Starting phenix.real_space_refine on Mon Sep 14 19:23:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7obb_12797/09_2026/7obb_12797.cif Found real_map, /net/cci-nas-00/data/ceres_data/7obb_12797/09_2026/7obb_12797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7obb_12797/09_2026/7obb_12797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7obb_12797/09_2026/7obb_12797.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7obb_12797/09_2026/7obb_12797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7obb_12797/09_2026/7obb_12797.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7obb_12797/09_2026/7obb_12797.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7obb_12797/09_2026/7obb_12797.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 17 5.49 5 S 231 5.16 5 C 20933 2.51 5 N 5757 2.21 5 O 6103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33048 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 12050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1510, 12050 Classifications: {'peptide': 1510} Link IDs: {'PCIS': 3, 'PTRANS': 71, 'TRANS': 1435} Chain breaks: 9 Chain: "B" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1130, 8962 Classifications: {'peptide': 1130} Link IDs: {'PTRANS': 66, 'TRANS': 1063} Chain breaks: 1 Chain: "C" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2474 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 16, 'TRANS': 292} Chain: "E" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1728 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 619 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "G" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1183 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain breaks: 1 Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 809 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 837 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "N" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1083 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 25, 'TRANS': 123} Chain: "T" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 64 48.575 68.603 75.920 1.00113.72 S ATOM 483 SG CYS A 67 47.852 65.685 72.267 1.00113.71 S ATOM 776 SG CYS A 104 69.013 90.787 33.082 1.00125.67 S ATOM 798 SG CYS A 107 65.958 89.702 30.366 1.00127.02 S ATOM 1582 SG CYS A 205 69.766 90.025 29.379 1.00121.24 S ATOM 20508 SG CYS B1070 54.056 58.067 58.260 1.00104.20 S ATOM 20728 SG CYS B1098 52.395 61.656 59.482 1.00108.00 S ATOM 20749 SG CYS B1101 52.409 60.424 56.063 1.00110.31 S ATOM 28292 SG CYS I 20 119.186 140.891 62.617 1.00 66.74 S ATOM 28312 SG CYS I 23 116.083 140.656 64.672 1.00 71.70 S ATOM 28412 SG CYS I 38 114.856 139.665 61.395 1.00 76.83 S ATOM 28437 SG CYS I 41 116.119 143.175 62.084 1.00 75.84 S ATOM 28708 SG CYS I 87 124.989 60.140 74.086 1.00 89.44 S ATOM 28732 SG CYS I 90 128.328 59.632 72.506 1.00 97.08 S ATOM 28931 SG CYS I 115 127.852 62.525 74.687 1.00 78.39 S ATOM 28952 SG CYS I 118 125.894 61.585 70.642 1.00 87.80 S ATOM 29077 SG CYS J 7 103.561 65.528 124.945 1.00 29.77 S ATOM 29101 SG CYS J 10 105.033 60.925 125.696 1.00 32.82 S ATOM 29365 SG CYS J 44 107.064 63.310 124.030 1.00 40.40 S ATOM 29371 SG CYS J 45 105.921 64.358 127.494 1.00 43.99 S ATOM 30443 SG CYS L 19 75.862 99.517 124.167 1.00 54.70 S ATOM 30462 SG CYS L 22 75.664 101.105 127.921 1.00 61.13 S ATOM 30579 SG CYS L 36 72.589 100.962 126.054 1.00 64.34 S ATOM 30605 SG CYS L 39 75.911 103.448 125.213 1.00 68.61 S Time building chain proxies: 5.54, per 1000 atoms: 0.17 Number of scatterers: 33048 At special positions: 0 Unit cell: (159.468, 170.976, 165.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 231 16.00 P 17 15.00 O 6103 8.00 N 5757 7.00 C 20933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 64 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 205 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 104 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1101 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1070 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 38 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 41 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 23 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 115 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 118 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 87 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 90 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 24 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7700 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 51 sheets defined 30.9% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 4.192A pdb=" N LEU A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 4.225A pdb=" N LEU A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 130 removed outlier: 3.584A pdb=" N LEU A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.820A pdb=" N VAL A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.602A pdb=" N ILE A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 removed outlier: 4.121A pdb=" N GLU A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 345 removed outlier: 4.001A pdb=" N LEU A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 403 removed outlier: 3.670A pdb=" N TRP A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.614A pdb=" N LEU A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.668A pdb=" N LEU A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 520 removed outlier: 4.133A pdb=" N ARG A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.858A pdb=" N LYS A 583 " --> pdb=" O ALA A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.542A pdb=" N ALA A 606 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 removed outlier: 3.940A pdb=" N ALA A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.856A pdb=" N TYR A 658 " --> pdb=" O MET A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 696 removed outlier: 3.576A pdb=" N VAL A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 760 through 765 Processing helix chain 'A' and resid 771 through 787 removed outlier: 3.940A pdb=" N LEU A 778 " --> pdb=" O SER A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.705A pdb=" N THR A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 832 removed outlier: 4.006A pdb=" N ALA A 829 " --> pdb=" O GLN A 825 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 850 Processing helix chain 'A' and resid 857 through 866 removed outlier: 3.504A pdb=" N ILE A 861 " --> pdb=" O ASP A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 881 removed outlier: 3.702A pdb=" N GLU A 875 " --> pdb=" O HIS A 871 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 876 " --> pdb=" O TYR A 872 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 944 through 949 Processing helix chain 'A' and resid 960 through 981 removed outlier: 3.656A pdb=" N GLY A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.768A pdb=" N ASP A1022 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1035 removed outlier: 3.613A pdb=" N THR A1029 " --> pdb=" O ILE A1026 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE A1031 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A1032 " --> pdb=" O THR A1029 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN A1033 " --> pdb=" O GLN A1030 " (cutoff:3.500A) Proline residue: A1034 - end of helix No H-bonds generated for 'chain 'A' and resid 1026 through 1035' Processing helix chain 'A' and resid 1036 through 1042 removed outlier: 3.622A pdb=" N LEU A1040 " --> pdb=" O GLN A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1049 Processing helix chain 'A' and resid 1062 through 1079 removed outlier: 3.909A pdb=" N HIS A1068 " --> pdb=" O LYS A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 removed outlier: 3.977A pdb=" N LYS A1095 " --> pdb=" O SER A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1102 Processing helix chain 'A' and resid 1114 through 1127 Processing helix chain 'A' and resid 1133 through 1138 Processing helix chain 'A' and resid 1160 through 1180 removed outlier: 4.196A pdb=" N LYS A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1203 Processing helix chain 'A' and resid 1210 through 1218 removed outlier: 3.824A pdb=" N LEU A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1253 removed outlier: 3.785A pdb=" N LEU A1248 " --> pdb=" O GLY A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1285 removed outlier: 3.527A pdb=" N LEU A1275 " --> pdb=" O THR A1271 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A1276 " --> pdb=" O LYS A1272 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A1283 " --> pdb=" O LYS A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1292 Processing helix chain 'A' and resid 1323 through 1327 Processing helix chain 'A' and resid 1334 through 1359 removed outlier: 4.140A pdb=" N ILE A1338 " --> pdb=" O ARG A1334 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE A1347 " --> pdb=" O GLU A1343 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A1353 " --> pdb=" O LEU A1349 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A1359 " --> pdb=" O LYS A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1507 Processing helix chain 'A' and resid 1539 through 1548 removed outlier: 3.865A pdb=" N LEU A1543 " --> pdb=" O ASP A1539 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1600 removed outlier: 3.519A pdb=" N LEU A1600 " --> pdb=" O LEU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1604 through 1612 removed outlier: 3.863A pdb=" N ILE A1608 " --> pdb=" O ASP A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1632 removed outlier: 4.151A pdb=" N TYR A1632 " --> pdb=" O VAL A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1649 removed outlier: 3.712A pdb=" N LEU A1641 " --> pdb=" O ASP A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1665 removed outlier: 3.552A pdb=" N ILE A1662 " --> pdb=" O ARG A1659 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG A1663 " --> pdb=" O PHE A1660 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A1664 " --> pdb=" O GLY A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1675 removed outlier: 4.006A pdb=" N GLU A1675 " --> pdb=" O GLN A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1686 Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 39 through 49 removed outlier: 4.040A pdb=" N SER B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'B' and resid 99 through 106 removed outlier: 3.594A pdb=" N CYS B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 removed outlier: 3.615A pdb=" N GLU B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.529A pdb=" N LYS B 199 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 200 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY B 202 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.658A pdb=" N VAL B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.694A pdb=" N LEU B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 269 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.805A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 338 through 358 removed outlier: 3.536A pdb=" N LEU B 348 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 358 " --> pdb=" O PHE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.646A pdb=" N LEU B 380 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 437 removed outlier: 4.550A pdb=" N LEU B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 468 removed outlier: 3.554A pdb=" N TYR B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.646A pdb=" N ARG B 488 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 529 through 537 Processing helix chain 'B' and resid 571 through 584 removed outlier: 3.944A pdb=" N SER B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 584 " --> pdb=" O HIS B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 681 through 692 removed outlier: 4.172A pdb=" N GLN B 690 " --> pdb=" O MET B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 730 removed outlier: 3.654A pdb=" N TYR B 730 " --> pdb=" O MET B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 735 removed outlier: 3.626A pdb=" N ASN B 734 " --> pdb=" O ASP B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 767 removed outlier: 3.509A pdb=" N GLY B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 804 removed outlier: 3.570A pdb=" N VAL B 803 " --> pdb=" O ASP B 800 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 804 " --> pdb=" O PRO B 801 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 800 through 804' Processing helix chain 'B' and resid 898 through 902 Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.917A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 969 removed outlier: 3.861A pdb=" N PHE B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 964 " --> pdb=" O GLU B 960 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 969 " --> pdb=" O MET B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1049 removed outlier: 3.504A pdb=" N GLY B1049 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1060 removed outlier: 3.712A pdb=" N LEU B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1124 Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.689A pdb=" N LYS C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 83 removed outlier: 4.187A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 82 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.608A pdb=" N ALA C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.662A pdb=" N LEU C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 185' Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.569A pdb=" N ALA C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.776A pdb=" N ASP C 281 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 Processing helix chain 'C' and resid 322 through 344 removed outlier: 4.250A pdb=" N VAL C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET C 330 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 19 removed outlier: 3.762A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG E 9 " --> pdb=" O GLU E 5 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE E 17 " --> pdb=" O ILE E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.584A pdb=" N GLY E 25 " --> pdb=" O HIS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 37 through 43 removed outlier: 3.543A pdb=" N LYS E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 removed outlier: 3.735A pdb=" N ILE E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 162 Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'F' and resid 58 through 72 Processing helix chain 'F' and resid 88 through 100 removed outlier: 3.654A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 67 through 77 Processing helix chain 'H' and resid 84 through 88 removed outlier: 3.637A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 53 removed outlier: 3.964A pdb=" N GLU I 51 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY I 52 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.993A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 60 removed outlier: 3.654A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG K 56 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET K 60 " --> pdb=" O ARG K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 126 removed outlier: 3.898A pdb=" N LEU K 103 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS K 109 " --> pdb=" O ASN K 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA K 116 " --> pdb=" O ASP K 112 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS K 119 " --> pdb=" O GLU K 115 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 removed outlier: 4.074A pdb=" N GLY A 14 " --> pdb=" O ASP B1133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 88 removed outlier: 6.922A pdb=" N ASP A 300 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N LEU A 85 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N PHE A 298 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 218 Processing sheet with id=AA4, first strand: chain 'A' and resid 436 through 437 removed outlier: 3.675A pdb=" N ILE B1035 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 565 removed outlier: 7.676A pdb=" N LEU A 575 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 444 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU A 577 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS A 446 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 561 through 565 removed outlier: 3.804A pdb=" N ALA A 440 " --> pdb=" O ARG B1013 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 458 through 459 removed outlier: 6.250A pdb=" N ILE A 458 " --> pdb=" O LEU A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 467 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 675 through 677 removed outlier: 6.316A pdb=" N VAL H 91 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1007 through 1008 removed outlier: 6.587A pdb=" N VAL A1007 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1264 through 1265 Processing sheet with id=AB3, first strand: chain 'A' and resid 1512 through 1517 removed outlier: 4.339A pdb=" N ASP A1514 " --> pdb=" O THR A1528 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A1317 " --> pdb=" O VAL A1527 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A1315 " --> pdb=" O VAL A1529 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1304 through 1305 Processing sheet with id=AB5, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.527A pdb=" N GLU F 116 " --> pdb=" O ARG F 108 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A1714 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A1715 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 68 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 82 removed outlier: 6.635A pdb=" N ASP B 117 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA B 80 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR B 115 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE B 82 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LYS B 113 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 135 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA B 116 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N PHE B 133 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE B 118 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS B 131 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AB9, first strand: chain 'B' and resid 372 through 375 removed outlier: 3.637A pdb=" N LEU B 182 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N MET B 181 " --> pdb=" O HIS B 473 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 191 through 194 removed outlier: 5.348A pdb=" N TYR B 208 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR B 228 " --> pdb=" O TYR B 208 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN B 223 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE B 239 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 238 " --> pdb=" O PHE B 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC3, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC4, first strand: chain 'B' and resid 540 through 541 removed outlier: 3.763A pdb=" N THR B 540 " --> pdb=" O TRP B 565 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N MET B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 558 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY B 564 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 556 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU B 610 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU B 612 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU B 557 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 695 through 696 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 695 through 696 current: chain 'B' and resid 913 through 915 removed outlier: 7.241A pdb=" N MET B 757 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 896 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 759 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS B 882 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 712 through 714 removed outlier: 7.441A pdb=" N CYS B 866 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL B 854 " --> pdb=" O CYS B 866 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 868 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE B 852 " --> pdb=" O CYS B 868 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR B 870 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 714 removed outlier: 7.441A pdb=" N CYS B 866 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL B 854 " --> pdb=" O CYS B 866 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 868 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE B 852 " --> pdb=" O CYS B 868 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR B 870 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 722 through 723 Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 794 Processing sheet with id=AD1, first strand: chain 'B' and resid 824 through 826 removed outlier: 6.891A pdb=" N MET B 839 " --> pdb=" O TYR B 825 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1064 through 1070 Processing sheet with id=AD3, first strand: chain 'B' and resid 1079 through 1081 Processing sheet with id=AD4, first strand: chain 'C' and resid 53 through 55 removed outlier: 6.582A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C 236 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 138 through 140 removed outlier: 3.870A pdb=" N PHE C 140 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN C 97 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU C 207 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 138 through 140 removed outlier: 3.870A pdb=" N PHE C 140 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AD8, first strand: chain 'C' and resid 228 through 232 removed outlier: 7.159A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA C 231 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER C 309 " --> pdb=" O ALA C 231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 262 through 267 removed outlier: 3.707A pdb=" N LYS C 270 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.763A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 150 removed outlier: 5.785A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 57 through 58 Processing sheet with id=AE5, first strand: chain 'G' and resid 89 through 98 removed outlier: 6.943A pdb=" N VAL G 121 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR G 93 " --> pdb=" O ASP G 119 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASP G 119 " --> pdb=" O TYR G 93 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN G 95 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU G 117 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 134 through 138 removed outlier: 6.116A pdb=" N VAL G 135 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU G 146 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS G 137 " --> pdb=" O GLY G 144 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 183 through 186 removed outlier: 4.376A pdb=" N ARG G 183 " --> pdb=" O ARG G 195 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP G 185 " --> pdb=" O CYS G 193 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS G 193 " --> pdb=" O ASP G 185 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 12 through 14 removed outlier: 7.634A pdb=" N SER I 12 " --> pdb=" O GLN M 34 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN M 34 " --> pdb=" O SER I 12 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 35 through 37 Processing sheet with id=AF1, first strand: chain 'I' and resid 82 through 83 Processing sheet with id=AF2, first strand: chain 'K' and resid 27 through 28 Processing sheet with id=AF3, first strand: chain 'K' and resid 39 through 41 Processing sheet with id=AF4, first strand: chain 'L' and resid 16 through 18 Processing sheet with id=AF5, first strand: chain 'N' and resid 24 through 25 removed outlier: 4.540A pdb=" N HIS M 87 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN N 67 " --> pdb=" O VAL N 82 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY N 65 " --> pdb=" O SER N 84 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 60 through 62 removed outlier: 7.009A pdb=" N MET M 99 " --> pdb=" O SER M 8 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG M 10 " --> pdb=" O MET M 99 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL M 101 " --> pdb=" O ARG M 10 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN M 12 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ASP M 103 " --> pdb=" O GLN M 12 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA M 23 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE M 107 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU M 25 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET M 109 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN M 27 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL M 24 " --> pdb=" O LEU N 95 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU N 95 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 26 " --> pdb=" O THR N 93 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR N 93 " --> pdb=" O VAL M 26 " (cutoff:3.500A) 1027 hydrogen bonds defined for protein. 2823 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.92 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8503 1.33 - 1.45: 7468 1.45 - 1.58: 17415 1.58 - 1.70: 33 1.70 - 1.83: 356 Bond restraints: 33775 Sorted by residual: bond pdb=" CA ALA A 463 " pdb=" CB ALA A 463 " ideal model delta sigma weight residual 1.531 1.446 0.085 1.72e-02 3.38e+03 2.45e+01 bond pdb=" N MET A 460 " pdb=" CA MET A 460 " ideal model delta sigma weight residual 1.459 1.404 0.055 1.21e-02 6.83e+03 2.05e+01 bond pdb=" C ARG A 558 " pdb=" N PRO A 559 " ideal model delta sigma weight residual 1.334 1.369 -0.036 8.40e-03 1.42e+04 1.81e+01 bond pdb=" CA TYR A 468 " pdb=" CB TYR A 468 " ideal model delta sigma weight residual 1.534 1.471 0.063 1.57e-02 4.06e+03 1.59e+01 bond pdb=" C LEU B 489 " pdb=" N LEU B 490 " ideal model delta sigma weight residual 1.333 1.234 0.099 2.74e-02 1.33e+03 1.30e+01 ... (remaining 33770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 43807 2.47 - 4.95: 1634 4.95 - 7.42: 212 7.42 - 9.90: 55 9.90 - 12.37: 13 Bond angle restraints: 45721 Sorted by residual: angle pdb=" N THR A 464 " pdb=" CA THR A 464 " pdb=" C THR A 464 " ideal model delta sigma weight residual 113.72 102.71 11.01 1.30e+00 5.92e-01 7.17e+01 angle pdb=" N GLN A 133 " pdb=" CA GLN A 133 " pdb=" C GLN A 133 " ideal model delta sigma weight residual 113.50 105.80 7.70 1.23e+00 6.61e-01 3.92e+01 angle pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N PRO A 459 " ideal model delta sigma weight residual 119.33 114.63 4.70 8.00e-01 1.56e+00 3.45e+01 angle pdb=" C LYS B 69 " pdb=" N ASP B 70 " pdb=" CA ASP B 70 " ideal model delta sigma weight residual 121.54 132.08 -10.54 1.91e+00 2.74e-01 3.05e+01 angle pdb=" N THR A 467 " pdb=" CA THR A 467 " pdb=" C THR A 467 " ideal model delta sigma weight residual 108.90 117.63 -8.73 1.63e+00 3.76e-01 2.87e+01 ... (remaining 45716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 18909 15.61 - 31.22: 1219 31.22 - 46.83: 317 46.83 - 62.43: 68 62.43 - 78.04: 22 Dihedral angle restraints: 20535 sinusoidal: 8601 harmonic: 11934 Sorted by residual: dihedral pdb=" CA HIS A 491 " pdb=" C HIS A 491 " pdb=" N PRO A 492 " pdb=" CA PRO A 492 " ideal model delta harmonic sigma weight residual 180.00 134.83 45.17 0 5.00e+00 4.00e-02 8.16e+01 dihedral pdb=" CA LEU G 86 " pdb=" C LEU G 86 " pdb=" N LEU G 87 " pdb=" CA LEU G 87 " ideal model delta harmonic sigma weight residual 180.00 -144.25 -35.75 0 5.00e+00 4.00e-02 5.11e+01 dihedral pdb=" N LYS A 465 " pdb=" C LYS A 465 " pdb=" CA LYS A 465 " pdb=" CB LYS A 465 " ideal model delta harmonic sigma weight residual 122.80 138.79 -15.99 0 2.50e+00 1.60e-01 4.09e+01 ... (remaining 20532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 4888 0.139 - 0.278: 154 0.278 - 0.416: 3 0.416 - 0.555: 0 0.555 - 0.694: 3 Chirality restraints: 5048 Sorted by residual: chirality pdb=" CA LYS A 465 " pdb=" N LYS A 465 " pdb=" C LYS A 465 " pdb=" CB LYS A 465 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ALA A 463 " pdb=" N ALA A 463 " pdb=" C ALA A 463 " pdb=" CB ALA A 463 " both_signs ideal model delta sigma weight residual False 2.48 1.84 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA MET A 460 " pdb=" N MET A 460 " pdb=" C MET A 460 " pdb=" CB MET A 460 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.60e+00 ... (remaining 5045 not shown) Planarity restraints: 5872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 387 " 0.031 2.00e-02 2.50e+03 6.29e-02 3.96e+01 pdb=" C LEU A 387 " -0.109 2.00e-02 2.50e+03 pdb=" O LEU A 387 " 0.043 2.00e-02 2.50e+03 pdb=" N TYR A 388 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 458 " 0.029 2.00e-02 2.50e+03 5.96e-02 3.55e+01 pdb=" C ILE A 458 " -0.103 2.00e-02 2.50e+03 pdb=" O ILE A 458 " 0.040 2.00e-02 2.50e+03 pdb=" N PRO A 459 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY N 154 " -0.029 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C GLY N 154 " 0.098 2.00e-02 2.50e+03 pdb=" O GLY N 154 " -0.036 2.00e-02 2.50e+03 pdb=" N ASN N 155 " -0.033 2.00e-02 2.50e+03 ... (remaining 5869 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 6736 2.78 - 3.31: 29120 3.31 - 3.84: 53554 3.84 - 4.37: 63850 4.37 - 4.90: 111020 Nonbonded interactions: 264280 Sorted by model distance: nonbonded pdb=" O ALA A 639 " pdb=" OG1 THR A 643 " model vdw 2.245 3.040 nonbonded pdb=" OG SER B 260 " pdb=" OG SER M 29 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A1601 " pdb=" OE2 GLU A1624 " model vdw 2.268 3.040 nonbonded pdb=" O LEU A 745 " pdb=" OG SER H 117 " model vdw 2.268 3.040 nonbonded pdb=" O ARG A 37 " pdb=" OG SER A 46 " model vdw 2.277 3.040 ... (remaining 264275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.110 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.614 33800 Z= 0.469 Angle : 1.196 45.700 45745 Z= 0.623 Chirality : 0.065 0.694 5048 Planarity : 0.009 0.084 5872 Dihedral : 11.910 78.042 12835 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.76 % Favored : 92.22 % Rotamer: Outliers : 0.64 % Allowed : 4.64 % Favored : 94.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.18 (0.11), residues: 4061 helix: -3.51 (0.09), residues: 1214 sheet: -2.26 (0.19), residues: 621 loop : -2.50 (0.11), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG J 47 TYR 0.066 0.004 TYR B 999 PHE 0.050 0.004 PHE C 308 TRP 0.061 0.004 TRP A 846 HIS 0.025 0.003 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00956 / 0.41 (33775) covalent geometry : angle 1.12129 / 0.62 (45721) hydrogen bonds : bond 0.22105 / 14.39 ( 992) hydrogen bonds : angle 9.17522 / 6.43 ( 2823) metal coordination : bond 0.24694 / 12.64 ( 25) metal coordination : angle 18.15535 / 10.26 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 643 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7168 (tpp) cc_final: 0.6688 (tpp) REVERT: A 449 MET cc_start: 0.6889 (tmm) cc_final: 0.6421 (ttp) REVERT: A 1048 MET cc_start: 0.6041 (mtp) cc_final: 0.5663 (ttm) REVERT: E 98 ASN cc_start: 0.8315 (m-40) cc_final: 0.7947 (p0) REVERT: F 125 ILE cc_start: 0.8288 (pt) cc_final: 0.7593 (pt) REVERT: H 123 MET cc_start: 0.5604 (ttt) cc_final: 0.5329 (ttt) REVERT: K 76 SER cc_start: 0.8098 (m) cc_final: 0.7640 (t) REVERT: M 92 LEU cc_start: 0.7488 (tp) cc_final: 0.7153 (tp) outliers start: 23 outliers final: 4 residues processed: 662 average time/residue: 0.2121 time to fit residues: 223.3642 Evaluate side-chains 350 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 346 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 1594 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 180 HIS ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 HIS ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 ASN A 832 ASN A 886 HIS A 995 HIS A1036 GLN A1076 GLN ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 ASN A1584 ASN B 123 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 227 HIS B 231 ASN B 237 ASN B 313 ASN B 365 ASN B 371 ASN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 846 ASN ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 918 HIS ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 HIS B1097 ASN C 160 ASN C 166 HIS C 172 HIS ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS G 42 ASN G 56 HIS G 148 HIS H 131 ASN I 92 HIS I 117 ASN J 52 HIS K 45 HIS K 105 ASN K 109 HIS L 23 HIS L 26 ASN ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 GLN M 30 ASN M 93 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.098614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.077156 restraints weight = 124740.623| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.05 r_work: 0.3288 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33800 Z= 0.170 Angle : 0.750 13.850 45745 Z= 0.384 Chirality : 0.047 0.276 5048 Planarity : 0.006 0.064 5872 Dihedral : 9.091 60.870 4685 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.08 % Allowed : 10.11 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.12), residues: 4061 helix: -2.06 (0.13), residues: 1216 sheet: -1.83 (0.19), residues: 648 loop : -2.11 (0.12), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 181 TYR 0.022 0.002 TYR C 95 PHE 0.025 0.002 PHE M 107 TRP 0.028 0.002 TRP A 846 HIS 0.011 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (33775) covalent geometry : angle 0.73720 / 0.38 (45721) hydrogen bonds : bond 0.04761 / 3.15 ( 992) hydrogen bonds : angle 6.52366 / 4.59 ( 2823) metal coordination : bond 0.01136 / 0.61 ( 25) metal coordination : angle 6.03616 / 3.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 404 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7600 (pt) cc_final: 0.7270 (mt) REVERT: A 170 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8686 (mm-40) REVERT: A 200 MET cc_start: 0.6716 (tpp) cc_final: 0.6201 (tpp) REVERT: A 300 ASP cc_start: 0.8504 (p0) cc_final: 0.8013 (t70) REVERT: A 345 MET cc_start: 0.7241 (tpt) cc_final: 0.6717 (mmp) REVERT: A 391 TRP cc_start: 0.6891 (m-10) cc_final: 0.6363 (m-90) REVERT: A 400 ILE cc_start: 0.8204 (mm) cc_final: 0.7974 (mm) REVERT: A 406 MET cc_start: 0.7516 (mmm) cc_final: 0.7310 (mmm) REVERT: A 433 MET cc_start: 0.8083 (tpp) cc_final: 0.7449 (mmt) REVERT: A 897 MET cc_start: 0.8569 (mtm) cc_final: 0.8297 (mtm) REVERT: A 929 MET cc_start: 0.8580 (mtt) cc_final: 0.8202 (mtm) REVERT: A 1123 MET cc_start: 0.9299 (mtp) cc_final: 0.8835 (mtp) REVERT: A 1288 VAL cc_start: 0.7515 (OUTLIER) cc_final: 0.7243 (m) REVERT: B 184 MET cc_start: 0.8928 (mmm) cc_final: 0.8690 (mmm) REVERT: B 639 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8418 (pt0) REVERT: B 932 SER cc_start: 0.8769 (t) cc_final: 0.8558 (m) REVERT: B 1080 LEU cc_start: 0.8559 (tp) cc_final: 0.8186 (tt) REVERT: B 1097 ASN cc_start: 0.8412 (m110) cc_final: 0.7747 (p0) REVERT: C 56 MET cc_start: 0.8506 (ttt) cc_final: 0.8262 (ttt) REVERT: E 24 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8691 (mtt180) REVERT: E 44 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7581 (m-10) REVERT: E 98 ASN cc_start: 0.9295 (m-40) cc_final: 0.8451 (p0) REVERT: E 121 MET cc_start: 0.9002 (tpt) cc_final: 0.8584 (ttt) REVERT: E 147 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8624 (mm-30) REVERT: F 95 LYS cc_start: 0.9221 (tppt) cc_final: 0.8957 (ttmt) REVERT: G 62 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7261 (ttm110) REVERT: G 73 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8915 (pp20) REVERT: G 76 ASP cc_start: 0.8921 (t0) cc_final: 0.8639 (m-30) REVERT: I 107 GLU cc_start: 0.8492 (pm20) cc_final: 0.7959 (pm20) REVERT: I 113 TYR cc_start: 0.8971 (m-80) cc_final: 0.7684 (m-80) REVERT: J 26 GLN cc_start: 0.9219 (tp40) cc_final: 0.8628 (tm-30) REVERT: K 76 SER cc_start: 0.8867 (m) cc_final: 0.8632 (t) REVERT: M 25 LEU cc_start: 0.8524 (mm) cc_final: 0.8122 (mm) REVERT: M 53 ARG cc_start: 0.7108 (ptp90) cc_final: 0.6877 (ptp90) REVERT: M 64 THR cc_start: 0.7887 (m) cc_final: 0.7402 (p) REVERT: M 80 LYS cc_start: 0.8043 (pttm) cc_final: 0.7490 (mmtt) REVERT: M 88 PHE cc_start: 0.8655 (m-10) cc_final: 0.8356 (m-10) REVERT: M 98 GLN cc_start: 0.8173 (pp30) cc_final: 0.7962 (pp30) REVERT: M 105 GLU cc_start: 0.5259 (pm20) cc_final: 0.4956 (pm20) REVERT: N 26 GLU cc_start: 0.8364 (pm20) cc_final: 0.8039 (tm-30) REVERT: N 57 ASN cc_start: 0.8728 (t0) cc_final: 0.8509 (m-40) REVERT: N 59 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8426 (mmm160) outliers start: 75 outliers final: 39 residues processed: 453 average time/residue: 0.1936 time to fit residues: 144.2285 Evaluate side-chains 377 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 334 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1094 GLN Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 103 ASP Chi-restraints excluded: chain N residue 51 PHE Chi-restraints excluded: chain N residue 56 PHE Chi-restraints excluded: chain N residue 146 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 47 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 354 optimal weight: 3.9990 chunk 5 optimal weight: 40.0000 chunk 240 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN A 634 HIS A1030 GLN ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1526 GLN A1690 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1093 ASN ** C 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN H 131 ASN K 105 ASN ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.095920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.074177 restraints weight = 124627.102| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.96 r_work: 0.3205 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 33800 Z= 0.195 Angle : 0.708 14.536 45745 Z= 0.359 Chirality : 0.046 0.242 5048 Planarity : 0.005 0.055 5872 Dihedral : 8.671 59.986 4680 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.39 % Allowed : 11.39 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.12), residues: 4061 helix: -1.16 (0.14), residues: 1208 sheet: -1.69 (0.19), residues: 639 loop : -1.81 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 77 TYR 0.019 0.002 TYR A 792 PHE 0.019 0.002 PHE A1341 TRP 0.022 0.002 TRP N 43 HIS 0.012 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (33775) covalent geometry : angle 0.69758 / 0.36 (45721) hydrogen bonds : bond 0.04237 / 2.80 ( 992) hydrogen bonds : angle 5.86544 / 4.13 ( 2823) metal coordination : bond 0.00800 / 0.49 ( 25) metal coordination : angle 5.44505 / 3.42 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 347 time to evaluate : 1.310 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 200 MET cc_start: 0.6760 (tpp) cc_final: 0.6204 (tpp) REVERT: A 300 ASP cc_start: 0.8608 (p0) cc_final: 0.8143 (t70) REVERT: A 345 MET cc_start: 0.6999 (tpt) cc_final: 0.6370 (mmp) REVERT: A 400 ILE cc_start: 0.8279 (mm) cc_final: 0.8021 (mm) REVERT: A 460 MET cc_start: 0.7192 (tpt) cc_final: 0.6970 (tpt) REVERT: A 896 MET cc_start: 0.8840 (tpp) cc_final: 0.8592 (tpp) REVERT: A 915 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8055 (pp) REVERT: A 929 MET cc_start: 0.8697 (mtt) cc_final: 0.8265 (mtm) REVERT: B 639 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: B 1053 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9061 (mm) REVERT: B 1080 LEU cc_start: 0.8811 (tp) cc_final: 0.8446 (tt) REVERT: B 1097 ASN cc_start: 0.8581 (m110) cc_final: 0.7912 (p0) REVERT: E 20 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8701 (tp) REVERT: E 24 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8555 (mtt180) REVERT: E 33 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7943 (pp) REVERT: E 44 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: E 61 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8191 (tp) REVERT: E 98 ASN cc_start: 0.9338 (m-40) cc_final: 0.8541 (p0) REVERT: E 121 MET cc_start: 0.9041 (tpt) cc_final: 0.8629 (ttt) REVERT: F 75 MET cc_start: 0.8463 (mtm) cc_final: 0.7982 (mtm) REVERT: G 62 ARG cc_start: 0.7821 (ttp-110) cc_final: 0.7347 (ttm110) REVERT: G 73 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8953 (pp20) REVERT: G 76 ASP cc_start: 0.8945 (t0) cc_final: 0.8682 (m-30) REVERT: G 91 ILE cc_start: 0.8863 (mm) cc_final: 0.8650 (mp) REVERT: G 97 LYS cc_start: 0.7555 (mmpt) cc_final: 0.7318 (tptt) REVERT: I 107 GLU cc_start: 0.8365 (pm20) cc_final: 0.8160 (pm20) REVERT: I 113 TYR cc_start: 0.9206 (m-80) cc_final: 0.8499 (m-80) REVERT: J 26 GLN cc_start: 0.9315 (tp40) cc_final: 0.8919 (tm-30) REVERT: K 64 GLU cc_start: 0.8728 (mp0) cc_final: 0.8504 (mp0) REVERT: K 119 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8610 (tppp) REVERT: L 15 MET cc_start: 0.7958 (mmm) cc_final: 0.7311 (mtm) REVERT: M 88 PHE cc_start: 0.8859 (m-10) cc_final: 0.8450 (m-10) REVERT: M 98 GLN cc_start: 0.8291 (pp30) cc_final: 0.8009 (pp30) REVERT: M 99 MET cc_start: 0.8516 (mmm) cc_final: 0.8200 (mmm) REVERT: N 57 ASN cc_start: 0.8884 (t0) cc_final: 0.8654 (m-40) REVERT: N 79 ARG cc_start: 0.8215 (mmp-170) cc_final: 0.7855 (tpp-160) REVERT: N 81 ARG cc_start: 0.9037 (ttt-90) cc_final: 0.8390 (tpt-90) REVERT: N 82 VAL cc_start: 0.8342 (t) cc_final: 0.8115 (p) outliers start: 86 outliers final: 38 residues processed: 406 average time/residue: 0.1972 time to fit residues: 133.1557 Evaluate side-chains 357 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 311 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 56 PHE Chi-restraints excluded: chain N residue 118 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 306 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 312 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 379 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** A 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1569 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** C 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN C 305 HIS H 131 ASN L 26 ASN M 12 GLN M 21 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.094154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.072300 restraints weight = 124728.205| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.93 r_work: 0.3159 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33800 Z= 0.181 Angle : 0.662 9.263 45745 Z= 0.338 Chirality : 0.045 0.271 5048 Planarity : 0.005 0.061 5872 Dihedral : 8.461 59.903 4680 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.42 % Allowed : 11.86 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.13), residues: 4061 helix: -0.67 (0.15), residues: 1208 sheet: -1.56 (0.19), residues: 644 loop : -1.61 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 22 TYR 0.016 0.001 TYR A 792 PHE 0.015 0.001 PHE A1341 TRP 0.015 0.001 TRP E 11 HIS 0.008 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (33775) covalent geometry : angle 0.65343 / 0.34 (45721) hydrogen bonds : bond 0.03767 / 2.50 ( 992) hydrogen bonds : angle 5.50637 / 3.87 ( 2823) metal coordination : bond 0.00848 / 0.51 ( 25) metal coordination : angle 4.64966 / 2.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 329 time to evaluate : 1.317 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 200 MET cc_start: 0.7010 (tpp) cc_final: 0.6452 (tpp) REVERT: A 283 MET cc_start: 0.6113 (tpp) cc_final: 0.4050 (ptp) REVERT: A 300 ASP cc_start: 0.8642 (p0) cc_final: 0.8193 (t70) REVERT: A 345 MET cc_start: 0.6957 (tpt) cc_final: 0.6364 (mmp) REVERT: A 896 MET cc_start: 0.8807 (tpp) cc_final: 0.8581 (tpp) REVERT: A 915 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8227 (pp) REVERT: A 929 MET cc_start: 0.8757 (mtt) cc_final: 0.8397 (mtm) REVERT: A 1305 MET cc_start: 0.8168 (tpt) cc_final: 0.7657 (mmm) REVERT: B 796 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8697 (pt) REVERT: B 1043 ASP cc_start: 0.8280 (t0) cc_final: 0.8077 (m-30) REVERT: B 1080 LEU cc_start: 0.9069 (tp) cc_final: 0.8762 (tt) REVERT: B 1097 ASN cc_start: 0.8706 (m110) cc_final: 0.8116 (p0) REVERT: B 1103 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.7662 (ptt-90) REVERT: E 33 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7873 (pp) REVERT: E 61 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8196 (tp) REVERT: E 98 ASN cc_start: 0.9339 (m-40) cc_final: 0.8663 (p0) REVERT: F 69 ARG cc_start: 0.9196 (tpt170) cc_final: 0.8937 (tpt90) REVERT: F 76 CYS cc_start: 0.8804 (t) cc_final: 0.8065 (t) REVERT: G 62 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7336 (ttm110) REVERT: G 76 ASP cc_start: 0.8906 (t0) cc_final: 0.8667 (m-30) REVERT: G 91 ILE cc_start: 0.8974 (mm) cc_final: 0.8752 (mp) REVERT: G 97 LYS cc_start: 0.7643 (mmpt) cc_final: 0.7343 (tptm) REVERT: I 107 GLU cc_start: 0.8488 (pm20) cc_final: 0.7946 (pm20) REVERT: I 113 TYR cc_start: 0.9317 (m-80) cc_final: 0.8478 (m-80) REVERT: J 26 GLN cc_start: 0.9352 (tp40) cc_final: 0.8982 (tm-30) REVERT: K 64 GLU cc_start: 0.8866 (mp0) cc_final: 0.8544 (mp0) REVERT: K 104 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8445 (mtp) REVERT: L 15 MET cc_start: 0.8002 (mmm) cc_final: 0.7444 (mtm) REVERT: M 64 THR cc_start: 0.7954 (m) cc_final: 0.7570 (p) REVERT: M 88 PHE cc_start: 0.8886 (m-10) cc_final: 0.8390 (m-10) REVERT: M 98 GLN cc_start: 0.8394 (pp30) cc_final: 0.8193 (pp30) REVERT: N 26 GLU cc_start: 0.8002 (mp0) cc_final: 0.7739 (tm-30) REVERT: N 59 ARG cc_start: 0.8633 (mmm-85) cc_final: 0.8426 (mmm160) REVERT: N 81 ARG cc_start: 0.9127 (ttt-90) cc_final: 0.8661 (tpt-90) REVERT: N 82 VAL cc_start: 0.8486 (t) cc_final: 0.8260 (p) outliers start: 87 outliers final: 48 residues processed: 387 average time/residue: 0.1980 time to fit residues: 126.1412 Evaluate side-chains 348 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1094 GLN Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 56 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 185 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 156 optimal weight: 0.1980 chunk 275 optimal weight: 10.0000 chunk 263 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1569 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 740 ASN ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** C 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN G 53 HIS K 49 HIS M 21 GLN N 46 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.091251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069381 restraints weight = 125917.752| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.87 r_work: 0.3074 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 33800 Z= 0.252 Angle : 0.723 11.396 45745 Z= 0.364 Chirality : 0.047 0.206 5048 Planarity : 0.005 0.053 5872 Dihedral : 8.454 59.183 4680 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.50 % Allowed : 13.25 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.13), residues: 4061 helix: -0.43 (0.15), residues: 1204 sheet: -1.60 (0.19), residues: 672 loop : -1.49 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 53 TYR 0.021 0.002 TYR B 999 PHE 0.025 0.002 PHE B1059 TRP 0.013 0.002 TRP A 846 HIS 0.011 0.002 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (33775) covalent geometry : angle 0.71200 / 0.36 (45721) hydrogen bonds : bond 0.03913 / 2.56 ( 992) hydrogen bonds : angle 5.47779 / 3.85 ( 2823) metal coordination : bond 0.01220 / 0.78 ( 25) metal coordination : angle 5.41238 / 3.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 308 time to evaluate : 1.172 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 200 MET cc_start: 0.7242 (tpp) cc_final: 0.6334 (tpp) REVERT: A 300 ASP cc_start: 0.8727 (p0) cc_final: 0.8240 (t70) REVERT: A 345 MET cc_start: 0.6953 (tpt) cc_final: 0.6354 (mmp) REVERT: A 450 TYR cc_start: 0.8009 (m-80) cc_final: 0.7407 (m-80) REVERT: A 915 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8492 (pp) REVERT: A 1123 MET cc_start: 0.9178 (mtp) cc_final: 0.8970 (mtp) REVERT: A 1305 MET cc_start: 0.8172 (tpt) cc_final: 0.7866 (mmm) REVERT: A 1529 VAL cc_start: 0.8547 (t) cc_final: 0.8260 (p) REVERT: B 796 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8825 (pt) REVERT: B 1080 LEU cc_start: 0.9257 (tp) cc_final: 0.8919 (tt) REVERT: B 1097 ASN cc_start: 0.8878 (m110) cc_final: 0.8278 (p0) REVERT: C 345 MET cc_start: 0.5300 (mpt) cc_final: 0.3245 (mmt) REVERT: E 33 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7884 (pp) REVERT: E 61 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8205 (tp) REVERT: E 98 ASN cc_start: 0.9352 (m-40) cc_final: 0.8648 (p0) REVERT: E 121 MET cc_start: 0.9050 (tpt) cc_final: 0.8698 (ttt) REVERT: F 56 TYR cc_start: 0.8493 (m-10) cc_final: 0.8158 (m-10) REVERT: F 76 CYS cc_start: 0.8882 (t) cc_final: 0.8306 (t) REVERT: G 62 ARG cc_start: 0.7830 (ttp-110) cc_final: 0.7453 (ttm110) REVERT: G 75 LEU cc_start: 0.8991 (mt) cc_final: 0.8552 (pp) REVERT: G 76 ASP cc_start: 0.8868 (t0) cc_final: 0.8523 (m-30) REVERT: G 97 LYS cc_start: 0.7728 (mmpt) cc_final: 0.7437 (tptp) REVERT: H 15 ILE cc_start: 0.9359 (pt) cc_final: 0.9023 (mt) REVERT: I 107 GLU cc_start: 0.8439 (pm20) cc_final: 0.7807 (pm20) REVERT: I 113 TYR cc_start: 0.9403 (m-80) cc_final: 0.8496 (m-80) REVERT: J 26 GLN cc_start: 0.9393 (tp40) cc_final: 0.9033 (tm-30) REVERT: K 64 GLU cc_start: 0.8932 (mp0) cc_final: 0.8460 (pm20) REVERT: K 66 GLU cc_start: 0.9142 (tp30) cc_final: 0.8797 (tp30) REVERT: L 15 MET cc_start: 0.8169 (mmm) cc_final: 0.7708 (mtm) REVERT: M 21 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: M 64 THR cc_start: 0.7990 (m) cc_final: 0.7585 (p) REVERT: N 26 GLU cc_start: 0.8047 (mp0) cc_final: 0.7805 (tm-30) REVERT: N 79 ARG cc_start: 0.8423 (mmp80) cc_final: 0.7884 (tpp-160) REVERT: N 81 ARG cc_start: 0.9178 (ttt-90) cc_final: 0.8805 (tpt-90) outliers start: 90 outliers final: 55 residues processed: 372 average time/residue: 0.1961 time to fit residues: 120.9567 Evaluate side-chains 343 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 283 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1569 ASN Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 56 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 140 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 120 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 351 optimal weight: 7.9990 chunk 204 optimal weight: 0.7980 chunk 232 optimal weight: 0.1980 chunk 218 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS A 199 HIS ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN A 686 GLN ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.093177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.071246 restraints weight = 122663.414| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.92 r_work: 0.3128 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33800 Z= 0.115 Angle : 0.632 10.061 45745 Z= 0.316 Chirality : 0.044 0.248 5048 Planarity : 0.004 0.046 5872 Dihedral : 8.296 59.981 4679 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.94 % Allowed : 14.11 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.13), residues: 4061 helix: -0.18 (0.15), residues: 1205 sheet: -1.55 (0.19), residues: 676 loop : -1.30 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 53 TYR 0.021 0.001 TYR M 102 PHE 0.013 0.001 PHE A1346 TRP 0.011 0.001 TRP A 682 HIS 0.016 0.001 HIS K 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (33775) covalent geometry : angle 0.62504 / 0.32 (45721) hydrogen bonds : bond 0.03424 / 2.28 ( 992) hydrogen bonds : angle 5.19485 / 3.64 ( 2823) metal coordination : bond 0.00589 / 0.37 ( 25) metal coordination : angle 4.06026 / 2.67 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 312 time to evaluate : 1.162 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 20 TYR cc_start: 0.5042 (OUTLIER) cc_final: 0.4793 (m-80) REVERT: A 200 MET cc_start: 0.7197 (tpp) cc_final: 0.6589 (tpp) REVERT: A 300 ASP cc_start: 0.8688 (p0) cc_final: 0.8208 (t70) REVERT: A 319 MET cc_start: 0.4595 (tpt) cc_final: 0.1658 (ppp) REVERT: A 345 MET cc_start: 0.6907 (tpt) cc_final: 0.6289 (mmp) REVERT: A 449 MET cc_start: 0.7399 (ttm) cc_final: 0.7194 (ttm) REVERT: A 450 TYR cc_start: 0.7871 (m-80) cc_final: 0.7295 (m-80) REVERT: A 586 ASN cc_start: 0.8409 (t0) cc_final: 0.7880 (t0) REVERT: A 1123 MET cc_start: 0.9160 (mtp) cc_final: 0.8732 (mtp) REVERT: A 1305 MET cc_start: 0.8024 (tpt) cc_final: 0.7765 (mmm) REVERT: B 184 MET cc_start: 0.9197 (mmm) cc_final: 0.8944 (mmm) REVERT: B 796 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8790 (pt) REVERT: B 895 ARG cc_start: 0.8611 (tpp-160) cc_final: 0.8288 (ttt180) REVERT: B 1040 MET cc_start: 0.5614 (mtm) cc_final: 0.5274 (mmt) REVERT: B 1097 ASN cc_start: 0.8908 (m110) cc_final: 0.8315 (p0) REVERT: C 334 ARG cc_start: 0.9017 (mmm-85) cc_final: 0.8814 (mmm-85) REVERT: C 345 MET cc_start: 0.5367 (mpt) cc_final: 0.3372 (mmt) REVERT: E 33 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7758 (pp) REVERT: E 61 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8235 (tp) REVERT: E 98 ASN cc_start: 0.9343 (m-40) cc_final: 0.8693 (p0) REVERT: E 121 MET cc_start: 0.8968 (tpt) cc_final: 0.8628 (ttt) REVERT: F 69 ARG cc_start: 0.9305 (tpt170) cc_final: 0.8987 (tpt90) REVERT: F 76 CYS cc_start: 0.8917 (t) cc_final: 0.8520 (t) REVERT: F 84 GLU cc_start: 0.8794 (pp20) cc_final: 0.8299 (pp20) REVERT: G 66 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7680 (ttt-90) REVERT: G 75 LEU cc_start: 0.8956 (mt) cc_final: 0.8485 (pp) REVERT: G 76 ASP cc_start: 0.8835 (t0) cc_final: 0.8486 (m-30) REVERT: G 97 LYS cc_start: 0.7767 (mmpt) cc_final: 0.7491 (tptp) REVERT: H 15 ILE cc_start: 0.9367 (pt) cc_final: 0.9043 (mt) REVERT: H 21 LYS cc_start: 0.9391 (mtpt) cc_final: 0.8812 (mtpp) REVERT: H 145 MET cc_start: 0.8980 (tpp) cc_final: 0.8585 (tpt) REVERT: I 107 GLU cc_start: 0.8448 (pm20) cc_final: 0.7860 (pm20) REVERT: I 113 TYR cc_start: 0.9382 (m-80) cc_final: 0.8544 (m-80) REVERT: J 26 GLN cc_start: 0.9403 (tp40) cc_final: 0.9005 (tm-30) REVERT: J 28 GLU cc_start: 0.8854 (mp0) cc_final: 0.8637 (mp0) REVERT: K 64 GLU cc_start: 0.8885 (mp0) cc_final: 0.8397 (pm20) REVERT: K 66 GLU cc_start: 0.9110 (tp30) cc_final: 0.8800 (tp30) REVERT: L 15 MET cc_start: 0.8154 (mmm) cc_final: 0.7621 (mtm) REVERT: M 39 MET cc_start: 0.8835 (mpp) cc_final: 0.8485 (mpp) REVERT: M 92 LEU cc_start: 0.9262 (tt) cc_final: 0.8953 (tt) REVERT: M 99 MET cc_start: 0.8494 (mmp) cc_final: 0.7621 (tpt) REVERT: N 81 ARG cc_start: 0.9166 (ttt-90) cc_final: 0.8956 (tpt-90) outliers start: 70 outliers final: 35 residues processed: 364 average time/residue: 0.1973 time to fit residues: 118.7941 Evaluate side-chains 323 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 53 ARG Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 56 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 97 optimal weight: 0.5980 chunk 330 optimal weight: 0.7980 chunk 371 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 293 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 72 optimal weight: 0.0060 chunk 350 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS G 109 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.093373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.071409 restraints weight = 123738.984| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.95 r_work: 0.3140 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33800 Z= 0.109 Angle : 0.617 10.553 45745 Z= 0.308 Chirality : 0.044 0.291 5048 Planarity : 0.004 0.049 5872 Dihedral : 8.182 59.486 4679 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.00 % Allowed : 14.47 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.13), residues: 4061 helix: -0.03 (0.15), residues: 1206 sheet: -1.47 (0.19), residues: 667 loop : -1.21 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1103 TYR 0.013 0.001 TYR A1170 PHE 0.017 0.001 PHE M 88 TRP 0.009 0.001 TRP A1075 HIS 0.006 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (33775) covalent geometry : angle 0.60979 / 0.31 (45721) hydrogen bonds : bond 0.03219 / 2.14 ( 992) hydrogen bonds : angle 5.03130 / 3.52 ( 2823) metal coordination : bond 0.00515 / 0.31 ( 25) metal coordination : angle 4.04580 / 2.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 297 time to evaluate : 1.228 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 20 TYR cc_start: 0.5151 (OUTLIER) cc_final: 0.4891 (m-80) REVERT: A 200 MET cc_start: 0.7120 (tpp) cc_final: 0.6456 (tpp) REVERT: A 300 ASP cc_start: 0.8669 (p0) cc_final: 0.8181 (t70) REVERT: A 319 MET cc_start: 0.4431 (tpt) cc_final: 0.1472 (ppp) REVERT: A 345 MET cc_start: 0.6891 (tpt) cc_final: 0.6288 (mmp) REVERT: A 450 TYR cc_start: 0.7847 (m-80) cc_final: 0.7344 (m-80) REVERT: A 586 ASN cc_start: 0.8354 (t0) cc_final: 0.7814 (t0) REVERT: A 929 MET cc_start: 0.8832 (mtp) cc_final: 0.8619 (mtm) REVERT: A 1123 MET cc_start: 0.9167 (mtp) cc_final: 0.8821 (mtp) REVERT: A 1282 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8825 (tttp) REVERT: A 1305 MET cc_start: 0.8012 (tpt) cc_final: 0.7779 (mmm) REVERT: B 422 MET cc_start: 0.8997 (mpp) cc_final: 0.8764 (pmm) REVERT: B 547 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7108 (p90) REVERT: B 631 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8326 (tt0) REVERT: B 726 MET cc_start: 0.9351 (mmm) cc_final: 0.9073 (tpp) REVERT: B 796 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8800 (pt) REVERT: B 839 MET cc_start: 0.7970 (mmm) cc_final: 0.7740 (mmm) REVERT: B 895 ARG cc_start: 0.8563 (tpp-160) cc_final: 0.8248 (ttt180) REVERT: B 1040 MET cc_start: 0.5558 (mtm) cc_final: 0.5173 (mmt) REVERT: B 1097 ASN cc_start: 0.8925 (m110) cc_final: 0.8374 (p0) REVERT: C 334 ARG cc_start: 0.9032 (mmm-85) cc_final: 0.8831 (mmm-85) REVERT: C 345 MET cc_start: 0.5373 (mpt) cc_final: 0.3388 (mmt) REVERT: E 61 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8274 (tp) REVERT: E 98 ASN cc_start: 0.9343 (m-40) cc_final: 0.8686 (p0) REVERT: E 121 MET cc_start: 0.8895 (tpt) cc_final: 0.8658 (ttt) REVERT: F 76 CYS cc_start: 0.8909 (t) cc_final: 0.8514 (t) REVERT: G 66 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7745 (ttt-90) REVERT: G 73 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8855 (pp20) REVERT: G 75 LEU cc_start: 0.8925 (mt) cc_final: 0.8441 (pp) REVERT: G 76 ASP cc_start: 0.8805 (t0) cc_final: 0.8466 (m-30) REVERT: G 97 LYS cc_start: 0.7782 (mmpt) cc_final: 0.7483 (tptp) REVERT: H 15 ILE cc_start: 0.9384 (pt) cc_final: 0.9083 (mt) REVERT: H 145 MET cc_start: 0.8988 (tpp) cc_final: 0.8620 (tpt) REVERT: I 107 GLU cc_start: 0.8483 (pm20) cc_final: 0.7834 (pm20) REVERT: I 113 TYR cc_start: 0.9383 (m-80) cc_final: 0.8541 (m-80) REVERT: J 26 GLN cc_start: 0.9393 (tp40) cc_final: 0.8975 (tm-30) REVERT: J 28 GLU cc_start: 0.8818 (mp0) cc_final: 0.8601 (mp0) REVERT: K 28 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7772 (mp0) REVERT: K 64 GLU cc_start: 0.8871 (mp0) cc_final: 0.8402 (pm20) REVERT: K 66 GLU cc_start: 0.9118 (tp30) cc_final: 0.8765 (tp30) REVERT: L 15 MET cc_start: 0.8149 (mmm) cc_final: 0.7712 (mtm) REVERT: M 39 MET cc_start: 0.8842 (mpp) cc_final: 0.8519 (mpp) REVERT: M 92 LEU cc_start: 0.9291 (tt) cc_final: 0.8973 (tt) REVERT: M 99 MET cc_start: 0.8467 (mmp) cc_final: 0.7528 (tpt) REVERT: N 81 ARG cc_start: 0.9129 (ttt-90) cc_final: 0.8870 (tpt-90) outliers start: 72 outliers final: 43 residues processed: 352 average time/residue: 0.1849 time to fit residues: 108.7286 Evaluate side-chains 332 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1282 LYS Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 56 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 374 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 267 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 238 optimal weight: 8.9990 chunk 311 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 404 optimal weight: 20.0000 chunk 301 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1569 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.091799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.069869 restraints weight = 124420.316| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.88 r_work: 0.3092 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33800 Z= 0.176 Angle : 0.655 12.232 45745 Z= 0.324 Chirality : 0.045 0.215 5048 Planarity : 0.004 0.047 5872 Dihedral : 8.161 59.579 4679 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.89 % Allowed : 14.80 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 4061 helix: 0.11 (0.15), residues: 1215 sheet: -1.49 (0.19), residues: 671 loop : -1.16 (0.14), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 59 TYR 0.022 0.001 TYR B1096 PHE 0.014 0.001 PHE A1346 TRP 0.008 0.001 TRP C 40 HIS 0.007 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (33775) covalent geometry : angle 0.64673 / 0.32 (45721) hydrogen bonds : bond 0.03400 / 2.24 ( 992) hydrogen bonds : angle 5.06764 / 3.54 ( 2823) metal coordination : bond 0.00728 / 0.47 ( 25) metal coordination : angle 4.58975 / 2.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 288 time to evaluate : 1.107 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 20 TYR cc_start: 0.5098 (OUTLIER) cc_final: 0.4830 (m-80) REVERT: A 200 MET cc_start: 0.7214 (tpp) cc_final: 0.6415 (tpp) REVERT: A 300 ASP cc_start: 0.8808 (p0) cc_final: 0.8265 (t70) REVERT: A 319 MET cc_start: 0.4742 (tpt) cc_final: 0.1818 (ppp) REVERT: A 345 MET cc_start: 0.6884 (tpt) cc_final: 0.6248 (mmp) REVERT: A 433 MET cc_start: 0.8222 (mmt) cc_final: 0.7529 (mmt) REVERT: A 586 ASN cc_start: 0.8379 (t0) cc_final: 0.7816 (t0) REVERT: A 635 MET cc_start: 0.9297 (mpp) cc_final: 0.8856 (mpp) REVERT: A 915 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8559 (pp) REVERT: A 1123 MET cc_start: 0.9166 (mtp) cc_final: 0.8904 (mtp) REVERT: A 1282 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8863 (tttp) REVERT: B 547 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7230 (p90) REVERT: B 631 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8391 (tt0) REVERT: B 726 MET cc_start: 0.9323 (mmm) cc_final: 0.9107 (tpp) REVERT: B 796 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8861 (pt) REVERT: B 839 MET cc_start: 0.8094 (mmm) cc_final: 0.7831 (mmm) REVERT: B 1040 MET cc_start: 0.5791 (mtm) cc_final: 0.5447 (mmt) REVERT: B 1097 ASN cc_start: 0.8888 (m110) cc_final: 0.8454 (p0) REVERT: C 334 ARG cc_start: 0.9069 (mmm-85) cc_final: 0.8844 (mmm-85) REVERT: C 345 MET cc_start: 0.5301 (mpt) cc_final: 0.3375 (mmt) REVERT: E 33 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7754 (pp) REVERT: E 61 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8238 (tp) REVERT: E 98 ASN cc_start: 0.9338 (m-40) cc_final: 0.8702 (p0) REVERT: E 121 MET cc_start: 0.8964 (tpt) cc_final: 0.8694 (ttt) REVERT: F 76 CYS cc_start: 0.8932 (t) cc_final: 0.8448 (t) REVERT: G 62 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7504 (ttm110) REVERT: G 66 ARG cc_start: 0.8045 (mtp85) cc_final: 0.7815 (ttt-90) REVERT: G 73 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8909 (pp20) REVERT: G 86 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7146 (pp) REVERT: G 97 LYS cc_start: 0.7852 (mmpt) cc_final: 0.7524 (tptp) REVERT: H 15 ILE cc_start: 0.9389 (pt) cc_final: 0.9113 (mt) REVERT: H 145 MET cc_start: 0.9061 (tpp) cc_final: 0.8692 (tpt) REVERT: I 107 GLU cc_start: 0.8538 (pm20) cc_final: 0.7738 (pm20) REVERT: I 113 TYR cc_start: 0.9399 (m-80) cc_final: 0.8478 (m-80) REVERT: J 26 GLN cc_start: 0.9413 (tp40) cc_final: 0.8958 (tm-30) REVERT: K 31 GLN cc_start: 0.8735 (mm-40) cc_final: 0.7961 (tp-100) REVERT: K 64 GLU cc_start: 0.8921 (mp0) cc_final: 0.8438 (pm20) REVERT: K 79 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8798 (mtmm) REVERT: M 99 MET cc_start: 0.8513 (mmp) cc_final: 0.7681 (tpp) REVERT: N 81 ARG cc_start: 0.9150 (ttt-90) cc_final: 0.8891 (tpt-90) outliers start: 68 outliers final: 51 residues processed: 337 average time/residue: 0.2007 time to fit residues: 112.3443 Evaluate side-chains 339 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 280 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1282 LYS Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1569 ASN Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 53 ARG Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 56 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 146 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 143 optimal weight: 10.0000 chunk 393 optimal weight: 30.0000 chunk 402 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 chunk 392 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 40.0000 chunk 95 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1569 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.090614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068754 restraints weight = 123061.417| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.82 r_work: 0.3052 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 33800 Z= 0.233 Angle : 0.696 14.160 45745 Z= 0.348 Chirality : 0.047 0.506 5048 Planarity : 0.005 0.050 5872 Dihedral : 8.213 59.638 4679 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.05 % Allowed : 15.05 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 4061 helix: 0.14 (0.15), residues: 1218 sheet: -1.49 (0.19), residues: 672 loop : -1.19 (0.14), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 59 TYR 0.015 0.002 TYR B 999 PHE 0.026 0.001 PHE M 88 TRP 0.010 0.002 TRP F 118 HIS 0.008 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (33775) covalent geometry : angle 0.68643 / 0.35 (45721) hydrogen bonds : bond 0.03543 / 2.32 ( 992) hydrogen bonds : angle 5.15377 / 3.60 ( 2823) metal coordination : bond 0.01004 / 0.62 ( 25) metal coordination : angle 4.99216 / 3.09 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 284 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7263 (tpp) cc_final: 0.6397 (tpp) REVERT: A 300 ASP cc_start: 0.8862 (p0) cc_final: 0.8287 (t70) REVERT: A 319 MET cc_start: 0.4758 (tpt) cc_final: 0.1887 (ppp) REVERT: A 345 MET cc_start: 0.6849 (tpt) cc_final: 0.6199 (mmp) REVERT: A 433 MET cc_start: 0.8208 (mmt) cc_final: 0.7535 (mmt) REVERT: A 450 TYR cc_start: 0.7893 (m-10) cc_final: 0.7601 (m-80) REVERT: A 586 ASN cc_start: 0.8474 (t0) cc_final: 0.7919 (t0) REVERT: A 635 MET cc_start: 0.9340 (mpp) cc_final: 0.8933 (mpp) REVERT: A 896 MET cc_start: 0.8873 (tpp) cc_final: 0.8589 (tpp) REVERT: A 1123 MET cc_start: 0.9146 (mtp) cc_final: 0.8895 (mtp) REVERT: A 1154 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 1282 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8892 (tttp) REVERT: A 1285 LEU cc_start: 0.9342 (tp) cc_final: 0.9011 (tp) REVERT: A 1305 MET cc_start: 0.8168 (tpt) cc_final: 0.7517 (mmm) REVERT: A 1529 VAL cc_start: 0.8526 (t) cc_final: 0.8304 (p) REVERT: B 422 MET cc_start: 0.9006 (mpp) cc_final: 0.8731 (pmm) REVERT: B 547 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7243 (p90) REVERT: B 796 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8848 (pt) REVERT: B 839 MET cc_start: 0.8273 (mmm) cc_final: 0.8002 (mmm) REVERT: B 1040 MET cc_start: 0.5857 (mtm) cc_final: 0.5069 (mmt) REVERT: B 1097 ASN cc_start: 0.8890 (m110) cc_final: 0.8511 (p0) REVERT: C 334 ARG cc_start: 0.9068 (mmm-85) cc_final: 0.8849 (mmm-85) REVERT: C 345 MET cc_start: 0.5297 (mpt) cc_final: 0.3355 (mmt) REVERT: E 33 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7839 (pp) REVERT: E 61 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8219 (tp) REVERT: E 98 ASN cc_start: 0.9337 (m-40) cc_final: 0.8715 (p0) REVERT: E 121 MET cc_start: 0.9004 (tpt) cc_final: 0.8704 (ttt) REVERT: F 76 CYS cc_start: 0.8950 (t) cc_final: 0.8539 (t) REVERT: G 62 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7511 (ttm110) REVERT: G 66 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7930 (ttt-90) REVERT: G 86 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7204 (pp) REVERT: G 93 TYR cc_start: 0.7873 (p90) cc_final: 0.7518 (p90) REVERT: G 97 LYS cc_start: 0.7889 (mmpt) cc_final: 0.7546 (tptp) REVERT: H 15 ILE cc_start: 0.9384 (pt) cc_final: 0.9140 (mt) REVERT: H 145 MET cc_start: 0.9070 (tpp) cc_final: 0.8657 (tpt) REVERT: I 107 GLU cc_start: 0.8565 (pm20) cc_final: 0.7614 (pm20) REVERT: I 113 TYR cc_start: 0.9430 (m-80) cc_final: 0.8459 (m-80) REVERT: J 26 GLN cc_start: 0.9378 (tp40) cc_final: 0.9048 (tm-30) REVERT: K 25 THR cc_start: 0.8133 (t) cc_final: 0.7869 (p) REVERT: K 31 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8098 (tp-100) REVERT: K 46 GLU cc_start: 0.9127 (mp0) cc_final: 0.8856 (mp0) REVERT: K 64 GLU cc_start: 0.8931 (mp0) cc_final: 0.8482 (pm20) REVERT: K 104 MET cc_start: 0.8803 (mtp) cc_final: 0.8343 (mtp) REVERT: L 15 MET cc_start: 0.8068 (mmm) cc_final: 0.7790 (mtm) REVERT: M 39 MET cc_start: 0.8871 (mpp) cc_final: 0.8517 (mpp) REVERT: M 66 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8217 (mtp-110) REVERT: M 79 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8135 (pp) REVERT: M 99 MET cc_start: 0.8613 (mmp) cc_final: 0.7888 (tpp) REVERT: N 81 ARG cc_start: 0.9182 (ttt-90) cc_final: 0.8926 (tpt-90) outliers start: 74 outliers final: 53 residues processed: 336 average time/residue: 0.2088 time to fit residues: 115.7004 Evaluate side-chains 343 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 282 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1282 LYS Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1568 THR Chi-restraints excluded: chain A residue 1569 ASN Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 56 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 146 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 196 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 236 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 403 optimal weight: 7.9990 chunk 364 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 334 optimal weight: 50.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 ASN A1569 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN G 74 GLN I 92 HIS I 117 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.091175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069211 restraints weight = 123727.943| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.88 r_work: 0.3075 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33800 Z= 0.153 Angle : 0.660 12.932 45745 Z= 0.326 Chirality : 0.045 0.338 5048 Planarity : 0.004 0.059 5872 Dihedral : 8.156 59.567 4679 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.69 % Allowed : 15.30 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4061 helix: 0.28 (0.15), residues: 1209 sheet: -1.46 (0.19), residues: 662 loop : -1.11 (0.14), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 59 TYR 0.018 0.001 TYR J 29 PHE 0.013 0.001 PHE A 955 TRP 0.012 0.001 TRP A1075 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (33775) covalent geometry : angle 0.65225 / 0.33 (45721) hydrogen bonds : bond 0.03333 / 2.19 ( 992) hydrogen bonds : angle 5.06256 / 3.53 ( 2823) metal coordination : bond 0.00738 / 0.45 ( 25) metal coordination : angle 4.35261 / 2.71 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 289 time to evaluate : 1.300 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 200 MET cc_start: 0.7219 (tpp) cc_final: 0.6625 (tpp) REVERT: A 300 ASP cc_start: 0.8842 (p0) cc_final: 0.8294 (t70) REVERT: A 319 MET cc_start: 0.4836 (tpt) cc_final: 0.2047 (ppp) REVERT: A 345 MET cc_start: 0.6879 (tpt) cc_final: 0.6275 (mmp) REVERT: A 433 MET cc_start: 0.8200 (mmt) cc_final: 0.7565 (mmt) REVERT: A 450 TYR cc_start: 0.7760 (m-10) cc_final: 0.7477 (m-80) REVERT: A 512 MET cc_start: 0.9119 (tpp) cc_final: 0.8665 (tpp) REVERT: A 586 ASN cc_start: 0.8407 (t0) cc_final: 0.7841 (t0) REVERT: A 635 MET cc_start: 0.9285 (mpp) cc_final: 0.8917 (mpp) REVERT: A 896 MET cc_start: 0.8815 (tpp) cc_final: 0.8567 (tpp) REVERT: A 1123 MET cc_start: 0.9139 (mtp) cc_final: 0.8889 (mtp) REVERT: A 1282 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8875 (tttp) REVERT: A 1305 MET cc_start: 0.8219 (tpt) cc_final: 0.7516 (mmm) REVERT: A 1529 VAL cc_start: 0.8510 (t) cc_final: 0.8292 (p) REVERT: B 422 MET cc_start: 0.8988 (mpp) cc_final: 0.8695 (pmm) REVERT: B 547 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7240 (p90) REVERT: B 796 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8841 (pt) REVERT: B 839 MET cc_start: 0.8268 (mmm) cc_final: 0.7989 (mmm) REVERT: B 1040 MET cc_start: 0.5679 (mtm) cc_final: 0.5280 (mmt) REVERT: B 1097 ASN cc_start: 0.8824 (m110) cc_final: 0.8515 (p0) REVERT: C 334 ARG cc_start: 0.9084 (mmm-85) cc_final: 0.8879 (mmm-85) REVERT: C 345 MET cc_start: 0.5245 (mpt) cc_final: 0.3412 (mmt) REVERT: E 33 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7847 (pp) REVERT: E 61 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8209 (tp) REVERT: E 98 ASN cc_start: 0.9349 (m-40) cc_final: 0.8733 (p0) REVERT: E 169 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: F 69 ARG cc_start: 0.9277 (tpt90) cc_final: 0.8972 (tpt-90) REVERT: F 76 CYS cc_start: 0.8944 (t) cc_final: 0.8591 (t) REVERT: G 66 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7939 (ttt-90) REVERT: G 73 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8808 (tt0) REVERT: G 74 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8981 (tt0) REVERT: G 86 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7147 (pp) REVERT: G 93 TYR cc_start: 0.7646 (p90) cc_final: 0.7182 (p90) REVERT: G 97 LYS cc_start: 0.7999 (mmpt) cc_final: 0.7596 (tptp) REVERT: H 15 ILE cc_start: 0.9385 (pt) cc_final: 0.9160 (mt) REVERT: I 107 GLU cc_start: 0.8607 (pm20) cc_final: 0.8013 (pm20) REVERT: I 113 TYR cc_start: 0.9411 (m-80) cc_final: 0.8486 (m-80) REVERT: K 31 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8071 (tp-100) REVERT: K 46 GLU cc_start: 0.9103 (mp0) cc_final: 0.8837 (mp0) REVERT: K 64 GLU cc_start: 0.8988 (mp0) cc_final: 0.8515 (pm20) REVERT: K 66 GLU cc_start: 0.9269 (tp30) cc_final: 0.8679 (tp30) REVERT: K 104 MET cc_start: 0.8755 (mtp) cc_final: 0.8320 (mtp) REVERT: L 15 MET cc_start: 0.8027 (mmm) cc_final: 0.7776 (mtm) REVERT: M 39 MET cc_start: 0.8883 (mpp) cc_final: 0.8533 (mpp) REVERT: M 79 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8177 (pp) REVERT: M 99 MET cc_start: 0.8631 (mmp) cc_final: 0.7935 (tpp) REVERT: N 81 ARG cc_start: 0.9183 (ttt-90) cc_final: 0.8955 (tpt-90) outliers start: 61 outliers final: 48 residues processed: 332 average time/residue: 0.2049 time to fit residues: 112.1327 Evaluate side-chains 338 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 281 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1282 LYS Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1569 ASN Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 56 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 146 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 20 optimal weight: 0.0060 chunk 381 optimal weight: 30.0000 chunk 201 optimal weight: 0.3980 chunk 330 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 400 optimal weight: 40.0000 chunk 276 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 overall best weight: 2.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1569 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN G 109 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.091305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.069550 restraints weight = 122782.498| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.81 r_work: 0.3089 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33800 Z= 0.131 Angle : 0.645 13.132 45745 Z= 0.319 Chirality : 0.044 0.181 5048 Planarity : 0.004 0.061 5872 Dihedral : 8.125 59.785 4679 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.78 % Allowed : 15.47 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 4061 helix: 0.33 (0.16), residues: 1210 sheet: -1.40 (0.19), residues: 663 loop : -1.08 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 59 TYR 0.013 0.001 TYR M 102 PHE 0.034 0.001 PHE M 88 TRP 0.012 0.001 TRP A1075 HIS 0.010 0.001 HIS K 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (33775) covalent geometry : angle 0.63806 / 0.32 (45721) hydrogen bonds : bond 0.03281 / 2.16 ( 992) hydrogen bonds : angle 5.02523 / 3.49 ( 2823) metal coordination : bond 0.00652 / 0.39 ( 25) metal coordination : angle 4.08494 / 2.51 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9840.86 seconds wall clock time: 168 minutes 48.36 seconds (10128.36 seconds total)