 (t) REVERT: M 259 TYR cc_start: 0.8520 (t80) cc_final: 0.8078 (t80) REVERT: M 277 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8507 (tt) REVERT: O 166 GLN cc_start: 0.7373 (tm-30) cc_final: 0.6865 (tm130) REVERT: O 277 HIS cc_start: 0.8866 (m90) cc_final: 0.8210 (m90) REVERT: O 322 TYR cc_start: 0.8363 (m-80) cc_final: 0.7764 (m-80) REVERT: Q 163 GLU cc_start: 0.5951 (pp20) cc_final: 0.5696 (tm-30) REVERT: Q 177 MET cc_start: 0.2434 (pmm) cc_final: 0.0852 (OUTLIER) REVERT: R 22 LYS cc_start: 0.6738 (ttmt) cc_final: 0.6469 (mptt) REVERT: U 358 MET cc_start: 0.4567 (tpt) cc_final: 0.2945 (mpp) outliers start: 51 outliers final: 35 residues processed: 617 average time/residue: 1.5198 time to fit residues: 1168.0095 Evaluate side-chains 610 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 570 time to evaluate : 5.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 326 GLU Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain U residue 51 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 333 optimal weight: 50.0000 chunk 447 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 386 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 420 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 431 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A1032 GLN B 143 GLN B 265 GLN C 5 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 ASN ** 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 = 0.4110 r_free = 0.4110 target = 0.173003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.091482 restraints weight = 59921.600| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.85 r_work: 0.2769 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 45954 Z= 0.343 Angle : 0.610 13.253 62578 Z= 0.307 Chirality : 0.043 0.208 6990 Planarity : 0.004 0.070 7668 Dihedral : 14.155 172.924 7152 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.14 % Allowed : 17.78 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.12), residues: 5211 helix: 1.80 (0.12), residues: 1920 sheet: -0.06 (0.18), residues: 801 loop : -0.48 (0.13), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A1334 HIS 0.005 0.001 HIS A1005 PHE 0.032 0.001 PHE A 397 TYR 0.057 0.001 TYR E 90 ARG 0.015 0.000 ARG A 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18288.04 seconds wall clock time: 321 minutes 49.58 seconds (19309.58 seconds total)