Starting phenix.real_space_refine on Mon Dec 30 01:26:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8trh_41580/12_2024/8trh_41580_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8trh_41580/12_2024/8trh_41580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8trh_41580/12_2024/8trh_41580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8trh_41580/12_2024/8trh_41580.map" model { file = "/net/cci-nas-00/data/ceres_data/8trh_41580/12_2024/8trh_41580_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8trh_41580/12_2024/8trh_41580_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 384 5.16 5 C 38174 2.51 5 N 10380 2.21 5 O 11017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 59957 Number of models: 1 Model: "" Number of chains: 28 Chain: "0" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2159 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 9, 'TRANS': 257} Chain breaks: 2 Chain: "1" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 1 Chain: "2" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 899 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain breaks: 1 Chain: "3" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1022 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 3 Chain: "4" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 932 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "A" Number of atoms: 3578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3578 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 30, 'TRANS': 436} Chain breaks: 5 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1266 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1374 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 9, 'TRANS': 157} Chain breaks: 1 Chain: "G" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1284 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 148} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain breaks: 1 Chain: "I" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 605 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Chain: "J" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 834 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 106 Chain: "K" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "N" Number of atoms: 7768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7768 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 61, 'TRANS': 955} Chain breaks: 10 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 469 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "O" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1226 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 16, 'TRANS': 140} Chain breaks: 1 Chain: "P" Number of atoms: 5875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5875 Classifications: {'peptide': 753} Link IDs: {'PTRANS': 36, 'TRANS': 716} Chain breaks: 4 Chain: "Q" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4387 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 27, 'TRANS': 528} Chain breaks: 5 Chain: "R" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1532 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 8, 'TRANS': 182} Chain: "T" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1499 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "V" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1063 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain: "W" Number of atoms: 10774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10774 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 70, 'TRANS': 1263} Chain: "X" Number of atoms: 7061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 7061 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 35, 'TRANS': 861} Chain breaks: 9 Chain: "d" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 435 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 7, 'TRANS': 66} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "U" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1914 SG CYS 0 281 120.498 200.396 141.373 1.00 24.29 S ATOM 1940 SG CYS 0 284 119.303 203.204 143.675 1.00 31.49 S ATOM 2148 SG CYS 0 309 116.731 201.195 141.621 1.00 26.61 S ATOM 31795 SG CYS P 798 142.164 231.552 68.728 1.00 29.08 S ATOM 31819 SG CYS P 801 144.345 229.463 69.196 1.00 28.83 S ATOM 32032 SG CYS P 827 146.281 232.624 69.393 1.00 41.12 S Time building chain proxies: 23.91, per 1000 atoms: 0.40 Number of scatterers: 59957 At special positions: 0 Unit cell: (204.604, 371.371, 281.681, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 384 16.00 O 11017 8.00 N 10380 7.00 C 38174 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: 11.07 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 401 " pdb="ZN ZN 0 401 " - pdb=" ND1 HIS 0 306 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 284 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 281 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 309 " pdb=" ZN P 901 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 798 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 801 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 827 " Number of angles added : 3 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14620 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 39 sheets defined 58.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain '0' and resid 8 through 38 removed outlier: 3.743A pdb=" N GLU 0 12 " --> pdb=" O SER 0 8 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY 0 38 " --> pdb=" O CYS 0 34 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 77 removed outlier: 3.791A pdb=" N PHE 0 52 " --> pdb=" O ARG 0 48 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE 0 53 " --> pdb=" O GLU 0 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP 0 58 " --> pdb=" O ALA 0 54 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN 0 59 " --> pdb=" O HIS 0 55 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU 0 60 " --> pdb=" O PHE 0 56 " (cutoff:3.500A) Processing helix chain '0' and resid 104 through 129 removed outlier: 3.997A pdb=" N LYS 0 116 " --> pdb=" O LYS 0 112 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR 0 119 " --> pdb=" O ASN 0 115 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS 0 120 " --> pdb=" O LYS 0 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA 0 124 " --> pdb=" O HIS 0 120 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN 0 129 " --> pdb=" O SER 0 125 " (cutoff:3.500A) Processing helix chain '0' and resid 158 through 172 removed outlier: 3.571A pdb=" N VAL 0 162 " --> pdb=" O PRO 0 158 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET 0 172 " --> pdb=" O ARG 0 168 " (cutoff:3.500A) Processing helix chain '0' and resid 236 through 253 Processing helix chain '0' and resid 259 through 272 removed outlier: 3.595A pdb=" N VAL 0 263 " --> pdb=" O PRO 0 259 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER 0 272 " --> pdb=" O THR 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 273 through 276 Processing helix chain '1' and resid 43 through 56 removed outlier: 4.160A pdb=" N GLU 1 47 " --> pdb=" O THR 1 43 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE 1 56 " --> pdb=" O PHE 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 106 Processing helix chain '1' and resid 107 through 145 Processing helix chain '2' and resid 56 through 90 Proline residue: 2 65 - end of helix Processing helix chain '2' and resid 101 through 136 removed outlier: 3.842A pdb=" N CYS 2 105 " --> pdb=" O ARG 2 101 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS 2 135 " --> pdb=" O CYS 2 131 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS 2 136 " --> pdb=" O ASP 2 132 " (cutoff:3.500A) Processing helix chain '2' and resid 156 through 186 Processing helix chain '3' and resid 30 through 58 Processing helix chain '3' and resid 70 through 102 removed outlier: 4.215A pdb=" N GLU 3 101 " --> pdb=" O ASP 3 97 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN 3 102 " --> pdb=" O LYS 3 98 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 176 removed outlier: 3.965A pdb=" N GLU 3 144 " --> pdb=" O ARG 3 140 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL 3 145 " --> pdb=" O GLU 3 141 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET 3 176 " --> pdb=" O ALA 3 172 " (cutoff:3.500A) Processing helix chain '4' and resid 11 through 28 Processing helix chain '4' and resid 30 through 41 removed outlier: 3.580A pdb=" N GLY 4 41 " --> pdb=" O LEU 4 37 " (cutoff:3.500A) Processing helix chain '4' and resid 46 through 55 removed outlier: 3.733A pdb=" N ASN 4 50 " --> pdb=" O LYS 4 46 " (cutoff:3.500A) Processing helix chain '4' and resid 56 through 59 removed outlier: 3.741A pdb=" N LYS 4 59 " --> pdb=" O LEU 4 56 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 56 through 59' Processing helix chain '4' and resid 60 through 66 removed outlier: 4.418A pdb=" N TYR 4 66 " --> pdb=" O GLU 4 62 " (cutoff:3.500A) Processing helix chain '4' and resid 70 through 80 removed outlier: 4.081A pdb=" N HIS 4 74 " --> pdb=" O PRO 4 70 " (cutoff:3.500A) Processing helix chain '4' and resid 91 through 115 removed outlier: 3.657A pdb=" N GLN 4 101 " --> pdb=" O ILE 4 97 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 4 102 " --> pdb=" O ASP 4 98 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN 4 106 " --> pdb=" O ILE 4 102 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER 4 109 " --> pdb=" O TRP 4 105 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG 4 112 " --> pdb=" O TYR 4 108 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET 4 113 " --> pdb=" O SER 4 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 73 through 89 Processing helix chain 'A' and resid 135 through 144 removed outlier: 4.119A pdb=" N VAL A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 160 Processing helix chain 'A' and resid 168 through 195 removed outlier: 3.506A pdb=" N SER A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.706A pdb=" N LYS A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.538A pdb=" N ILE A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 18 Processing helix chain 'D' and resid 27 through 52 removed outlier: 3.526A pdb=" N SER D 51 " --> pdb=" O MET D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 109 removed outlier: 3.532A pdb=" N GLU D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU D 75 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 95 " --> pdb=" O HIS D 91 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 97 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 140 removed outlier: 4.540A pdb=" N GLN D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 158 removed outlier: 3.656A pdb=" N ILE D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 185 removed outlier: 4.138A pdb=" N GLU D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.527A pdb=" N ASN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 removed outlier: 3.771A pdb=" N TRP F 20 " --> pdb=" O ASP F 17 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE F 21 " --> pdb=" O SER F 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 17 through 21' Processing helix chain 'F' and resid 25 through 34 removed outlier: 3.516A pdb=" N VAL F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 54 removed outlier: 4.468A pdb=" N VAL F 49 " --> pdb=" O CYS F 45 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN F 53 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 63 removed outlier: 3.685A pdb=" N GLN F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET F 63 " --> pdb=" O HIS F 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 58 through 63' Processing helix chain 'F' and resid 112 through 135 removed outlier: 4.270A pdb=" N SER F 135 " --> pdb=" O ASP F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 5.258A pdb=" N ALA F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 26 removed outlier: 4.368A pdb=" N ILE G 26 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 99 removed outlier: 3.555A pdb=" N GLU G 77 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU G 96 " --> pdb=" O LEU G 92 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 124 removed outlier: 3.971A pdb=" N GLU G 107 " --> pdb=" O ILE G 103 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS G 120 " --> pdb=" O PHE G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 171 removed outlier: 4.442A pdb=" N HIS G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG G 136 " --> pdb=" O ARG G 132 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET G 138 " --> pdb=" O THR G 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET G 139 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN G 142 " --> pdb=" O MET G 138 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS G 143 " --> pdb=" O MET G 139 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU G 148 " --> pdb=" O ARG G 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 36 Processing helix chain 'H' and resid 41 through 66 removed outlier: 3.785A pdb=" N LEU H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU H 66 " --> pdb=" O VAL H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 74 removed outlier: 3.517A pdb=" N ASN H 73 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 93 Processing helix chain 'H' and resid 103 through 109 removed outlier: 3.583A pdb=" N ASP H 107 " --> pdb=" O GLU H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 129 removed outlier: 3.813A pdb=" N GLU H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 157 removed outlier: 3.736A pdb=" N GLU H 157 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 186 Processing helix chain 'I' and resid 66 through 79 Processing helix chain 'I' and resid 86 through 103 Processing helix chain 'I' and resid 110 through 138 Processing helix chain 'J' and resid 8 through 29 removed outlier: 4.548A pdb=" N PHE J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 60 removed outlier: 3.925A pdb=" N GLN J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 74 removed outlier: 3.620A pdb=" N GLN J 73 " --> pdb=" O GLU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 113 removed outlier: 4.325A pdb=" N TYR J 80 " --> pdb=" O ASN J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 128 Processing helix chain 'K' and resid 7 through 34 Processing helix chain 'K' and resid 41 through 72 Processing helix chain 'K' and resid 84 through 115 Processing helix chain 'N' and resid 51 through 76 Proline residue: N 74 - end of helix Processing helix chain 'N' and resid 77 through 106 Processing helix chain 'N' and resid 109 through 148 removed outlier: 3.766A pdb=" N GLU N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU N 144 " --> pdb=" O ALA N 140 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL N 145 " --> pdb=" O ARG N 141 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA N 147 " --> pdb=" O ALA N 143 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG N 148 " --> pdb=" O LEU N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 162 Processing helix chain 'N' and resid 171 through 178 removed outlier: 3.592A pdb=" N ASP N 175 " --> pdb=" O THR N 171 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE N 177 " --> pdb=" O ILE N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 205 removed outlier: 3.689A pdb=" N GLN N 189 " --> pdb=" O LYS N 185 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA N 190 " --> pdb=" O ILE N 186 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN N 194 " --> pdb=" O ALA N 190 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN N 197 " --> pdb=" O HIS N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 217 through 221 removed outlier: 3.686A pdb=" N GLY N 220 " --> pdb=" O VAL N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 283 removed outlier: 3.598A pdb=" N ILE N 271 " --> pdb=" O HIS N 267 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN N 276 " --> pdb=" O SER N 272 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU N 277 " --> pdb=" O PHE N 273 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE N 283 " --> pdb=" O GLN N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 318 removed outlier: 3.889A pdb=" N TYR N 293 " --> pdb=" O LEU N 289 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN N 294 " --> pdb=" O GLN N 290 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS N 295 " --> pdb=" O ASP N 291 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN N 304 " --> pdb=" O CYS N 300 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU N 305 " --> pdb=" O LEU N 301 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG N 317 " --> pdb=" O LEU N 313 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU N 318 " --> pdb=" O MET N 314 " (cutoff:3.500A) Processing helix chain 'N' and resid 397 through 424 removed outlier: 4.531A pdb=" N ASP N 403 " --> pdb=" O LYS N 399 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN N 411 " --> pdb=" O ALA N 407 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN N 414 " --> pdb=" O HIS N 410 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU N 416 " --> pdb=" O LYS N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 471 through 483 removed outlier: 4.100A pdb=" N ASP N 477 " --> pdb=" O ALA N 473 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS N 480 " --> pdb=" O ASP N 476 " (cutoff:3.500A) Processing helix chain 'N' and resid 488 through 493 removed outlier: 3.693A pdb=" N TRP N 492 " --> pdb=" O ARG N 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 496 through 507 removed outlier: 3.712A pdb=" N GLY N 501 " --> pdb=" O LYS N 497 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN N 502 " --> pdb=" O PHE N 498 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN N 507 " --> pdb=" O GLN N 503 " (cutoff:3.500A) Processing helix chain 'N' and resid 508 through 510 No H-bonds generated for 'chain 'N' and resid 508 through 510' Processing helix chain 'N' and resid 528 through 533 removed outlier: 3.944A pdb=" N LEU N 533 " --> pdb=" O ILE N 530 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 652 removed outlier: 3.761A pdb=" N ALA N 642 " --> pdb=" O ASN N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 652 through 664 removed outlier: 4.263A pdb=" N GLY N 656 " --> pdb=" O MET N 652 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU N 657 " --> pdb=" O PRO N 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 694 through 702 Processing helix chain 'N' and resid 714 through 717 removed outlier: 3.738A pdb=" N ASN N 717 " --> pdb=" O GLY N 714 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 714 through 717' Processing helix chain 'N' and resid 759 through 787 removed outlier: 4.300A pdb=" N VAL N 763 " --> pdb=" O GLY N 759 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS N 779 " --> pdb=" O ARG N 775 " (cutoff:3.500A) Processing helix chain 'N' and resid 848 through 850 No H-bonds generated for 'chain 'N' and resid 848 through 850' Processing helix chain 'N' and resid 851 through 862 Processing helix chain 'N' and resid 864 through 883 removed outlier: 3.819A pdb=" N LEU N 868 " --> pdb=" O ASN N 864 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ALA N 877 " --> pdb=" O PHE N 873 " (cutoff:3.500A) Proline residue: N 878 - end of helix removed outlier: 3.680A pdb=" N ALA N 881 " --> pdb=" O ALA N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 958 through 967 removed outlier: 3.610A pdb=" N PHE N 962 " --> pdb=" O GLY N 958 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE N 966 " --> pdb=" O PHE N 962 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL N 967 " --> pdb=" O LEU N 963 " (cutoff:3.500A) Processing helix chain 'N' and resid 1169 through 1173 removed outlier: 4.021A pdb=" N ILE N1173 " --> pdb=" O ALA N1170 " (cutoff:3.500A) Processing helix chain 'N' and resid 1180 through 1187 removed outlier: 3.645A pdb=" N ILE N1184 " --> pdb=" O SER N1180 " (cutoff:3.500A) Processing helix chain 'N' and resid 1205 through 1226 Processing helix chain 'N' and resid 1276 through 1288 removed outlier: 3.612A pdb=" N VAL N1280 " --> pdb=" O ASP N1276 " (cutoff:3.500A) Processing helix chain 'N' and resid 1295 through 1306 removed outlier: 3.974A pdb=" N LEU N1299 " --> pdb=" O LYS N1295 " (cutoff:3.500A) Processing helix chain 'N' and resid 1311 through 1325 removed outlier: 3.546A pdb=" N ASP N1315 " --> pdb=" O HIS N1311 " (cutoff:3.500A) Processing helix chain 'O' and resid 618 through 627 Processing helix chain 'O' and resid 633 through 651 Proline residue: O 644 - end of helix Processing helix chain 'O' and resid 675 through 684 Processing helix chain 'O' and resid 746 through 763 Processing helix chain 'O' and resid 768 through 788 removed outlier: 3.632A pdb=" N LEU O 772 " --> pdb=" O SER O 768 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 60 Processing helix chain 'P' and resid 154 through 158 Processing helix chain 'P' and resid 364 through 374 removed outlier: 3.567A pdb=" N LEU P 368 " --> pdb=" O THR P 364 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS P 369 " --> pdb=" O ASN P 365 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL P 370 " --> pdb=" O THR P 366 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR P 374 " --> pdb=" O VAL P 370 " (cutoff:3.500A) Processing helix chain 'P' and resid 466 through 484 removed outlier: 3.587A pdb=" N CYS P 481 " --> pdb=" O LEU P 477 " (cutoff:3.500A) Processing helix chain 'P' and resid 488 through 493 Processing helix chain 'P' and resid 499 through 512 Processing helix chain 'P' and resid 517 through 522 removed outlier: 3.690A pdb=" N VAL P 521 " --> pdb=" O ALA P 517 " (cutoff:3.500A) Processing helix chain 'P' and resid 522 through 535 removed outlier: 3.568A pdb=" N LYS P 530 " --> pdb=" O ILE P 526 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS P 535 " --> pdb=" O ALA P 531 " (cutoff:3.500A) Processing helix chain 'P' and resid 540 through 542 No H-bonds generated for 'chain 'P' and resid 540 through 542' Processing helix chain 'P' and resid 543 through 562 removed outlier: 3.642A pdb=" N THR P 549 " --> pdb=" O CYS P 545 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS P 550 " --> pdb=" O ASP P 546 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU P 560 " --> pdb=" O ILE P 556 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS P 561 " --> pdb=" O SER P 557 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER P 562 " --> pdb=" O SER P 558 " (cutoff:3.500A) Processing helix chain 'P' and resid 575 through 587 Processing helix chain 'P' and resid 591 through 597 removed outlier: 4.304A pdb=" N VAL P 595 " --> pdb=" O ASP P 591 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE P 597 " --> pdb=" O ASP P 593 " (cutoff:3.500A) Processing helix chain 'P' and resid 598 through 600 No H-bonds generated for 'chain 'P' and resid 598 through 600' Processing helix chain 'P' and resid 609 through 614 removed outlier: 4.100A pdb=" N ALA P 613 " --> pdb=" O ASN P 609 " (cutoff:3.500A) Processing helix chain 'P' and resid 614 through 631 Processing helix chain 'P' and resid 648 through 669 removed outlier: 3.775A pdb=" N LEU P 652 " --> pdb=" O ASP P 648 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET P 659 " --> pdb=" O LEU P 655 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL P 660 " --> pdb=" O ARG P 656 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL P 661 " --> pdb=" O GLU P 657 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE P 662 " --> pdb=" O LEU P 658 " (cutoff:3.500A) Processing helix chain 'P' and resid 670 through 673 removed outlier: 3.536A pdb=" N LEU P 673 " --> pdb=" O PRO P 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 670 through 673' Processing helix chain 'P' and resid 684 through 699 removed outlier: 3.990A pdb=" N CYS P 699 " --> pdb=" O LYS P 695 " (cutoff:3.500A) Processing helix chain 'P' and resid 710 through 719 Processing helix chain 'P' and resid 720 through 723 Processing helix chain 'P' and resid 816 through 821 Processing helix chain 'Q' and resid 35 through 47 removed outlier: 3.574A pdb=" N ILE Q 47 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 120 Processing helix chain 'Q' and resid 139 through 172 removed outlier: 3.741A pdb=" N THR Q 172 " --> pdb=" O THR Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 194 removed outlier: 3.886A pdb=" N LEU Q 188 " --> pdb=" O ASN Q 184 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG Q 189 " --> pdb=" O SER Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 289 through 318 removed outlier: 3.679A pdb=" N THR Q 293 " --> pdb=" O PRO Q 289 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS Q 305 " --> pdb=" O VAL Q 301 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU Q 306 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE Q 307 " --> pdb=" O LEU Q 303 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE Q 308 " --> pdb=" O CYS Q 304 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL Q 316 " --> pdb=" O SER Q 312 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE Q 318 " --> pdb=" O GLU Q 314 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 385 removed outlier: 3.631A pdb=" N GLU Q 372 " --> pdb=" O LEU Q 368 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS Q 376 " --> pdb=" O GLU Q 372 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU Q 377 " --> pdb=" O HIS Q 373 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN Q 385 " --> pdb=" O GLU Q 381 " (cutoff:3.500A) Processing helix chain 'Q' and resid 386 through 387 No H-bonds generated for 'chain 'Q' and resid 386 through 387' Processing helix chain 'Q' and resid 388 through 392 removed outlier: 3.701A pdb=" N MET Q 391 " --> pdb=" O SER Q 388 " (cutoff:3.500A) Processing helix chain 'Q' and resid 403 through 408 Processing helix chain 'Q' and resid 414 through 420 Processing helix chain 'Q' and resid 426 through 455 removed outlier: 3.669A pdb=" N LYS Q 430 " --> pdb=" O GLY Q 426 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE Q 431 " --> pdb=" O LEU Q 427 " (cutoff:3.500A) Processing helix chain 'Q' and resid 517 through 530 removed outlier: 4.145A pdb=" N LEU Q 521 " --> pdb=" O GLN Q 517 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU Q 525 " --> pdb=" O LEU Q 521 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU Q 526 " --> pdb=" O GLN Q 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 531 through 544 removed outlier: 3.566A pdb=" N VAL Q 543 " --> pdb=" O GLN Q 539 " (cutoff:3.500A) Processing helix chain 'Q' and resid 613 through 617 Processing helix chain 'Q' and resid 634 through 646 removed outlier: 3.565A pdb=" N LEU Q 641 " --> pdb=" O TYR Q 637 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 43 removed outlier: 3.749A pdb=" N LEU R 35 " --> pdb=" O SER R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 122 removed outlier: 3.585A pdb=" N PHE R 117 " --> pdb=" O ASN R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 192 Processing helix chain 'T' and resid 16 through 32 removed outlier: 3.521A pdb=" N THR T 20 " --> pdb=" O SER T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 99 removed outlier: 3.541A pdb=" N LYS T 99 " --> pdb=" O MET T 95 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 166 Processing helix chain 'T' and resid 173 through 178 removed outlier: 3.982A pdb=" N ASN T 178 " --> pdb=" O VAL T 175 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 204 removed outlier: 4.409A pdb=" N THR T 189 " --> pdb=" O GLY T 185 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET T 190 " --> pdb=" O PRO T 186 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 39 Processing helix chain 'V' and resid 49 through 90 removed outlier: 3.701A pdb=" N GLN V 53 " --> pdb=" O SER V 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE V 87 " --> pdb=" O LYS V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 135 removed outlier: 3.522A pdb=" N ALA V 97 " --> pdb=" O SER V 93 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN V 103 " --> pdb=" O ASP V 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 13 Processing helix chain 'W' and resid 32 through 50 removed outlier: 4.028A pdb=" N ILE W 38 " --> pdb=" O LYS W 34 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER W 39 " --> pdb=" O THR W 35 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY W 50 " --> pdb=" O GLN W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 68 removed outlier: 4.111A pdb=" N CYS W 59 " --> pdb=" O SER W 55 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE W 60 " --> pdb=" O HIS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 89 removed outlier: 4.037A pdb=" N THR W 89 " --> pdb=" O MET W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 103 Processing helix chain 'W' and resid 111 through 125 Processing helix chain 'W' and resid 126 through 129 removed outlier: 3.998A pdb=" N VAL W 129 " --> pdb=" O ILE W 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 126 through 129' Processing helix chain 'W' and resid 130 through 146 Processing helix chain 'W' and resid 156 through 161 Processing helix chain 'W' and resid 161 through 171 Processing helix chain 'W' and resid 179 through 191 removed outlier: 3.740A pdb=" N ALA W 183 " --> pdb=" O PRO W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 211 removed outlier: 3.800A pdb=" N SER W 206 " --> pdb=" O GLY W 202 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE W 208 " --> pdb=" O LEU W 204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL W 209 " --> pdb=" O VAL W 205 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 219 removed outlier: 3.556A pdb=" N ALA W 216 " --> pdb=" O PHE W 212 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN W 219 " --> pdb=" O THR W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 238 through 242 removed outlier: 3.697A pdb=" N LYS W 242 " --> pdb=" O ASN W 239 " (cutoff:3.500A) Processing helix chain 'W' and resid 259 through 263 Processing helix chain 'W' and resid 266 through 276 removed outlier: 4.174A pdb=" N LEU W 270 " --> pdb=" O GLN W 266 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN W 276 " --> pdb=" O TYR W 272 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 287 removed outlier: 3.735A pdb=" N CYS W 284 " --> pdb=" O ARG W 280 " (cutoff:3.500A) Processing helix chain 'W' and resid 297 through 318 removed outlier: 3.748A pdb=" N GLU W 301 " --> pdb=" O CYS W 297 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU W 318 " --> pdb=" O ARG W 314 " (cutoff:3.500A) Processing helix chain 'W' and resid 327 through 344 removed outlier: 3.620A pdb=" N PHE W 344 " --> pdb=" O PHE W 340 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 361 Processing helix chain 'W' and resid 368 through 383 removed outlier: 3.683A pdb=" N LEU W 372 " --> pdb=" O GLY W 368 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER W 383 " --> pdb=" O PHE W 379 " (cutoff:3.500A) Processing helix chain 'W' and resid 388 through 393 removed outlier: 3.591A pdb=" N ASP W 391 " --> pdb=" O ALA W 388 " (cutoff:3.500A) Processing helix chain 'W' and resid 394 through 403 Processing helix chain 'W' and resid 416 through 436 removed outlier: 3.790A pdb=" N THR W 420 " --> pdb=" O LYS W 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS W 421 " --> pdb=" O PRO W 417 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET W 425 " --> pdb=" O HIS W 421 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR W 426 " --> pdb=" O ALA W 422 " (cutoff:3.500A) Processing helix chain 'W' and resid 450 through 464 removed outlier: 4.434A pdb=" N HIS W 454 " --> pdb=" O SER W 450 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE W 457 " --> pdb=" O LEU W 453 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU W 458 " --> pdb=" O HIS W 454 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN W 459 " --> pdb=" O HIS W 455 " (cutoff:3.500A) Processing helix chain 'W' and resid 472 through 482 Processing helix chain 'W' and resid 488 through 501 removed outlier: 4.091A pdb=" N THR W 498 " --> pdb=" O ALA W 494 " (cutoff:3.500A) Processing helix chain 'W' and resid 524 through 529 Processing helix chain 'W' and resid 532 through 553 Processing helix chain 'W' and resid 560 through 570 Processing helix chain 'W' and resid 573 through 577 removed outlier: 3.826A pdb=" N ILE W 576 " --> pdb=" O TYR W 573 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU W 577 " --> pdb=" O MET W 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 573 through 577' Processing helix chain 'W' and resid 580 through 596 removed outlier: 4.472A pdb=" N LEU W 589 " --> pdb=" O ILE W 585 " (cutoff:3.500A) Proline residue: W 590 - end of helix removed outlier: 3.511A pdb=" N HIS W 596 " --> pdb=" O VAL W 592 " (cutoff:3.500A) Processing helix chain 'W' and resid 599 through 611 Processing helix chain 'W' and resid 616 through 633 removed outlier: 3.526A pdb=" N VAL W 633 " --> pdb=" O THR W 629 " (cutoff:3.500A) Processing helix chain 'W' and resid 638 through 654 removed outlier: 3.624A pdb=" N ILE W 653 " --> pdb=" O ALA W 649 " (cutoff:3.500A) Processing helix chain 'W' and resid 660 through 666 removed outlier: 3.546A pdb=" N THR W 666 " --> pdb=" O GLN W 662 " (cutoff:3.500A) Processing helix chain 'W' and resid 671 through 675 Processing helix chain 'W' and resid 680 through 698 removed outlier: 4.324A pdb=" N ASN W 684 " --> pdb=" O SER W 680 " (cutoff:3.500A) Processing helix chain 'W' and resid 712 through 721 Processing helix chain 'W' and resid 728 through 733 Processing helix chain 'W' and resid 736 through 744 Processing helix chain 'W' and resid 752 through 770 removed outlier: 3.893A pdb=" N MET W 770 " --> pdb=" O LYS W 766 " (cutoff:3.500A) Processing helix chain 'W' and resid 773 through 782 Processing helix chain 'W' and resid 789 through 798 Processing helix chain 'W' and resid 804 through 815 removed outlier: 3.899A pdb=" N TYR W 808 " --> pdb=" O ASN W 804 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY W 815 " --> pdb=" O LEU W 811 " (cutoff:3.500A) Processing helix chain 'W' and resid 818 through 836 removed outlier: 3.792A pdb=" N HIS W 822 " --> pdb=" O ALA W 818 " (cutoff:3.500A) Processing helix chain 'W' and resid 840 through 856 Processing helix chain 'W' and resid 861 through 871 Processing helix chain 'W' and resid 876 through 891 removed outlier: 4.311A pdb=" N GLN W 880 " --> pdb=" O GLY W 876 " (cutoff:3.500A) Processing helix chain 'W' and resid 893 through 907 removed outlier: 3.860A pdb=" N ARG W 897 " --> pdb=" O PRO W 893 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG W 899 " --> pdb=" O ASP W 895 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL W 900 " --> pdb=" O PHE W 896 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP W 902 " --> pdb=" O ASN W 898 " (cutoff:3.500A) Processing helix chain 'W' and resid 916 through 928 removed outlier: 3.797A pdb=" N LYS W 920 " --> pdb=" O ASP W 916 " (cutoff:3.500A) Processing helix chain 'W' and resid 934 through 940 Processing helix chain 'W' and resid 958 through 976 Proline residue: W 965 - end of helix Processing helix chain 'W' and resid 980 through 992 Processing helix chain 'W' and resid 993 through 998 removed outlier: 3.734A pdb=" N PHE W 997 " --> pdb=" O LEU W 994 " (cutoff:3.500A) Processing helix chain 'W' and resid 1000 through 1012 removed outlier: 3.581A pdb=" N TYR W1004 " --> pdb=" O ARG W1000 " (cutoff:3.500A) Processing helix chain 'W' and resid 1019 through 1034 removed outlier: 3.642A pdb=" N LYS W1023 " --> pdb=" O ARG W1019 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU W1034 " --> pdb=" O ILE W1030 " (cutoff:3.500A) Processing helix chain 'W' and resid 1045 through 1051 Processing helix chain 'W' and resid 1064 through 1081 removed outlier: 4.111A pdb=" N TYR W1068 " --> pdb=" O ASP W1064 " (cutoff:3.500A) Processing helix chain 'W' and resid 1099 through 1114 Processing helix chain 'W' and resid 1118 through 1132 removed outlier: 4.315A pdb=" N VAL W1130 " --> pdb=" O LEU W1126 " (cutoff:3.500A) Processing helix chain 'W' and resid 1141 through 1156 removed outlier: 3.824A pdb=" N TRP W1145 " --> pdb=" O ASN W1141 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA W1155 " --> pdb=" O LEU W1151 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU W1156 " --> pdb=" O ILE W1152 " (cutoff:3.500A) Processing helix chain 'W' and resid 1157 through 1162 removed outlier: 3.655A pdb=" N TRP W1161 " --> pdb=" O PRO W1157 " (cutoff:3.500A) Processing helix chain 'W' and resid 1162 through 1173 removed outlier: 4.392A pdb=" N ASP W1166 " --> pdb=" O ILE W1162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER W1173 " --> pdb=" O VAL W1169 " (cutoff:3.500A) Processing helix chain 'W' and resid 1174 through 1179 Processing helix chain 'W' and resid 1192 through 1198 Processing helix chain 'W' and resid 1203 through 1218 removed outlier: 4.162A pdb=" N TYR W1207 " --> pdb=" O MET W1203 " (cutoff:3.500A) Processing helix chain 'W' and resid 1220 through 1225 Processing helix chain 'W' and resid 1226 through 1234 removed outlier: 3.843A pdb=" N PHE W1230 " --> pdb=" O LEU W1226 " (cutoff:3.500A) Processing helix chain 'W' and resid 1241 through 1253 removed outlier: 3.571A pdb=" N LEU W1245 " --> pdb=" O THR W1241 " (cutoff:3.500A) Processing helix chain 'W' and resid 1255 through 1263 Processing helix chain 'W' and resid 1263 through 1285 removed outlier: 3.606A pdb=" N MET W1267 " --> pdb=" O ARG W1263 " (cutoff:3.500A) Processing helix chain 'W' and resid 1290 through 1305 removed outlier: 3.520A pdb=" N ILE W1294 " --> pdb=" O TYR W1290 " (cutoff:3.500A) Processing helix chain 'W' and resid 1314 through 1320 removed outlier: 3.866A pdb=" N ASN W1320 " --> pdb=" O LYS W1316 " (cutoff:3.500A) Processing helix chain 'W' and resid 1322 through 1328 Processing helix chain 'W' and resid 1329 through 1333 removed outlier: 3.534A pdb=" N ILE W1332 " --> pdb=" O LEU W1329 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 16 removed outlier: 3.989A pdb=" N GLU X 16 " --> pdb=" O GLN X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 31 removed outlier: 3.679A pdb=" N LYS X 28 " --> pdb=" O ALA X 24 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS X 29 " --> pdb=" O ILE X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 34 through 38 removed outlier: 3.514A pdb=" N TRP X 37 " --> pdb=" O GLY X 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 51 removed outlier: 3.501A pdb=" N LEU X 47 " --> pdb=" O ALA X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 70 removed outlier: 3.612A pdb=" N LEU X 61 " --> pdb=" O ASN X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 86 removed outlier: 4.081A pdb=" N VAL X 78 " --> pdb=" O SER X 74 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE X 85 " --> pdb=" O ALA X 81 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP X 86 " --> pdb=" O ILE X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 105 removed outlier: 3.725A pdb=" N VAL X 94 " --> pdb=" O ARG X 90 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE X 104 " --> pdb=" O ILE X 100 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 146 Processing helix chain 'X' and resid 156 through 171 removed outlier: 3.714A pdb=" N MET X 160 " --> pdb=" O LYS X 156 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER X 171 " --> pdb=" O LYS X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 171 through 185 removed outlier: 3.528A pdb=" N ARG X 175 " --> pdb=" O SER X 171 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU X 183 " --> pdb=" O HIS X 179 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU X 184 " --> pdb=" O ILE X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 206 removed outlier: 3.535A pdb=" N LEU X 206 " --> pdb=" O ILE X 202 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 225 removed outlier: 3.566A pdb=" N GLN X 214 " --> pdb=" O GLN X 210 " (cutoff:3.500A) Processing helix chain 'X' and resid 241 through 254 removed outlier: 3.838A pdb=" N HIS X 245 " --> pdb=" O PHE X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 259 through 274 removed outlier: 3.986A pdb=" N LEU X 263 " --> pdb=" O GLU X 259 " (cutoff:3.500A) Processing helix chain 'X' and resid 277 through 296 removed outlier: 3.583A pdb=" N SER X 296 " --> pdb=" O GLY X 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 324 removed outlier: 3.758A pdb=" N LEU X 303 " --> pdb=" O GLY X 299 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE X 313 " --> pdb=" O THR X 309 " (cutoff:3.500A) Proline residue: X 314 - end of helix Processing helix chain 'X' and resid 330 through 342 Processing helix chain 'X' and resid 344 through 356 removed outlier: 3.668A pdb=" N LEU X 348 " --> pdb=" O LEU X 344 " (cutoff:3.500A) Processing helix chain 'X' and resid 358 through 370 removed outlier: 3.628A pdb=" N PHE X 362 " --> pdb=" O ASP X 358 " (cutoff:3.500A) Processing helix chain 'X' and resid 374 through 391 removed outlier: 3.803A pdb=" N HIS X 391 " --> pdb=" O ALA X 387 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 424 Proline residue: X 415 - end of helix Processing helix chain 'X' and resid 426 through 431 removed outlier: 3.672A pdb=" N LYS X 430 " --> pdb=" O ALA X 426 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 442 Processing helix chain 'X' and resid 446 through 459 Processing helix chain 'X' and resid 460 through 478 removed outlier: 3.621A pdb=" N PHE X 464 " --> pdb=" O LYS X 460 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR X 477 " --> pdb=" O GLU X 473 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY X 478 " --> pdb=" O PHE X 474 " (cutoff:3.500A) Processing helix chain 'X' and resid 482 through 507 Processing helix chain 'X' and resid 523 through 533 removed outlier: 3.549A pdb=" N THR X 527 " --> pdb=" O PRO X 523 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N MET X 533 " --> pdb=" O MET X 529 " (cutoff:3.500A) Processing helix chain 'X' and resid 544 through 548 Processing helix chain 'X' and resid 552 through 564 removed outlier: 3.603A pdb=" N SER X 564 " --> pdb=" O LEU X 560 " (cutoff:3.500A) Processing helix chain 'X' and resid 573 through 595 removed outlier: 4.358A pdb=" N SER X 582 " --> pdb=" O CYS X 578 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA X 583 " --> pdb=" O LEU X 579 " (cutoff:3.500A) Processing helix chain 'X' and resid 598 through 612 removed outlier: 3.516A pdb=" N ILE X 602 " --> pdb=" O ALA X 598 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS X 612 " --> pdb=" O ASN X 608 " (cutoff:3.500A) Processing helix chain 'X' and resid 614 through 631 removed outlier: 4.021A pdb=" N MET X 630 " --> pdb=" O ALA X 626 " (cutoff:3.500A) Processing helix chain 'X' and resid 632 through 647 removed outlier: 4.497A pdb=" N GLU X 637 " --> pdb=" O LEU X 633 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS X 638 " --> pdb=" O ASP X 634 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER X 639 " --> pdb=" O GLU X 635 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU X 640 " --> pdb=" O ARG X 636 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN X 641 " --> pdb=" O GLU X 637 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET X 642 " --> pdb=" O LYS X 638 " (cutoff:3.500A) Processing helix chain 'X' and resid 659 through 681 removed outlier: 5.487A pdb=" N ASP X 676 " --> pdb=" O ARG X 672 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL X 677 " --> pdb=" O MET X 673 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN X 680 " --> pdb=" O ASP X 676 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR X 681 " --> pdb=" O VAL X 677 " (cutoff:3.500A) Processing helix chain 'X' and resid 706 through 722 removed outlier: 4.018A pdb=" N VAL X 710 " --> pdb=" O PRO X 706 " (cutoff:3.500A) Processing helix chain 'X' and resid 725 through 740 Processing helix chain 'X' and resid 740 through 753 Processing helix chain 'X' and resid 757 through 773 removed outlier: 3.721A pdb=" N SER X 770 " --> pdb=" O GLU X 766 " (cutoff:3.500A) Processing helix chain 'X' and resid 775 through 794 removed outlier: 5.463A pdb=" N LEU X 788 " --> pdb=" O LEU X 784 " (cutoff:3.500A) Proline residue: X 789 - end of helix Processing helix chain 'X' and resid 802 through 823 Processing helix chain 'X' and resid 829 through 839 removed outlier: 3.571A pdb=" N ASP X 839 " --> pdb=" O ARG X 835 " (cutoff:3.500A) Processing helix chain 'X' and resid 842 through 847 Processing helix chain 'X' and resid 895 through 914 Processing helix chain 'X' and resid 918 through 935 removed outlier: 3.592A pdb=" N GLN X 922 " --> pdb=" O GLY X 918 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU X 935 " --> pdb=" O CYS X 931 " (cutoff:3.500A) Processing helix chain 'X' and resid 943 through 947 removed outlier: 4.010A pdb=" N PHE X 946 " --> pdb=" O VAL X 943 " (cutoff:3.500A) Processing helix chain 'X' and resid 949 through 959 removed outlier: 4.386A pdb=" N SER X 953 " --> pdb=" O PHE X 949 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL X 956 " --> pdb=" O VAL X 952 " (cutoff:3.500A) Processing helix chain 'X' and resid 966 through 973 removed outlier: 3.639A pdb=" N ILE X 970 " --> pdb=" O VAL X 966 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR X 971 " --> pdb=" O VAL X 967 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU X 973 " --> pdb=" O ALA X 969 " (cutoff:3.500A) Processing helix chain 'X' and resid 975 through 988 removed outlier: 4.479A pdb=" N GLN X 980 " --> pdb=" O PRO X 976 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 87 Processing helix chain 'S' and resid 89 through 97 Processing helix chain 'S' and resid 112 through 118 Processing helix chain 'S' and resid 129 through 139 Proline residue: S 134 - end of helix removed outlier: 3.562A pdb=" N SER S 138 " --> pdb=" O PRO S 134 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER S 139 " --> pdb=" O PRO S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 154 Processing helix chain 'U' and resid 3 through 29 Processing helix chain 'U' and resid 49 through 76 removed outlier: 3.511A pdb=" N GLN U 56 " --> pdb=" O GLU U 52 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP U 74 " --> pdb=" O ASP U 70 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER U 75 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU U 76 " --> pdb=" O LEU U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 108 removed outlier: 3.720A pdb=" N LYS U 92 " --> pdb=" O ALA U 88 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) Processing helix chain 'U' and resid 109 through 133 Processing sheet with id=AA1, first strand: chain '0' and resid 176 through 181 removed outlier: 5.789A pdb=" N ARG 0 205 " --> pdb=" O ILE 0 209 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE 0 209 " --> pdb=" O ARG 0 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 296 through 297 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.712A pdb=" N GLY A 91 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 103 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N HIS A 93 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N CYS A 101 " --> pdb=" O HIS A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 212 removed outlier: 6.348A pdb=" N ASN A 221 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 257 " --> pdb=" O ASN A 221 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LYS A 223 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA A 255 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TYR A 225 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET A 253 " --> pdb=" O TYR A 225 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N ASN A 254 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 260 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 302 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 262 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N ALA A 264 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N ASP A 298 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N TYR A 266 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N SER A 296 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 303 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N SER A 394 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N GLN A 309 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N LEU A 392 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N ILE A 311 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N GLY A 390 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 278 removed outlier: 3.502A pdb=" N HIS A 278 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP A 281 " --> pdb=" O HIS A 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 362 through 366 removed outlier: 7.534A pdb=" N GLN A 439 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLN A 455 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 142 through 143 Processing sheet with id=AA8, first strand: chain 'F' and resid 66 through 73 removed outlier: 3.682A pdb=" N LEU F 71 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE F 80 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 137 through 140 Processing sheet with id=AB1, first strand: chain 'H' and resid 75 through 78 removed outlier: 3.539A pdb=" N ASP Q 128 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE H 77 " --> pdb=" O THR Q 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 224 through 225 removed outlier: 7.164A pdb=" N THR N 235 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU N 247 " --> pdb=" O THR N 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 325 through 330 removed outlier: 6.998A pdb=" N SER N 336 " --> pdb=" O GLU N 327 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR N 329 " --> pdb=" O CYS N 334 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N CYS N 334 " --> pdb=" O TYR N 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 430 through 432 removed outlier: 3.728A pdb=" N ALA N 437 " --> pdb=" O GLU N 432 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 514 through 517 removed outlier: 3.551A pdb=" N LEU N 542 " --> pdb=" O TYR N 548 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR N 548 " --> pdb=" O LEU N 542 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER N 572 " --> pdb=" O LEU N 587 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU N 587 " --> pdb=" O SER N 572 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 672 through 673 Processing sheet with id=AB7, first strand: chain 'N' and resid 705 through 713 removed outlier: 5.997A pdb=" N LEU N 705 " --> pdb=" O ALA N 727 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA N 727 " --> pdb=" O LEU N 705 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP N 707 " --> pdb=" O VAL N 725 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL N 725 " --> pdb=" O ASP N 707 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 798 through 803 removed outlier: 5.178A pdb=" N VAL N 800 " --> pdb=" O CYS N 811 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N CYS N 811 " --> pdb=" O VAL N 800 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN N 823 " --> pdb=" O HIS N 832 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN N 825 " --> pdb=" O LYS N 830 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS N 830 " --> pdb=" O ASN N 825 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 904 through 908 removed outlier: 3.640A pdb=" N VAL N 933 " --> pdb=" O ARG N 929 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 1240 through 1242 removed outlier: 4.034A pdb=" N ILE N1240 " --> pdb=" O VAL N1251 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL N1251 " --> pdb=" O ILE N1240 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS N1249 " --> pdb=" O PHE N1242 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 1338 through 1339 removed outlier: 3.503A pdb=" N PHE N1338 " --> pdb=" O THR N1354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 692 through 693 removed outlier: 3.569A pdb=" N SER O 724 " --> pdb=" O LEU O 735 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU O 735 " --> pdb=" O SER O 724 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 431 through 436 removed outlier: 3.814A pdb=" N ASP P 447 " --> pdb=" O LYS P 451 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS P 451 " --> pdb=" O ASP P 447 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR P 17 " --> pdb=" O VAL P 454 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ARG P 456 " --> pdb=" O LEU P 15 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU P 15 " --> pdb=" O ARG P 456 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU P 748 " --> pdb=" O ALA P 16 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU P 750 " --> pdb=" O VAL P 18 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU P 20 " --> pdb=" O LEU P 750 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 37 through 39 removed outlier: 4.971A pdb=" N ASP P 66 " --> pdb=" O ASP P 72 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP P 72 " --> pdb=" O ASP P 66 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 84 through 89 removed outlier: 6.764A pdb=" N ILE P 105 " --> pdb=" O GLY P 123 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY P 123 " --> pdb=" O ILE P 105 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N CYS P 107 " --> pdb=" O SER P 121 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER P 121 " --> pdb=" O CYS P 107 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER P 117 " --> pdb=" O ALA P 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 131 through 136 removed outlier: 5.198A pdb=" N LEU P 187 " --> pdb=" O THR P 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 143 through 145 Processing sheet with id=AC9, first strand: chain 'P' and resid 215 through 221 removed outlier: 3.712A pdb=" N ASN P 225 " --> pdb=" O THR P 221 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL P 239 " --> pdb=" O SER P 262 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER P 262 " --> pdb=" O VAL P 239 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE P 241 " --> pdb=" O LEU P 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 279 through 287 removed outlier: 5.333A pdb=" N ILE P 280 " --> pdb=" O SER P 299 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER P 299 " --> pdb=" O ILE P 280 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLN P 293 " --> pdb=" O LEU P 286 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL P 306 " --> pdb=" O ALA P 344 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA P 344 " --> pdb=" O VAL P 306 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N CYS P 308 " --> pdb=" O LEU P 342 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 279 through 287 removed outlier: 5.333A pdb=" N ILE P 280 " --> pdb=" O SER P 299 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER P 299 " --> pdb=" O ILE P 280 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLN P 293 " --> pdb=" O LEU P 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 351 through 355 removed outlier: 3.711A pdb=" N ALA P 353 " --> pdb=" O ALA P 385 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE P 386 " --> pdb=" O SER P 390 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N SER P 390 " --> pdb=" O PHE P 386 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL P 391 " --> pdb=" O VAL P 404 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL P 404 " --> pdb=" O VAL P 391 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE P 393 " --> pdb=" O MET P 402 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 779 through 780 removed outlier: 3.997A pdb=" N LEU P 785 " --> pdb=" O ASP P 780 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 795 through 797 Processing sheet with id=AD6, first strand: chain 'Q' and resid 196 through 199 removed outlier: 4.516A pdb=" N ILE Q 203 " --> pdb=" O VAL Q 224 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 256 through 262 removed outlier: 3.692A pdb=" N GLN Q 340 " --> pdb=" O GLN Q 262 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE Q 325 " --> pdb=" O ILE Q 332 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 461 through 464 removed outlier: 4.134A pdb=" N ARG Q 510 " --> pdb=" O HIS Q 506 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 547 through 552 removed outlier: 6.497A pdb=" N THR Q 570 " --> pdb=" O LEU Q 549 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE Q 551 " --> pdb=" O ALA Q 568 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA Q 568 " --> pdb=" O PHE Q 551 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 160 through 162 removed outlier: 5.694A pdb=" N ILE R 148 " --> pdb=" O SER R 166 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N SER R 166 " --> pdb=" O ILE R 148 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET R 18 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS R 105 " --> pdb=" O MET R 18 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU R 88 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL R 69 " --> pdb=" O LEU R 88 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE R 51 " --> pdb=" O LYS R 132 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS R 132 " --> pdb=" O PHE R 51 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP R 53 " --> pdb=" O VAL R 130 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL R 130 " --> pdb=" O ASP R 53 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU R 55 " --> pdb=" O GLU R 128 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU R 128 " --> pdb=" O GLU R 55 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL R 57 " --> pdb=" O ASP R 126 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU R 128 " --> pdb=" O ILE R 151 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE R 151 " --> pdb=" O GLU R 128 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL R 130 " --> pdb=" O PHE R 149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 4 through 8 removed outlier: 3.872A pdb=" N GLY T 137 " --> pdb=" O VAL T 129 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL T 126 " --> pdb=" O THR T 115 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR T 115 " --> pdb=" O VAL T 126 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE T 110 " --> pdb=" O CYS T 43 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG T 116 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY T 37 " --> pdb=" O ARG T 116 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN T 118 " --> pdb=" O LYS T 35 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LYS T 35 " --> pdb=" O GLN T 118 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP T 42 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS T 67 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASN T 68 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER T 74 " --> pdb=" O ASN T 68 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 506 through 508 3365 hydrogen bonds defined for protein. 9849 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: 26.37 Time building geometry restraints manager: 13.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18977 1.34 - 1.46: 11124 1.46 - 1.58: 30442 1.58 - 1.70: 2 1.70 - 1.82: 588 Bond restraints: 61133 Sorted by residual: bond pdb=" CA SER S 129 " pdb=" C SER S 129 " ideal model delta sigma weight residual 1.522 1.601 -0.078 1.36e-02 5.41e+03 3.30e+01 bond pdb=" CA THR Q 273 " pdb=" CB THR Q 273 " ideal model delta sigma weight residual 1.530 1.584 -0.054 1.69e-02 3.50e+03 1.02e+01 bond pdb=" N CYS N 300 " pdb=" CA CYS N 300 " ideal model delta sigma weight residual 1.459 1.426 0.033 1.21e-02 6.83e+03 7.53e+00 bond pdb=" CA THR Q 273 " pdb=" C THR Q 273 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.34e-02 5.57e+03 7.51e+00 bond pdb=" C ASP Q 457 " pdb=" N PRO Q 458 " ideal model delta sigma weight residual 1.330 1.363 -0.033 1.23e-02 6.61e+03 7.00e+00 ... (remaining 61128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 80790 2.64 - 5.27: 1711 5.27 - 7.91: 244 7.91 - 10.54: 43 10.54 - 13.18: 7 Bond angle restraints: 82795 Sorted by residual: angle pdb=" N VAL N 204 " pdb=" CA VAL N 204 " pdb=" C VAL N 204 " ideal model delta sigma weight residual 110.53 121.44 -10.91 9.40e-01 1.13e+00 1.35e+02 angle pdb=" N SER S 129 " pdb=" CA SER S 129 " pdb=" C SER S 129 " ideal model delta sigma weight residual 111.71 98.96 12.75 1.15e+00 7.56e-01 1.23e+02 angle pdb=" C PRO d 929 " pdb=" N PRO d 930 " pdb=" CA PRO d 930 " ideal model delta sigma weight residual 119.28 130.87 -11.59 1.10e+00 8.26e-01 1.11e+02 angle pdb=" C HIS G 68 " pdb=" N PRO G 69 " pdb=" CA PRO G 69 " ideal model delta sigma weight residual 120.03 129.07 -9.04 9.90e-01 1.02e+00 8.35e+01 angle pdb=" C LEU d 923 " pdb=" N PRO d 924 " pdb=" CA PRO d 924 " ideal model delta sigma weight residual 119.28 128.94 -9.66 1.10e+00 8.26e-01 7.71e+01 ... (remaining 82790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 33314 17.94 - 35.88: 3244 35.88 - 53.82: 568 53.82 - 71.76: 121 71.76 - 89.70: 56 Dihedral angle restraints: 37303 sinusoidal: 14942 harmonic: 22361 Sorted by residual: dihedral pdb=" N GLN N 547 " pdb=" C GLN N 547 " pdb=" CA GLN N 547 " pdb=" CB GLN N 547 " ideal model delta harmonic sigma weight residual 122.80 138.46 -15.66 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" C GLN N 547 " pdb=" N GLN N 547 " pdb=" CA GLN N 547 " pdb=" CB GLN N 547 " ideal model delta harmonic sigma weight residual -122.60 -138.17 15.57 0 2.50e+00 1.60e-01 3.88e+01 dihedral pdb=" CA THR N 259 " pdb=" C THR N 259 " pdb=" N GLY N 260 " pdb=" CA GLY N 260 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 37300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 9155 0.124 - 0.249: 326 0.249 - 0.373: 32 0.373 - 0.497: 6 0.497 - 0.621: 2 Chirality restraints: 9521 Sorted by residual: chirality pdb=" CA GLN N 547 " pdb=" N GLN N 547 " pdb=" C GLN N 547 " pdb=" CB GLN N 547 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.65e+00 chirality pdb=" CG LEU Q 112 " pdb=" CB LEU Q 112 " pdb=" CD1 LEU Q 112 " pdb=" CD2 LEU Q 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.96e+00 chirality pdb=" CA ASP N 285 " pdb=" N ASP N 285 " pdb=" C ASP N 285 " pdb=" CB ASP N 285 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 9518 not shown) Planarity restraints: 10565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE N 666 " 0.087 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO N 667 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO N 667 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO N 667 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER N 298 " 0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C SER N 298 " -0.088 2.00e-02 2.50e+03 pdb=" O SER N 298 " 0.033 2.00e-02 2.50e+03 pdb=" N PHE N 299 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN K 77 " -0.074 5.00e-02 4.00e+02 1.14e-01 2.06e+01 pdb=" N PRO K 78 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO K 78 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO K 78 " -0.061 5.00e-02 4.00e+02 ... (remaining 10562 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 792 2.64 - 3.21: 55324 3.21 - 3.77: 90070 3.77 - 4.34: 115138 4.34 - 4.90: 190092 Nonbonded interactions: 451416 Sorted by model distance: nonbonded pdb=" O LYS N 691 " pdb=" NZ LYS N 691 " model vdw 2.076 3.120 nonbonded pdb=" N GLU Q 12 " pdb=" OE1 GLU Q 12 " model vdw 2.168 3.120 nonbonded pdb=" N GLU D 28 " pdb=" OE1 GLU D 28 " model vdw 2.175 3.120 nonbonded pdb=" OD1 ASN U 49 " pdb=" CD PRO U 50 " model vdw 2.181 3.440 nonbonded pdb=" N GLU N 227 " pdb=" OE1 GLU N 227 " model vdw 2.188 3.120 ... (remaining 451411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 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: 0.090 Extract box with map and model: 1.830 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 113.550 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 61133 Z= 0.306 Angle : 0.918 13.180 82795 Z= 0.549 Chirality : 0.058 0.621 9521 Planarity : 0.006 0.134 10565 Dihedral : 14.822 89.700 22683 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.25 % Favored : 94.63 % Rotamer: Outliers : 1.44 % Allowed : 2.46 % Favored : 96.09 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.10), residues: 7453 helix: 1.12 (0.08), residues: 3967 sheet: 0.13 (0.19), residues: 701 loop : -1.83 (0.11), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP X 798 HIS 0.013 0.001 HIS W 822 PHE 0.062 0.002 PHE W 584 TYR 0.037 0.002 TYR W1200 ARG 0.031 0.001 ARG W 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 919 time to evaluate : 5.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7607 (tmm-80) REVERT: 0 234 SER cc_start: 0.9148 (p) cc_final: 0.8889 (t) REVERT: 0 300 ARG cc_start: 0.6526 (mtm110) cc_final: 0.5876 (ptp-170) REVERT: 1 111 ILE cc_start: 0.4875 (mt) cc_final: 0.4634 (mt) REVERT: 2 62 MET cc_start: 0.6592 (ttp) cc_final: 0.6159 (tpp) REVERT: 3 39 GLU cc_start: 0.7327 (tp30) cc_final: 0.7052 (tp30) REVERT: 3 145 VAL cc_start: 0.6653 (p) cc_final: 0.6421 (p) REVERT: 3 157 LYS cc_start: 0.8185 (tppt) cc_final: 0.7751 (tptt) REVERT: A 170 LYS cc_start: 0.4633 (OUTLIER) cc_final: 0.4272 (mtpt) REVERT: A 400 HIS cc_start: 0.1388 (p90) cc_final: 0.0708 (m90) REVERT: D 182 MET cc_start: 0.2467 (ppp) cc_final: 0.2172 (ptp) REVERT: F 138 ARG cc_start: 0.3882 (mpt-90) cc_final: 0.3618 (mmm160) REVERT: G 64 ILE cc_start: -0.0156 (mp) cc_final: -0.0683 (mp) REVERT: G 139 MET cc_start: 0.2860 (mtp) cc_final: 0.1782 (tpt) REVERT: H 145 LYS cc_start: 0.6239 (mttp) cc_final: 0.5834 (tttm) REVERT: I 97 MET cc_start: 0.2275 (ppp) cc_final: 0.1619 (mtm) REVERT: I 100 LEU cc_start: 0.0858 (mt) cc_final: 0.0543 (mt) REVERT: I 104 MET cc_start: -0.0529 (mmp) cc_final: -0.0820 (ppp) REVERT: N 593 GLU cc_start: 0.3989 (OUTLIER) cc_final: 0.3573 (mm-30) REVERT: N 954 TYR cc_start: 0.8213 (m-80) cc_final: 0.7994 (m-80) REVERT: O 653 PRO cc_start: 0.4380 (Cg_endo) cc_final: 0.4120 (Cg_exo) REVERT: P 341 ILE cc_start: 0.8279 (mp) cc_final: 0.7739 (tt) REVERT: P 578 ASP cc_start: 0.6381 (m-30) cc_final: 0.5410 (t0) REVERT: Q 480 THR cc_start: 0.7682 (p) cc_final: 0.7480 (p) REVERT: R 186 MET cc_start: 0.6520 (mtm) cc_final: 0.6293 (mtp) REVERT: V 121 ASP cc_start: 0.7264 (m-30) cc_final: 0.6763 (t0) REVERT: W 607 MET cc_start: 0.7202 (ttm) cc_final: 0.6627 (ttp) REVERT: W 720 MET cc_start: 0.5667 (ttt) cc_final: 0.5466 (tmm) REVERT: W 763 GLU cc_start: 0.4555 (pp20) cc_final: 0.4117 (mm-30) REVERT: W 782 MET cc_start: 0.4567 (ppp) cc_final: 0.3360 (tpt) REVERT: W 867 LEU cc_start: 0.6667 (tt) cc_final: 0.6376 (tp) REVERT: W 1079 MET cc_start: 0.8356 (ttp) cc_final: 0.8107 (ttp) REVERT: X 36 THR cc_start: 0.6026 (OUTLIER) cc_final: 0.5665 (p) outliers start: 95 outliers final: 20 residues processed: 993 average time/residue: 0.6092 time to fit residues: 1017.5795 Evaluate side-chains 568 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 545 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 295 THR Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 315 LEU Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 593 GLU Chi-restraints excluded: chain N residue 678 PHE Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 625 VAL Chi-restraints excluded: chain W residue 152 VAL Chi-restraints excluded: chain W residue 610 TYR Chi-restraints excluded: chain W residue 830 LEU Chi-restraints excluded: chain W residue 935 GLU Chi-restraints excluded: chain W residue 1276 ASP Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain U residue 7 GLN Chi-restraints excluded: chain U residue 97 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 633 optimal weight: 0.9980 chunk 568 optimal weight: 3.9990 chunk 315 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 383 optimal weight: 0.6980 chunk 303 optimal weight: 10.0000 chunk 587 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 357 optimal weight: 3.9990 chunk 437 optimal weight: 1.9990 chunk 681 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 130 GLN 1 132 HIS 3 29 ASN 3 146 ASN ** 4 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 GLN ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS H 7 GLN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 ASN I 108 HIS I 113 GLN I 116 GLN I 124 GLN K 77 GLN K 79 HIS N 189 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 297 HIS N 330 HIS N 669 GLN N 832 HIS N1183 ASN N1297 ASN ** O 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 746 ASN P 80 HIS P 400 GLN P 548 HIS P 751 GLN Q 394 HIS Q 595 GLN Q 611 GLN R 37 HIS R 192 GLN T 168 HIS V 89 ASN V 109 GLN W 239 ASN W 351 HIS W 552 HIS W 628 HIS ** W 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 408 GLN X 737 HIS U 7 GLN U 13 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 61133 Z= 0.254 Angle : 0.699 12.153 82795 Z= 0.360 Chirality : 0.044 0.221 9521 Planarity : 0.005 0.085 10565 Dihedral : 5.370 77.990 8150 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer: Outliers : 1.67 % Allowed : 10.10 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 7453 helix: 1.28 (0.08), residues: 4083 sheet: 0.27 (0.19), residues: 721 loop : -1.93 (0.11), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 798 HIS 0.014 0.001 HIS F 148 PHE 0.038 0.002 PHE U 19 TYR 0.023 0.002 TYR D 126 ARG 0.031 0.001 ARG G 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 604 time to evaluate : 5.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 64 ASN cc_start: 0.6557 (m-40) cc_final: 0.6284 (m-40) REVERT: 2 62 MET cc_start: 0.6676 (ttp) cc_final: 0.6220 (tpp) REVERT: 3 80 ASP cc_start: 0.6641 (t0) cc_final: 0.6410 (t0) REVERT: 3 137 GLU cc_start: 0.5532 (mm-30) cc_final: 0.5300 (pt0) REVERT: 3 157 LYS cc_start: 0.8137 (tppt) cc_final: 0.7721 (tptt) REVERT: 3 176 MET cc_start: 0.6423 (ttt) cc_final: 0.6036 (ttm) REVERT: A 71 VAL cc_start: 0.1679 (t) cc_final: 0.1403 (t) REVERT: A 400 HIS cc_start: 0.1533 (p90) cc_final: 0.0734 (m90) REVERT: D 73 ASP cc_start: 0.1561 (OUTLIER) cc_final: 0.1290 (m-30) REVERT: D 98 LYS cc_start: 0.5910 (mmmt) cc_final: 0.5284 (ttmm) REVERT: G 127 ARG cc_start: 0.2225 (ppt170) cc_final: 0.1920 (tmm160) REVERT: G 139 MET cc_start: 0.3091 (mtp) cc_final: 0.0597 (tpt) REVERT: G 151 GLU cc_start: 0.3972 (pp20) cc_final: 0.2976 (tp30) REVERT: H 74 GLN cc_start: 0.4905 (mm-40) cc_final: 0.4654 (tp40) REVERT: H 87 GLU cc_start: 0.3108 (tt0) cc_final: 0.1730 (mm-30) REVERT: I 97 MET cc_start: 0.2430 (ppp) cc_final: 0.1569 (mtm) REVERT: I 130 GLU cc_start: 0.2024 (OUTLIER) cc_final: 0.1698 (pp20) REVERT: N 749 TYR cc_start: 0.6716 (m-80) cc_final: 0.6423 (m-80) REVERT: N 1299 LEU cc_start: 0.7952 (tp) cc_final: 0.7684 (tp) REVERT: P 341 ILE cc_start: 0.7896 (mp) cc_final: 0.7692 (tt) REVERT: P 578 ASP cc_start: 0.6482 (m-30) cc_final: 0.5538 (t0) REVERT: Q 557 LEU cc_start: 0.7044 (mt) cc_final: 0.6762 (mt) REVERT: Q 592 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8482 (mm) REVERT: Q 611 GLN cc_start: 0.6135 (OUTLIER) cc_final: 0.5911 (pm20) REVERT: R 186 MET cc_start: 0.6685 (mtm) cc_final: 0.6466 (mtm) REVERT: V 12 GLU cc_start: 0.5209 (OUTLIER) cc_final: 0.4875 (mt-10) REVERT: V 121 ASP cc_start: 0.7572 (m-30) cc_final: 0.6891 (t0) REVERT: W 396 MET cc_start: 0.7004 (mmp) cc_final: 0.6790 (mtm) REVERT: W 515 MET cc_start: 0.4225 (pmm) cc_final: 0.3938 (mmm) REVERT: W 607 MET cc_start: 0.6946 (ttm) cc_final: 0.6431 (ttp) REVERT: W 763 GLU cc_start: 0.4673 (pp20) cc_final: 0.4159 (mm-30) REVERT: X 66 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.4718 (m-80) REVERT: X 103 MET cc_start: 0.7305 (ttm) cc_final: 0.6922 (ttm) REVERT: X 330 PHE cc_start: 0.6878 (t80) cc_final: 0.6524 (t80) REVERT: X 424 MET cc_start: 0.4225 (tpp) cc_final: 0.3937 (tpt) REVERT: X 937 GLN cc_start: 0.0826 (pm20) cc_final: 0.0348 (mt0) REVERT: U 1 MET cc_start: -0.0043 (tpp) cc_final: -0.1216 (mmt) outliers start: 110 outliers final: 63 residues processed: 685 average time/residue: 0.5274 time to fit residues: 629.7205 Evaluate side-chains 588 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 519 time to evaluate : 5.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 58 ASP Chi-restraints excluded: chain 0 residue 214 VAL Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 295 THR Chi-restraints excluded: chain 3 residue 49 MET Chi-restraints excluded: chain 3 residue 76 THR Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain N residue 261 ASP Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 322 ASP Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 678 PHE Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain O residue 744 ASP Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 575 SER Chi-restraints excluded: chain P residue 590 VAL Chi-restraints excluded: chain P residue 599 LEU Chi-restraints excluded: chain P residue 739 VAL Chi-restraints excluded: chain P residue 816 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 263 LYS Chi-restraints excluded: chain Q residue 485 GLU Chi-restraints excluded: chain Q residue 487 ILE Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 604 LEU Chi-restraints excluded: chain Q residue 609 VAL Chi-restraints excluded: chain Q residue 611 GLN Chi-restraints excluded: chain Q residue 625 VAL Chi-restraints excluded: chain Q residue 637 TYR Chi-restraints excluded: chain R residue 30 HIS Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 147 LYS Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain V residue 12 GLU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 618 HIS Chi-restraints excluded: chain W residue 830 LEU Chi-restraints excluded: chain W residue 1074 ARG Chi-restraints excluded: chain W residue 1129 VAL Chi-restraints excluded: chain W residue 1314 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 20 ASP Chi-restraints excluded: chain X residue 66 TYR Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 174 ASN Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 798 TRP Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 97 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 378 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 566 optimal weight: 4.9990 chunk 463 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 682 optimal weight: 4.9990 chunk 737 optimal weight: 0.3980 chunk 607 optimal weight: 1.9990 chunk 676 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 547 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 130 GLN 3 29 ASN 3 154 GLN ** 4 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 201 HIS N 270 GLN ** N 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 713 GLN N 832 HIS N 846 ASN P 751 GLN Q 219 HIS Q 394 HIS ** Q 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 293 HIS W 552 HIS ** W 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 737 HIS ** X 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 61133 Z= 0.186 Angle : 0.614 12.034 82795 Z= 0.315 Chirality : 0.042 0.234 9521 Planarity : 0.005 0.088 10565 Dihedral : 4.805 71.873 8123 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 2.01 % Allowed : 12.73 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.10), residues: 7453 helix: 1.49 (0.08), residues: 4106 sheet: 0.31 (0.19), residues: 726 loop : -1.86 (0.11), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP X 798 HIS 0.016 0.001 HIS W 552 PHE 0.054 0.001 PHE W 379 TYR 0.019 0.001 TYR W 924 ARG 0.007 0.000 ARG 4 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 579 time to evaluate : 5.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 37 ASP cc_start: 0.6728 (t0) cc_final: 0.6440 (t0) REVERT: 0 64 ASN cc_start: 0.6584 (m-40) cc_final: 0.6342 (m-40) REVERT: 2 62 MET cc_start: 0.6635 (ttp) cc_final: 0.6229 (tpp) REVERT: 3 80 ASP cc_start: 0.6246 (t0) cc_final: 0.6010 (t0) REVERT: 3 137 GLU cc_start: 0.5454 (mm-30) cc_final: 0.4956 (pm20) REVERT: 3 157 LYS cc_start: 0.8134 (tppt) cc_final: 0.7732 (tptt) REVERT: 3 160 MET cc_start: 0.7501 (ttp) cc_final: 0.7255 (ttt) REVERT: 4 113 MET cc_start: 0.0453 (mtp) cc_final: -0.0348 (ttt) REVERT: A 503 SER cc_start: -0.0194 (OUTLIER) cc_final: -0.0597 (t) REVERT: D 73 ASP cc_start: 0.1607 (OUTLIER) cc_final: 0.1403 (m-30) REVERT: D 98 LYS cc_start: 0.5645 (mmmt) cc_final: 0.5215 (ttmm) REVERT: G 64 ILE cc_start: -0.0097 (mp) cc_final: -0.0688 (mp) REVERT: G 139 MET cc_start: 0.2937 (mtp) cc_final: 0.0445 (tpt) REVERT: G 151 GLU cc_start: 0.3917 (pp20) cc_final: 0.3523 (tp30) REVERT: H 42 TRP cc_start: 0.5689 (t-100) cc_final: 0.5415 (t60) REVERT: H 87 GLU cc_start: 0.3429 (tt0) cc_final: 0.2126 (mm-30) REVERT: I 97 MET cc_start: 0.2216 (ppp) cc_final: 0.1550 (mtm) REVERT: I 130 GLU cc_start: 0.2118 (OUTLIER) cc_final: 0.1805 (pp20) REVERT: N 261 ASP cc_start: 0.5607 (OUTLIER) cc_final: 0.5249 (p0) REVERT: N 584 MET cc_start: 0.6470 (ttm) cc_final: 0.5868 (mtp) REVERT: N 749 TYR cc_start: 0.6805 (m-80) cc_final: 0.6520 (m-80) REVERT: P 187 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8361 (mp) REVERT: P 578 ASP cc_start: 0.6522 (m-30) cc_final: 0.5248 (t0) REVERT: P 800 ARG cc_start: 0.4371 (mtm180) cc_final: 0.3923 (mtm180) REVERT: Q 109 MET cc_start: 0.2464 (tpp) cc_final: 0.1526 (tmm) REVERT: W 343 LEU cc_start: 0.7726 (tt) cc_final: 0.7324 (tt) REVERT: W 515 MET cc_start: 0.4400 (pmm) cc_final: 0.3890 (mmp) REVERT: W 607 MET cc_start: 0.6934 (ttm) cc_final: 0.6335 (ttp) REVERT: W 763 GLU cc_start: 0.5048 (pp20) cc_final: 0.4405 (mm-30) REVERT: W 782 MET cc_start: 0.5126 (ppp) cc_final: 0.3217 (tpt) REVERT: W 893 PRO cc_start: 0.1041 (Cg_exo) cc_final: 0.0838 (Cg_endo) REVERT: W 1131 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8150 (mt) REVERT: X 103 MET cc_start: 0.7308 (ttm) cc_final: 0.6957 (ttm) REVERT: X 330 PHE cc_start: 0.6790 (t80) cc_final: 0.6520 (t80) REVERT: X 424 MET cc_start: 0.4454 (tpp) cc_final: 0.4056 (tpt) REVERT: U 1 MET cc_start: 0.0301 (tpp) cc_final: -0.0816 (mmt) outliers start: 132 outliers final: 75 residues processed: 672 average time/residue: 0.5711 time to fit residues: 669.9960 Evaluate side-chains 581 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 500 time to evaluate : 5.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 58 ASP Chi-restraints excluded: chain 0 residue 214 VAL Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 295 THR Chi-restraints excluded: chain 3 residue 49 MET Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain N residue 261 ASP Chi-restraints excluded: chain N residue 322 ASP Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 678 PHE Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain O residue 744 ASP Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 171 PHE Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 452 LEU Chi-restraints excluded: chain P residue 548 HIS Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 590 VAL Chi-restraints excluded: chain P residue 599 LEU Chi-restraints excluded: chain P residue 814 THR Chi-restraints excluded: chain P residue 816 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 219 HIS Chi-restraints excluded: chain Q residue 263 LYS Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Q residue 394 HIS Chi-restraints excluded: chain Q residue 485 GLU Chi-restraints excluded: chain Q residue 604 LEU Chi-restraints excluded: chain Q residue 609 VAL Chi-restraints excluded: chain Q residue 625 VAL Chi-restraints excluded: chain Q residue 637 TYR Chi-restraints excluded: chain R residue 30 HIS Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain V residue 19 ASN Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 618 HIS Chi-restraints excluded: chain W residue 830 LEU Chi-restraints excluded: chain W residue 1074 ARG Chi-restraints excluded: chain W residue 1129 VAL Chi-restraints excluded: chain W residue 1131 LEU Chi-restraints excluded: chain W residue 1281 VAL Chi-restraints excluded: chain W residue 1314 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 20 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 174 ASN Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 714 ILE Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 798 TRP Chi-restraints excluded: chain X residue 949 PHE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 97 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 674 optimal weight: 5.9990 chunk 512 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 325 optimal weight: 0.6980 chunk 458 optimal weight: 7.9990 chunk 684 optimal weight: 6.9990 chunk 724 optimal weight: 0.8980 chunk 357 optimal weight: 1.9990 chunk 648 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 120 HIS 2 92 GLN 3 29 ASN ** 4 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN N 275 HIS ** N 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 832 HIS N 846 ASN N 856 GLN ** N1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 705 HIS P 29 HIS P 519 GLN Q 411 GLN ** Q 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 626 GLN R 54 HIS ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 HIS ** V 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 GLN W 616 GLN W 914 GLN W1147 ASN ** X 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 737 HIS S 86 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 61133 Z= 0.356 Angle : 0.749 11.641 82795 Z= 0.386 Chirality : 0.047 0.216 9521 Planarity : 0.006 0.092 10565 Dihedral : 5.208 67.554 8119 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 2.98 % Allowed : 15.52 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.10), residues: 7453 helix: 1.14 (0.08), residues: 4101 sheet: 0.13 (0.19), residues: 727 loop : -2.09 (0.11), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP X 798 HIS 0.049 0.002 HIS Q 394 PHE 0.037 0.003 PHE W 379 TYR 0.026 0.002 TYR W 995 ARG 0.011 0.001 ARG V 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 538 time to evaluate : 5.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7216 (t0) REVERT: 0 46 GLU cc_start: 0.6504 (mm-30) cc_final: 0.6099 (mm-30) REVERT: 0 64 ASN cc_start: 0.6972 (m-40) cc_final: 0.6716 (m-40) REVERT: 0 274 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7288 (mt) REVERT: 1 131 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6569 (tptm) REVERT: 3 80 ASP cc_start: 0.6595 (t0) cc_final: 0.6317 (t0) REVERT: 3 137 GLU cc_start: 0.5884 (mm-30) cc_final: 0.5037 (pm20) REVERT: 3 157 LYS cc_start: 0.8166 (tppt) cc_final: 0.7782 (tptt) REVERT: 4 106 GLN cc_start: 0.1796 (OUTLIER) cc_final: 0.0652 (pt0) REVERT: A 181 GLU cc_start: 0.4865 (OUTLIER) cc_final: 0.3455 (mm-30) REVERT: D 98 LYS cc_start: 0.5378 (mmmt) cc_final: 0.5177 (mmmt) REVERT: D 182 MET cc_start: 0.3085 (ptp) cc_final: 0.2781 (ptp) REVERT: G 139 MET cc_start: 0.2711 (mtp) cc_final: 0.0413 (tpt) REVERT: G 151 GLU cc_start: 0.3999 (pp20) cc_final: 0.3444 (tp30) REVERT: H 87 GLU cc_start: 0.2837 (tt0) cc_final: 0.1768 (mm-30) REVERT: I 97 MET cc_start: 0.2678 (ppp) cc_final: 0.1594 (mmm) REVERT: I 104 MET cc_start: -0.1495 (ppp) cc_final: -0.1997 (ppp) REVERT: I 130 GLU cc_start: 0.2497 (OUTLIER) cc_final: 0.1938 (pp20) REVERT: N 230 PHE cc_start: 0.5458 (p90) cc_final: 0.5160 (p90) REVERT: N 584 MET cc_start: 0.6647 (ttm) cc_final: 0.6015 (mtp) REVERT: N 678 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7484 (m-10) REVERT: O 622 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7541 (mm) REVERT: P 131 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8741 (mt) REVERT: P 187 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8409 (mp) REVERT: P 431 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8379 (mt) REVERT: P 461 MET cc_start: 0.6873 (mtp) cc_final: 0.6402 (mtt) REVERT: P 578 ASP cc_start: 0.6510 (m-30) cc_final: 0.5308 (t0) REVERT: Q 350 ASN cc_start: 0.7607 (t0) cc_final: 0.7250 (t0) REVERT: R 46 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6837 (ptp) REVERT: T 47 HIS cc_start: 0.3986 (OUTLIER) cc_final: 0.3622 (p90) REVERT: T 61 LYS cc_start: 0.3453 (OUTLIER) cc_final: 0.3053 (ptpp) REVERT: V 70 ARG cc_start: 0.4485 (mtp85) cc_final: 0.4086 (mmp80) REVERT: W 343 LEU cc_start: 0.7848 (tt) cc_final: 0.7450 (tt) REVERT: W 380 ILE cc_start: 0.7495 (mt) cc_final: 0.7276 (mt) REVERT: W 515 MET cc_start: 0.4858 (pmm) cc_final: 0.4113 (mmp) REVERT: W 607 MET cc_start: 0.7066 (ttm) cc_final: 0.6639 (ttp) REVERT: W 623 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7302 (tt) REVERT: W 763 GLU cc_start: 0.5030 (pp20) cc_final: 0.4513 (mp0) REVERT: W 796 MET cc_start: 0.5794 (mmp) cc_final: 0.5591 (mmp) REVERT: X 103 MET cc_start: 0.7340 (ttm) cc_final: 0.7052 (ttm) REVERT: X 256 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8260 (tp) REVERT: U 1 MET cc_start: 0.0377 (tpp) cc_final: -0.0799 (mmt) outliers start: 196 outliers final: 106 residues processed: 693 average time/residue: 0.5378 time to fit residues: 652.1834 Evaluate side-chains 607 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 485 time to evaluate : 5.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 37 ASP Chi-restraints excluded: chain 0 residue 58 ASP Chi-restraints excluded: chain 0 residue 204 MET Chi-restraints excluded: chain 0 residue 214 VAL Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 295 THR Chi-restraints excluded: chain 1 residue 45 VAL Chi-restraints excluded: chain 1 residue 73 ILE Chi-restraints excluded: chain 1 residue 131 LYS Chi-restraints excluded: chain 2 residue 92 GLN Chi-restraints excluded: chain 3 residue 49 MET Chi-restraints excluded: chain 3 residue 76 THR Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 4 residue 106 GLN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain N residue 439 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 500 LEU Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 678 PHE Chi-restraints excluded: chain N residue 780 VAL Chi-restraints excluded: chain N residue 1183 ASN Chi-restraints excluded: chain N residue 1282 GLU Chi-restraints excluded: chain O residue 622 LEU Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 171 PHE Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 431 LEU Chi-restraints excluded: chain P residue 515 THR Chi-restraints excluded: chain P residue 548 HIS Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 575 SER Chi-restraints excluded: chain P residue 589 ASP Chi-restraints excluded: chain P residue 590 VAL Chi-restraints excluded: chain P residue 599 LEU Chi-restraints excluded: chain P residue 739 VAL Chi-restraints excluded: chain P residue 805 THR Chi-restraints excluded: chain P residue 814 THR Chi-restraints excluded: chain Q residue 219 HIS Chi-restraints excluded: chain Q residue 263 LYS Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Q residue 427 LEU Chi-restraints excluded: chain Q residue 472 GLU Chi-restraints excluded: chain Q residue 485 GLU Chi-restraints excluded: chain Q residue 604 LEU Chi-restraints excluded: chain Q residue 609 VAL Chi-restraints excluded: chain Q residue 625 VAL Chi-restraints excluded: chain Q residue 637 TYR Chi-restraints excluded: chain R residue 30 HIS Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain T residue 47 HIS Chi-restraints excluded: chain T residue 61 LYS Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain V residue 12 GLU Chi-restraints excluded: chain V residue 19 ASN Chi-restraints excluded: chain V residue 30 MET Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 338 LEU Chi-restraints excluded: chain W residue 521 THR Chi-restraints excluded: chain W residue 618 HIS Chi-restraints excluded: chain W residue 623 LEU Chi-restraints excluded: chain W residue 820 VAL Chi-restraints excluded: chain W residue 830 LEU Chi-restraints excluded: chain W residue 860 VAL Chi-restraints excluded: chain W residue 1074 ARG Chi-restraints excluded: chain W residue 1129 VAL Chi-restraints excluded: chain W residue 1142 ILE Chi-restraints excluded: chain W residue 1281 VAL Chi-restraints excluded: chain W residue 1314 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 20 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 174 ASN Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 214 GLN Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 423 THR Chi-restraints excluded: chain X residue 442 MET Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 695 MET Chi-restraints excluded: chain X residue 710 VAL Chi-restraints excluded: chain X residue 714 ILE Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 770 SER Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 97 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 603 optimal weight: 2.9990 chunk 411 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 539 optimal weight: 0.7980 chunk 299 optimal weight: 0.9980 chunk 618 optimal weight: 0.1980 chunk 501 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 370 optimal weight: 1.9990 chunk 650 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 132 HIS 2 87 ASN 3 29 ASN ** 4 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 832 HIS N 856 GLN O 628 ASN Q 219 HIS Q 459 GLN ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 HIS ** W 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 GLN X 737 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 61133 Z= 0.181 Angle : 0.609 10.149 82795 Z= 0.312 Chirality : 0.041 0.197 9521 Planarity : 0.005 0.092 10565 Dihedral : 4.792 62.587 8119 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 2.68 % Allowed : 16.80 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.10), residues: 7453 helix: 1.50 (0.08), residues: 4089 sheet: 0.32 (0.19), residues: 726 loop : -1.99 (0.11), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP X 798 HIS 0.007 0.001 HIS V 62 PHE 0.026 0.001 PHE W 379 TYR 0.018 0.001 TYR W 995 ARG 0.006 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 536 time to evaluate : 5.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 ASP cc_start: 0.7457 (t0) cc_final: 0.7121 (t0) REVERT: 0 60 LEU cc_start: 0.8148 (mp) cc_final: 0.7773 (mp) REVERT: 0 64 ASN cc_start: 0.6853 (m-40) cc_final: 0.6491 (m-40) REVERT: 0 71 GLU cc_start: 0.7849 (mm-30) cc_final: 0.6596 (mt-10) REVERT: 0 274 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7280 (mm) REVERT: 1 131 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6648 (tptm) REVERT: 3 80 ASP cc_start: 0.6254 (t0) cc_final: 0.5920 (t0) REVERT: 3 137 GLU cc_start: 0.5874 (mm-30) cc_final: 0.5084 (pm20) REVERT: 3 141 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5565 (tt0) REVERT: 3 170 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7593 (mt) REVERT: 4 106 GLN cc_start: 0.1507 (OUTLIER) cc_final: 0.0326 (pt0) REVERT: A 181 GLU cc_start: 0.4709 (OUTLIER) cc_final: 0.2723 (mm-30) REVERT: D 182 MET cc_start: 0.3332 (ptp) cc_final: 0.3121 (ptp) REVERT: F 146 TRP cc_start: 0.3407 (p90) cc_final: 0.3051 (p90) REVERT: G 137 VAL cc_start: 0.3133 (OUTLIER) cc_final: 0.2928 (t) REVERT: G 138 MET cc_start: 0.2266 (ppp) cc_final: 0.0801 (mmt) REVERT: G 139 MET cc_start: 0.2384 (mtp) cc_final: 0.0448 (tpt) REVERT: G 151 GLU cc_start: 0.4002 (pp20) cc_final: 0.3465 (tp30) REVERT: G 158 GLU cc_start: 0.5103 (tm-30) cc_final: 0.4901 (tm-30) REVERT: H 87 GLU cc_start: 0.4230 (tt0) cc_final: 0.2564 (mm-30) REVERT: I 97 MET cc_start: 0.2541 (ppp) cc_final: 0.1560 (mmm) REVERT: I 130 GLU cc_start: 0.1980 (OUTLIER) cc_final: 0.1530 (pp20) REVERT: J 69 GLU cc_start: 0.4803 (OUTLIER) cc_final: 0.4546 (mp0) REVERT: K 57 GLN cc_start: 0.2216 (OUTLIER) cc_final: 0.1926 (pt0) REVERT: K 71 THR cc_start: 0.5972 (p) cc_final: 0.5580 (t) REVERT: N 230 PHE cc_start: 0.5551 (p90) cc_final: 0.5302 (p90) REVERT: N 261 ASP cc_start: 0.4842 (p0) cc_final: 0.4487 (p0) REVERT: N 416 LEU cc_start: 0.8090 (tp) cc_final: 0.7886 (tp) REVERT: N 465 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7604 (mt) REVERT: N 584 MET cc_start: 0.6587 (ttm) cc_final: 0.5858 (mtp) REVERT: N 652 MET cc_start: 0.7085 (tpp) cc_final: 0.6399 (mmm) REVERT: O 622 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7665 (mm) REVERT: O 700 ASN cc_start: 0.4208 (p0) cc_final: 0.3530 (m110) REVERT: P 49 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6871 (ttm) REVERT: P 131 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8630 (mt) REVERT: P 187 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8327 (mp) REVERT: P 460 SER cc_start: 0.7076 (p) cc_final: 0.6824 (t) REVERT: P 578 ASP cc_start: 0.6466 (m-30) cc_final: 0.5265 (t0) REVERT: Q 350 ASN cc_start: 0.7523 (t0) cc_final: 0.7198 (t0) REVERT: Q 378 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8723 (mm) REVERT: Q 592 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8692 (mm) REVERT: R 46 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6853 (ptp) REVERT: T 61 LYS cc_start: 0.3600 (OUTLIER) cc_final: 0.3245 (ptpp) REVERT: V 70 ARG cc_start: 0.4750 (mtp85) cc_final: 0.4426 (mmm160) REVERT: V 87 ILE cc_start: 0.6323 (OUTLIER) cc_final: 0.5777 (pt) REVERT: W 339 ILE cc_start: 0.8623 (mm) cc_final: 0.8114 (mm) REVERT: W 396 MET cc_start: 0.6982 (mmp) cc_final: 0.6734 (mtm) REVERT: W 515 MET cc_start: 0.4426 (pmm) cc_final: 0.4026 (mmp) REVERT: W 607 MET cc_start: 0.6947 (ttm) cc_final: 0.6442 (ttp) REVERT: W 623 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7311 (tt) REVERT: W 782 MET cc_start: 0.4755 (ppp) cc_final: 0.3134 (tpp) REVERT: W 976 GLU cc_start: 0.6030 (mm-30) cc_final: 0.5802 (mm-30) REVERT: W 1189 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6964 (ttt-90) REVERT: X 47 LEU cc_start: 0.8148 (mt) cc_final: 0.7845 (mt) REVERT: X 103 MET cc_start: 0.7261 (ttm) cc_final: 0.6961 (ttm) REVERT: X 468 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7172 (t80) REVERT: X 557 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7296 (mm) REVERT: U 1 MET cc_start: 0.0036 (tpp) cc_final: -0.0989 (mmt) outliers start: 176 outliers final: 96 residues processed: 676 average time/residue: 0.5262 time to fit residues: 621.9449 Evaluate side-chains 607 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 487 time to evaluate : 5.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 58 ASP Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 204 MET Chi-restraints excluded: chain 0 residue 214 VAL Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 295 THR Chi-restraints excluded: chain 0 residue 301 THR Chi-restraints excluded: chain 1 residue 131 LYS Chi-restraints excluded: chain 2 residue 87 ASN Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 3 residue 49 MET Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 141 GLU Chi-restraints excluded: chain 3 residue 170 ILE Chi-restraints excluded: chain 4 residue 106 GLN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain N residue 201 HIS Chi-restraints excluded: chain N residue 322 ASP Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 780 VAL Chi-restraints excluded: chain N residue 833 ILE Chi-restraints excluded: chain O residue 622 LEU Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 171 PHE Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 452 LEU Chi-restraints excluded: chain P residue 515 THR Chi-restraints excluded: chain P residue 548 HIS Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 599 LEU Chi-restraints excluded: chain P residue 814 THR Chi-restraints excluded: chain Q residue 263 LYS Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain Q residue 405 MET Chi-restraints excluded: chain Q residue 427 LEU Chi-restraints excluded: chain Q residue 459 GLN Chi-restraints excluded: chain Q residue 472 GLU Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 604 LEU Chi-restraints excluded: chain Q residue 609 VAL Chi-restraints excluded: chain Q residue 625 VAL Chi-restraints excluded: chain Q residue 637 TYR Chi-restraints excluded: chain R residue 30 HIS Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain T residue 61 LYS Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain V residue 12 GLU Chi-restraints excluded: chain V residue 19 ASN Chi-restraints excluded: chain V residue 30 MET Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 618 HIS Chi-restraints excluded: chain W residue 623 LEU Chi-restraints excluded: chain W residue 798 LEU Chi-restraints excluded: chain W residue 820 VAL Chi-restraints excluded: chain W residue 830 LEU Chi-restraints excluded: chain W residue 854 VAL Chi-restraints excluded: chain W residue 1074 ARG Chi-restraints excluded: chain W residue 1113 MET Chi-restraints excluded: chain W residue 1129 VAL Chi-restraints excluded: chain W residue 1189 ARG Chi-restraints excluded: chain W residue 1200 TYR Chi-restraints excluded: chain W residue 1314 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 20 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 174 ASN Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 214 GLN Chi-restraints excluded: chain X residue 239 THR Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 458 THR Chi-restraints excluded: chain X residue 468 PHE Chi-restraints excluded: chain X residue 557 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 714 ILE Chi-restraints excluded: chain X residue 770 SER Chi-restraints excluded: chain X residue 908 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 97 ASN Chi-restraints excluded: chain U residue 130 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 243 optimal weight: 6.9990 chunk 652 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 chunk 425 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 725 optimal weight: 0.8980 chunk 602 optimal weight: 0.8980 chunk 335 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 240 optimal weight: 0.0050 chunk 380 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 29 ASN 4 107 HIS ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 832 HIS N 841 ASN N 846 ASN Q 219 HIS ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 HIS T 67 HIS ** V 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 89 ASN V 103 GLN ** W 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 737 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 61133 Z= 0.171 Angle : 0.590 9.965 82795 Z= 0.301 Chirality : 0.041 0.184 9521 Planarity : 0.005 0.097 10565 Dihedral : 4.577 61.523 8113 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.09 % Favored : 94.90 % Rotamer: Outliers : 2.71 % Allowed : 17.61 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 7453 helix: 1.63 (0.08), residues: 4093 sheet: 0.38 (0.19), residues: 724 loop : -1.92 (0.11), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP X 798 HIS 0.015 0.001 HIS V 62 PHE 0.044 0.001 PHE G 89 TYR 0.014 0.001 TYR T 184 ARG 0.005 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 528 time to evaluate : 5.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 60 LEU cc_start: 0.8156 (mp) cc_final: 0.7800 (mp) REVERT: 0 64 ASN cc_start: 0.6833 (m-40) cc_final: 0.6456 (m-40) REVERT: 0 71 GLU cc_start: 0.7841 (mm-30) cc_final: 0.6655 (mt-10) REVERT: 0 274 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7340 (mt) REVERT: 1 131 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6681 (tptm) REVERT: 2 108 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: 3 80 ASP cc_start: 0.6274 (t0) cc_final: 0.5951 (t0) REVERT: 3 137 GLU cc_start: 0.5405 (mm-30) cc_final: 0.4720 (pm20) REVERT: 4 106 GLN cc_start: 0.2379 (OUTLIER) cc_final: 0.1184 (pt0) REVERT: 4 113 MET cc_start: 0.2726 (ptp) cc_final: 0.1860 (mmt) REVERT: A 181 GLU cc_start: 0.4625 (OUTLIER) cc_final: 0.2770 (mm-30) REVERT: F 23 ILE cc_start: -0.1333 (OUTLIER) cc_final: -0.1626 (mm) REVERT: F 146 TRP cc_start: 0.3688 (p90) cc_final: 0.3302 (p90) REVERT: G 136 ARG cc_start: 0.2563 (ptt180) cc_final: 0.0012 (ttp-170) REVERT: G 138 MET cc_start: 0.2204 (ppp) cc_final: 0.0870 (mmt) REVERT: G 139 MET cc_start: 0.2401 (mtp) cc_final: 0.0740 (tpt) REVERT: G 151 GLU cc_start: 0.4018 (pp20) cc_final: 0.3462 (tp30) REVERT: H 87 GLU cc_start: 0.3396 (tt0) cc_final: 0.3069 (mm-30) REVERT: I 130 GLU cc_start: 0.2612 (OUTLIER) cc_final: 0.1932 (pp20) REVERT: J 69 GLU cc_start: 0.4860 (OUTLIER) cc_final: 0.4611 (mp0) REVERT: K 57 GLN cc_start: 0.2196 (OUTLIER) cc_final: 0.1954 (pt0) REVERT: K 71 THR cc_start: 0.6188 (p) cc_final: 0.5721 (t) REVERT: N 117 MET cc_start: 0.1420 (pmm) cc_final: 0.0624 (ttp) REVERT: N 261 ASP cc_start: 0.4790 (p0) cc_final: 0.4451 (p0) REVERT: N 465 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7689 (mt) REVERT: N 584 MET cc_start: 0.6327 (ttm) cc_final: 0.5899 (mtp) REVERT: N 652 MET cc_start: 0.7116 (tpp) cc_final: 0.6874 (mmt) REVERT: O 700 ASN cc_start: 0.4214 (p0) cc_final: 0.3545 (m110) REVERT: P 49 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6867 (ttm) REVERT: P 131 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8532 (mt) REVERT: P 187 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8287 (mp) REVERT: P 434 MET cc_start: 0.8126 (ptp) cc_final: 0.7810 (ptp) REVERT: P 460 SER cc_start: 0.7101 (p) cc_final: 0.6888 (t) REVERT: P 578 ASP cc_start: 0.6462 (m-30) cc_final: 0.5310 (t0) REVERT: Q 350 ASN cc_start: 0.7523 (t0) cc_final: 0.7156 (t0) REVERT: Q 378 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8726 (mm) REVERT: R 19 MET cc_start: 0.6568 (ptm) cc_final: 0.5669 (ttm) REVERT: R 46 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6861 (ptp) REVERT: R 93 MET cc_start: 0.4569 (mpp) cc_final: 0.3788 (mpp) REVERT: V 70 ARG cc_start: 0.4525 (mtp85) cc_final: 0.4084 (mmm160) REVERT: V 87 ILE cc_start: 0.6381 (OUTLIER) cc_final: 0.5821 (pt) REVERT: W 396 MET cc_start: 0.6950 (mmp) cc_final: 0.6721 (mtm) REVERT: W 515 MET cc_start: 0.4497 (pmm) cc_final: 0.4165 (mmp) REVERT: W 607 MET cc_start: 0.6893 (ttm) cc_final: 0.6374 (ttp) REVERT: W 903 PHE cc_start: 0.5934 (t80) cc_final: 0.5574 (t80) REVERT: W 976 GLU cc_start: 0.5983 (mm-30) cc_final: 0.5716 (mm-30) REVERT: W 1189 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6899 (ttt-90) REVERT: X 47 LEU cc_start: 0.8161 (mt) cc_final: 0.7864 (mt) REVERT: X 103 MET cc_start: 0.7225 (ttm) cc_final: 0.7023 (ttm) REVERT: X 221 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5456 (tp) REVERT: X 468 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7167 (t80) REVERT: X 557 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7228 (mm) outliers start: 178 outliers final: 106 residues processed: 667 average time/residue: 0.5295 time to fit residues: 618.2997 Evaluate side-chains 619 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 493 time to evaluate : 5.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 58 ASP Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 204 MET Chi-restraints excluded: chain 0 residue 214 VAL Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 295 THR Chi-restraints excluded: chain 0 residue 301 THR Chi-restraints excluded: chain 1 residue 131 LYS Chi-restraints excluded: chain 2 residue 92 GLN Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 108 GLU Chi-restraints excluded: chain 3 residue 49 MET Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 167 ILE Chi-restraints excluded: chain 4 residue 106 GLN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain N residue 201 HIS Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 780 VAL Chi-restraints excluded: chain N residue 815 THR Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 171 PHE Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 346 ASN Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 452 LEU Chi-restraints excluded: chain P residue 515 THR Chi-restraints excluded: chain P residue 548 HIS Chi-restraints excluded: chain P residue 599 LEU Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 814 THR Chi-restraints excluded: chain P residue 827 CYS Chi-restraints excluded: chain Q residue 140 ASN Chi-restraints excluded: chain Q residue 219 HIS Chi-restraints excluded: chain Q residue 263 LYS Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain Q residue 405 MET Chi-restraints excluded: chain Q residue 427 LEU Chi-restraints excluded: chain Q residue 472 GLU Chi-restraints excluded: chain Q residue 604 LEU Chi-restraints excluded: chain Q residue 609 VAL Chi-restraints excluded: chain Q residue 625 VAL Chi-restraints excluded: chain Q residue 637 TYR Chi-restraints excluded: chain R residue 30 HIS Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain V residue 12 GLU Chi-restraints excluded: chain V residue 19 ASN Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 618 HIS Chi-restraints excluded: chain W residue 707 ILE Chi-restraints excluded: chain W residue 798 LEU Chi-restraints excluded: chain W residue 820 VAL Chi-restraints excluded: chain W residue 830 LEU Chi-restraints excluded: chain W residue 844 ASN Chi-restraints excluded: chain W residue 1065 ASP Chi-restraints excluded: chain W residue 1074 ARG Chi-restraints excluded: chain W residue 1113 MET Chi-restraints excluded: chain W residue 1129 VAL Chi-restraints excluded: chain W residue 1189 ARG Chi-restraints excluded: chain W residue 1314 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 20 ASP Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 174 ASN Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 239 THR Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 458 THR Chi-restraints excluded: chain X residue 468 PHE Chi-restraints excluded: chain X residue 488 VAL Chi-restraints excluded: chain X residue 557 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 695 MET Chi-restraints excluded: chain X residue 714 ILE Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 770 SER Chi-restraints excluded: chain X residue 908 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 699 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 413 optimal weight: 4.9990 chunk 529 optimal weight: 0.9990 chunk 410 optimal weight: 0.5980 chunk 610 optimal weight: 3.9990 chunk 405 optimal weight: 0.3980 chunk 722 optimal weight: 0.9990 chunk 452 optimal weight: 0.7980 chunk 440 optimal weight: 0.9990 chunk 333 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 29 ASN ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 832 HIS ** O 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 HIS ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 HIS ** W 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 GLN X 737 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 61133 Z= 0.177 Angle : 0.591 10.338 82795 Z= 0.301 Chirality : 0.041 0.211 9521 Planarity : 0.005 0.099 10565 Dihedral : 4.491 61.005 8111 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.83 % Favored : 95.16 % Rotamer: Outliers : 2.62 % Allowed : 17.96 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.10), residues: 7453 helix: 1.71 (0.08), residues: 4092 sheet: 0.45 (0.19), residues: 713 loop : -1.91 (0.11), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP X 798 HIS 0.022 0.001 HIS Q 219 PHE 0.031 0.001 PHE G 89 TYR 0.016 0.001 TYR W 764 ARG 0.006 0.000 ARG W 864 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 532 time to evaluate : 5.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 60 LEU cc_start: 0.8158 (mp) cc_final: 0.7728 (mp) REVERT: 0 274 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7396 (mt) REVERT: 1 131 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6729 (tptm) REVERT: 2 108 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: 3 80 ASP cc_start: 0.6283 (t0) cc_final: 0.5958 (t0) REVERT: 3 137 GLU cc_start: 0.5102 (mm-30) cc_final: 0.4693 (pm20) REVERT: 4 106 GLN cc_start: 0.1899 (OUTLIER) cc_final: 0.0652 (pt0) REVERT: 4 113 MET cc_start: 0.2591 (ptp) cc_final: 0.1785 (mmt) REVERT: A 77 MET cc_start: 0.3150 (ptp) cc_final: 0.1525 (mmt) REVERT: A 181 GLU cc_start: 0.4593 (OUTLIER) cc_final: 0.3101 (mm-30) REVERT: A 220 MET cc_start: 0.3688 (ttt) cc_final: 0.3269 (pmm) REVERT: D 190 MET cc_start: 0.2750 (OUTLIER) cc_final: 0.2106 (pmm) REVERT: F 23 ILE cc_start: -0.1340 (OUTLIER) cc_final: -0.1630 (mm) REVERT: F 134 MET cc_start: 0.3368 (tmm) cc_final: 0.2879 (tmm) REVERT: F 146 TRP cc_start: 0.3670 (p90) cc_final: 0.3274 (p90) REVERT: G 15 MET cc_start: 0.2586 (ppp) cc_final: 0.1188 (ppp) REVERT: G 83 MET cc_start: 0.0250 (tmm) cc_final: -0.0313 (mtt) REVERT: G 114 LEU cc_start: 0.1304 (tt) cc_final: 0.0953 (mt) REVERT: G 136 ARG cc_start: 0.2603 (ptt180) cc_final: 0.0127 (ttp-170) REVERT: G 138 MET cc_start: 0.2266 (ppp) cc_final: 0.0997 (mmt) REVERT: G 139 MET cc_start: 0.2443 (mtp) cc_final: 0.0719 (tpt) REVERT: H 87 GLU cc_start: 0.3694 (tt0) cc_final: 0.3459 (mm-30) REVERT: I 130 GLU cc_start: 0.2721 (OUTLIER) cc_final: 0.2375 (mm-30) REVERT: J 69 GLU cc_start: 0.4909 (OUTLIER) cc_final: 0.4655 (mp0) REVERT: K 71 THR cc_start: 0.6159 (p) cc_final: 0.5753 (t) REVERT: N 261 ASP cc_start: 0.4782 (p0) cc_final: 0.4487 (p0) REVERT: N 465 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7670 (mt) REVERT: N 584 MET cc_start: 0.6417 (ttm) cc_final: 0.5983 (mtp) REVERT: N 652 MET cc_start: 0.7119 (tpp) cc_final: 0.6878 (mmt) REVERT: O 622 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7614 (mm) REVERT: O 700 ASN cc_start: 0.3846 (p0) cc_final: 0.3244 (m110) REVERT: P 49 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6895 (ttm) REVERT: P 131 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8532 (mt) REVERT: P 187 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8277 (mp) REVERT: P 460 SER cc_start: 0.7168 (p) cc_final: 0.6960 (t) REVERT: P 578 ASP cc_start: 0.6506 (m-30) cc_final: 0.5324 (t0) REVERT: Q 36 MET cc_start: 0.2948 (tpp) cc_final: -0.0953 (mtm) REVERT: Q 350 ASN cc_start: 0.7559 (t0) cc_final: 0.7161 (t0) REVERT: Q 378 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8660 (mm) REVERT: Q 592 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8715 (mm) REVERT: R 19 MET cc_start: 0.6585 (ptm) cc_final: 0.5691 (ttm) REVERT: R 46 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6870 (ptp) REVERT: R 93 MET cc_start: 0.4569 (mpp) cc_final: 0.3777 (mpp) REVERT: V 38 LYS cc_start: 0.5997 (mmtt) cc_final: 0.5659 (mmmt) REVERT: V 87 ILE cc_start: 0.6438 (OUTLIER) cc_final: 0.5840 (pt) REVERT: W 396 MET cc_start: 0.6928 (mmp) cc_final: 0.6706 (mtm) REVERT: W 515 MET cc_start: 0.4340 (pmm) cc_final: 0.3975 (mmp) REVERT: W 607 MET cc_start: 0.6860 (ttm) cc_final: 0.6285 (ttp) REVERT: W 782 MET cc_start: 0.4077 (tmm) cc_final: 0.3401 (tpt) REVERT: W 903 PHE cc_start: 0.5939 (t80) cc_final: 0.5577 (t80) REVERT: X 103 MET cc_start: 0.7175 (ttm) cc_final: 0.6950 (ttm) REVERT: X 221 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.5395 (tp) REVERT: X 424 MET cc_start: 0.4514 (tpp) cc_final: 0.4228 (tpt) REVERT: X 468 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7178 (t80) REVERT: X 557 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.5822 (tp) REVERT: X 838 GLU cc_start: 0.5568 (tt0) cc_final: 0.5351 (tp30) REVERT: U 1 MET cc_start: 0.1813 (tpt) cc_final: 0.0999 (mmm) outliers start: 172 outliers final: 116 residues processed: 665 average time/residue: 0.5156 time to fit residues: 602.1347 Evaluate side-chains 617 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 480 time to evaluate : 5.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 58 ASP Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 204 MET Chi-restraints excluded: chain 0 residue 214 VAL Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 295 THR Chi-restraints excluded: chain 0 residue 301 THR Chi-restraints excluded: chain 1 residue 96 LEU Chi-restraints excluded: chain 1 residue 131 LYS Chi-restraints excluded: chain 2 residue 92 GLN Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 108 GLU Chi-restraints excluded: chain 3 residue 49 MET Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 4 residue 106 GLN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain N residue 201 HIS Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 780 VAL Chi-restraints excluded: chain N residue 815 THR Chi-restraints excluded: chain N residue 833 ILE Chi-restraints excluded: chain O residue 622 LEU Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 171 PHE Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 346 ASN Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 452 LEU Chi-restraints excluded: chain P residue 515 THR Chi-restraints excluded: chain P residue 548 HIS Chi-restraints excluded: chain P residue 589 ASP Chi-restraints excluded: chain P residue 599 LEU Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 814 THR Chi-restraints excluded: chain P residue 827 CYS Chi-restraints excluded: chain Q residue 140 ASN Chi-restraints excluded: chain Q residue 219 HIS Chi-restraints excluded: chain Q residue 263 LYS Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain Q residue 427 LEU Chi-restraints excluded: chain Q residue 472 GLU Chi-restraints excluded: chain Q residue 499 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 604 LEU Chi-restraints excluded: chain Q residue 625 VAL Chi-restraints excluded: chain Q residue 637 TYR Chi-restraints excluded: chain R residue 30 HIS Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 99 HIS Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain V residue 12 GLU Chi-restraints excluded: chain V residue 19 ASN Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 612 MET Chi-restraints excluded: chain W residue 618 HIS Chi-restraints excluded: chain W residue 707 ILE Chi-restraints excluded: chain W residue 798 LEU Chi-restraints excluded: chain W residue 820 VAL Chi-restraints excluded: chain W residue 830 LEU Chi-restraints excluded: chain W residue 854 VAL Chi-restraints excluded: chain W residue 1065 ASP Chi-restraints excluded: chain W residue 1074 ARG Chi-restraints excluded: chain W residue 1113 MET Chi-restraints excluded: chain W residue 1129 VAL Chi-restraints excluded: chain W residue 1281 VAL Chi-restraints excluded: chain W residue 1314 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 20 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 174 ASN Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 214 GLN Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 239 THR Chi-restraints excluded: chain X residue 342 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 436 LEU Chi-restraints excluded: chain X residue 458 THR Chi-restraints excluded: chain X residue 468 PHE Chi-restraints excluded: chain X residue 488 VAL Chi-restraints excluded: chain X residue 557 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 601 SER Chi-restraints excluded: chain X residue 695 MET Chi-restraints excluded: chain X residue 714 ILE Chi-restraints excluded: chain X residue 741 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 770 SER Chi-restraints excluded: chain X residue 798 TRP Chi-restraints excluded: chain X residue 908 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 447 optimal weight: 0.5980 chunk 288 optimal weight: 0.7980 chunk 431 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 459 optimal weight: 0.9980 chunk 492 optimal weight: 0.9990 chunk 357 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 568 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 84 GLN 3 146 ASN ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN K 57 GLN ** N 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 832 HIS ** O 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 HIS ** W 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 737 HIS U 97 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 61133 Z= 0.192 Angle : 0.601 10.684 82795 Z= 0.305 Chirality : 0.041 0.259 9521 Planarity : 0.005 0.106 10565 Dihedral : 4.513 62.278 8111 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.18 % Favored : 94.81 % Rotamer: Outliers : 2.63 % Allowed : 18.43 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.10), residues: 7453 helix: 1.68 (0.08), residues: 4106 sheet: 0.45 (0.19), residues: 723 loop : -1.95 (0.11), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP X 798 HIS 0.020 0.001 HIS Q 218 PHE 0.031 0.001 PHE G 89 TYR 0.021 0.001 TYR F 145 ARG 0.007 0.000 ARG V 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 512 time to evaluate : 5.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 207 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7662 (tp) REVERT: 0 274 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7456 (mt) REVERT: 1 131 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6664 (tptm) REVERT: 2 108 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: 3 58 MET cc_start: 0.8277 (tmm) cc_final: 0.7022 (tmm) REVERT: 3 80 ASP cc_start: 0.6294 (t0) cc_final: 0.5949 (t0) REVERT: 3 137 GLU cc_start: 0.5346 (mm-30) cc_final: 0.4924 (pm20) REVERT: 4 106 GLN cc_start: 0.1978 (OUTLIER) cc_final: 0.0738 (pt0) REVERT: 4 113 MET cc_start: 0.2649 (ptp) cc_final: 0.1807 (mmt) REVERT: A 77 MET cc_start: 0.3042 (ptp) cc_final: 0.1479 (mmt) REVERT: A 181 GLU cc_start: 0.4607 (OUTLIER) cc_final: 0.2746 (mm-30) REVERT: D 94 GLN cc_start: 0.4292 (OUTLIER) cc_final: 0.3868 (mm-40) REVERT: D 190 MET cc_start: 0.2994 (OUTLIER) cc_final: 0.2404 (pmm) REVERT: F 23 ILE cc_start: -0.1344 (OUTLIER) cc_final: -0.1618 (mm) REVERT: F 134 MET cc_start: 0.3492 (tmm) cc_final: 0.3139 (tmm) REVERT: F 146 TRP cc_start: 0.3773 (p90) cc_final: 0.3307 (p90) REVERT: G 15 MET cc_start: 0.2616 (ppp) cc_final: 0.1239 (ppp) REVERT: G 83 MET cc_start: 0.0294 (tmm) cc_final: -0.0215 (mtt) REVERT: G 114 LEU cc_start: 0.0907 (tt) cc_final: 0.0585 (mt) REVERT: G 136 ARG cc_start: 0.2647 (ptt180) cc_final: 0.0176 (ttp-170) REVERT: G 138 MET cc_start: 0.2495 (ppp) cc_final: 0.1059 (mmt) REVERT: G 139 MET cc_start: 0.2497 (mtp) cc_final: 0.0862 (tpt) REVERT: H 30 ILE cc_start: 0.1684 (OUTLIER) cc_final: 0.1372 (mp) REVERT: I 130 GLU cc_start: 0.2791 (OUTLIER) cc_final: 0.2393 (mm-30) REVERT: J 69 GLU cc_start: 0.4934 (OUTLIER) cc_final: 0.4692 (mp0) REVERT: K 71 THR cc_start: 0.6050 (p) cc_final: 0.5672 (t) REVERT: N 117 MET cc_start: 0.1480 (pmm) cc_final: 0.0855 (ttp) REVERT: N 240 ASP cc_start: 0.5565 (t0) cc_final: 0.5090 (p0) REVERT: N 261 ASP cc_start: 0.4702 (p0) cc_final: 0.4469 (p0) REVERT: N 465 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7673 (mt) REVERT: N 584 MET cc_start: 0.6476 (ttm) cc_final: 0.6030 (mtp) REVERT: N 652 MET cc_start: 0.7160 (tpp) cc_final: 0.6931 (mmt) REVERT: O 622 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7599 (mm) REVERT: O 700 ASN cc_start: 0.3932 (p0) cc_final: 0.3238 (m110) REVERT: P 49 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6889 (ttm) REVERT: P 131 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8408 (mp) REVERT: P 187 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8269 (mp) REVERT: P 460 SER cc_start: 0.7223 (p) cc_final: 0.6961 (t) REVERT: P 578 ASP cc_start: 0.6539 (m-30) cc_final: 0.5327 (t0) REVERT: Q 36 MET cc_start: 0.3050 (tpp) cc_final: -0.0768 (mtm) REVERT: Q 350 ASN cc_start: 0.7569 (t0) cc_final: 0.7165 (t0) REVERT: Q 378 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8685 (mm) REVERT: Q 592 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8749 (mm) REVERT: R 19 MET cc_start: 0.6568 (ptm) cc_final: 0.5679 (ttm) REVERT: R 46 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6948 (ptp) REVERT: R 93 MET cc_start: 0.4595 (mpp) cc_final: 0.3788 (mpp) REVERT: R 142 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6240 (mtpt) REVERT: V 38 LYS cc_start: 0.6020 (mmtt) cc_final: 0.5670 (mmmt) REVERT: V 87 ILE cc_start: 0.6535 (OUTLIER) cc_final: 0.5909 (pt) REVERT: W 339 ILE cc_start: 0.8559 (mm) cc_final: 0.8168 (mm) REVERT: W 396 MET cc_start: 0.6933 (mmp) cc_final: 0.6726 (mtm) REVERT: W 515 MET cc_start: 0.4381 (pmm) cc_final: 0.4019 (mmp) REVERT: W 607 MET cc_start: 0.6824 (ttm) cc_final: 0.6309 (ttp) REVERT: W 720 MET cc_start: 0.4736 (tmm) cc_final: 0.4277 (tmm) REVERT: W 782 MET cc_start: 0.4091 (tmm) cc_final: 0.3460 (tpt) REVERT: W 883 TYR cc_start: 0.5756 (m-10) cc_final: 0.5554 (m-10) REVERT: W 903 PHE cc_start: 0.6103 (t80) cc_final: 0.5747 (t80) REVERT: W 976 GLU cc_start: 0.5765 (mm-30) cc_final: 0.5519 (mm-30) REVERT: X 103 MET cc_start: 0.7198 (ttm) cc_final: 0.6958 (ttm) REVERT: X 221 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5454 (tp) REVERT: X 424 MET cc_start: 0.4687 (tpp) cc_final: 0.4312 (tpt) REVERT: X 468 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7195 (t80) REVERT: X 557 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.5900 (tp) REVERT: U 1 MET cc_start: 0.2006 (tpt) cc_final: 0.1109 (mmm) outliers start: 173 outliers final: 121 residues processed: 643 average time/residue: 0.5297 time to fit residues: 598.9634 Evaluate side-chains 622 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 476 time to evaluate : 6.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 58 ASP Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 204 MET Chi-restraints excluded: chain 0 residue 207 LEU Chi-restraints excluded: chain 0 residue 214 VAL Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 295 THR Chi-restraints excluded: chain 0 residue 301 THR Chi-restraints excluded: chain 1 residue 73 ILE Chi-restraints excluded: chain 1 residue 96 LEU Chi-restraints excluded: chain 1 residue 131 LYS Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 108 GLU Chi-restraints excluded: chain 3 residue 49 MET Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 167 ILE Chi-restraints excluded: chain 4 residue 106 GLN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain N residue 201 HIS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 780 VAL Chi-restraints excluded: chain N residue 815 THR Chi-restraints excluded: chain O residue 622 LEU Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 171 PHE Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 346 ASN Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 452 LEU Chi-restraints excluded: chain P residue 515 THR Chi-restraints excluded: chain P residue 548 HIS Chi-restraints excluded: chain P residue 589 ASP Chi-restraints excluded: chain P residue 599 LEU Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 739 VAL Chi-restraints excluded: chain P residue 814 THR Chi-restraints excluded: chain P residue 827 CYS Chi-restraints excluded: chain Q residue 140 ASN Chi-restraints excluded: chain Q residue 263 LYS Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain Q residue 405 MET Chi-restraints excluded: chain Q residue 427 LEU Chi-restraints excluded: chain Q residue 472 GLU Chi-restraints excluded: chain Q residue 499 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 604 LEU Chi-restraints excluded: chain Q residue 625 VAL Chi-restraints excluded: chain Q residue 637 TYR Chi-restraints excluded: chain R residue 30 HIS Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 99 HIS Chi-restraints excluded: chain R residue 142 LYS Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain V residue 12 GLU Chi-restraints excluded: chain V residue 19 ASN Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 474 ILE Chi-restraints excluded: chain W residue 612 MET Chi-restraints excluded: chain W residue 618 HIS Chi-restraints excluded: chain W residue 707 ILE Chi-restraints excluded: chain W residue 798 LEU Chi-restraints excluded: chain W residue 820 VAL Chi-restraints excluded: chain W residue 830 LEU Chi-restraints excluded: chain W residue 844 ASN Chi-restraints excluded: chain W residue 1074 ARG Chi-restraints excluded: chain W residue 1113 MET Chi-restraints excluded: chain W residue 1129 VAL Chi-restraints excluded: chain W residue 1142 ILE Chi-restraints excluded: chain W residue 1281 VAL Chi-restraints excluded: chain W residue 1314 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 20 ASP Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 174 ASN Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 239 THR Chi-restraints excluded: chain X residue 253 THR Chi-restraints excluded: chain X residue 342 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 436 LEU Chi-restraints excluded: chain X residue 442 MET Chi-restraints excluded: chain X residue 458 THR Chi-restraints excluded: chain X residue 468 PHE Chi-restraints excluded: chain X residue 488 VAL Chi-restraints excluded: chain X residue 557 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 601 SER Chi-restraints excluded: chain X residue 695 MET Chi-restraints excluded: chain X residue 714 ILE Chi-restraints excluded: chain X residue 741 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 770 SER Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 130 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 657 optimal weight: 2.9990 chunk 692 optimal weight: 0.8980 chunk 631 optimal weight: 0.8980 chunk 673 optimal weight: 0.9990 chunk 405 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 528 optimal weight: 0.3980 chunk 206 optimal weight: 0.4980 chunk 608 optimal weight: 3.9990 chunk 637 optimal weight: 3.9990 chunk 671 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 502 GLN N 846 ASN ** O 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 HIS ** V 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 642 HIS X 214 GLN X 737 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 61133 Z= 0.174 Angle : 0.597 12.703 82795 Z= 0.302 Chirality : 0.041 0.225 9521 Planarity : 0.005 0.107 10565 Dihedral : 4.456 61.269 8111 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.87 % Favored : 95.12 % Rotamer: Outliers : 2.30 % Allowed : 18.90 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 7453 helix: 1.74 (0.08), residues: 4110 sheet: 0.52 (0.20), residues: 720 loop : -1.93 (0.11), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 192 HIS 0.018 0.001 HIS V 62 PHE 0.025 0.001 PHE G 89 TYR 0.018 0.001 TYR F 145 ARG 0.007 0.000 ARG X 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 521 time to evaluate : 5.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 64 ASN cc_start: 0.6604 (m-40) cc_final: 0.6351 (m110) REVERT: 0 207 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7654 (tp) REVERT: 0 274 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7483 (mt) REVERT: 1 131 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6650 (tptm) REVERT: 2 108 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: 3 58 MET cc_start: 0.8247 (tmm) cc_final: 0.6973 (tmm) REVERT: 3 80 ASP cc_start: 0.6310 (t0) cc_final: 0.5969 (t0) REVERT: 3 137 GLU cc_start: 0.4836 (mm-30) cc_final: 0.4409 (pm20) REVERT: 4 106 GLN cc_start: 0.2376 (OUTLIER) cc_final: 0.1070 (pt0) REVERT: 4 113 MET cc_start: 0.2656 (ptp) cc_final: 0.1828 (mmt) REVERT: A 77 MET cc_start: 0.3123 (ptp) cc_final: 0.1500 (mmt) REVERT: A 181 GLU cc_start: 0.4300 (OUTLIER) cc_final: 0.2644 (mm-30) REVERT: D 94 GLN cc_start: 0.4282 (OUTLIER) cc_final: 0.3884 (mt0) REVERT: D 190 MET cc_start: 0.3006 (OUTLIER) cc_final: 0.2315 (pmm) REVERT: F 23 ILE cc_start: -0.1343 (OUTLIER) cc_final: -0.1596 (mm) REVERT: F 134 MET cc_start: 0.3532 (tmm) cc_final: 0.3108 (tmm) REVERT: F 146 TRP cc_start: 0.3514 (p90) cc_final: 0.3036 (p90) REVERT: G 15 MET cc_start: 0.2907 (ppp) cc_final: 0.1527 (ppp) REVERT: G 54 LEU cc_start: 0.3863 (tp) cc_final: 0.2918 (mt) REVERT: G 83 MET cc_start: 0.0187 (tmm) cc_final: -0.0261 (mtt) REVERT: G 114 LEU cc_start: 0.0885 (tt) cc_final: 0.0586 (mt) REVERT: G 136 ARG cc_start: 0.2161 (ptt180) cc_final: 0.0152 (ttp-170) REVERT: G 138 MET cc_start: 0.2182 (ppp) cc_final: 0.0525 (mmt) REVERT: G 139 MET cc_start: 0.2489 (mtp) cc_final: 0.0875 (tpt) REVERT: I 130 GLU cc_start: 0.2841 (OUTLIER) cc_final: 0.2419 (mm-30) REVERT: J 69 GLU cc_start: 0.4921 (OUTLIER) cc_final: 0.4684 (mp0) REVERT: K 71 THR cc_start: 0.6008 (p) cc_final: 0.5664 (t) REVERT: N 117 MET cc_start: 0.1372 (pmm) cc_final: 0.0779 (ttp) REVERT: N 240 ASP cc_start: 0.5444 (t0) cc_final: 0.5095 (p0) REVERT: N 584 MET cc_start: 0.6563 (ttm) cc_final: 0.6102 (mtp) REVERT: N 652 MET cc_start: 0.7186 (tpp) cc_final: 0.6979 (mmt) REVERT: N 749 TYR cc_start: 0.6966 (m-80) cc_final: 0.6675 (m-80) REVERT: O 622 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7532 (mm) REVERT: O 700 ASN cc_start: 0.4220 (p0) cc_final: 0.3549 (m110) REVERT: O 743 TYR cc_start: 0.6556 (m-80) cc_final: 0.6302 (m-10) REVERT: P 49 MET cc_start: 0.7067 (ttp) cc_final: 0.6854 (ttm) REVERT: P 131 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8351 (mp) REVERT: P 187 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8236 (mp) REVERT: P 460 SER cc_start: 0.7277 (p) cc_final: 0.6980 (t) REVERT: P 578 ASP cc_start: 0.6714 (m-30) cc_final: 0.5495 (t0) REVERT: Q 36 MET cc_start: 0.2911 (tpp) cc_final: -0.0875 (mtm) REVERT: Q 378 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8682 (mm) REVERT: Q 592 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8789 (mm) REVERT: R 19 MET cc_start: 0.6547 (ptm) cc_final: 0.5687 (ttm) REVERT: R 46 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7255 (ptp) REVERT: R 93 MET cc_start: 0.4603 (mpp) cc_final: 0.3778 (mpp) REVERT: V 38 LYS cc_start: 0.5970 (mmtt) cc_final: 0.5441 (mmmt) REVERT: V 87 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.5731 (pt) REVERT: W 312 MET cc_start: 0.7238 (mmm) cc_final: 0.7017 (mtp) REVERT: W 339 ILE cc_start: 0.8723 (mm) cc_final: 0.8353 (mm) REVERT: W 515 MET cc_start: 0.4443 (pmm) cc_final: 0.4102 (mmp) REVERT: W 607 MET cc_start: 0.6759 (ttm) cc_final: 0.6238 (ttp) REVERT: W 720 MET cc_start: 0.4610 (tmm) cc_final: 0.4246 (tmm) REVERT: W 782 MET cc_start: 0.4069 (tmm) cc_final: 0.3472 (tpt) REVERT: W 883 TYR cc_start: 0.5770 (m-10) cc_final: 0.5530 (m-10) REVERT: W 903 PHE cc_start: 0.6119 (t80) cc_final: 0.5701 (t80) REVERT: W 976 GLU cc_start: 0.5902 (mm-30) cc_final: 0.5646 (mm-30) REVERT: X 30 PHE cc_start: 0.7960 (t80) cc_final: 0.7716 (t80) REVERT: X 103 MET cc_start: 0.7418 (ttm) cc_final: 0.7157 (ttm) REVERT: X 164 ARG cc_start: 0.6183 (mmp80) cc_final: 0.5855 (mmp80) REVERT: X 221 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.5506 (tp) REVERT: X 254 MET cc_start: 0.6860 (ttm) cc_final: 0.6567 (tpt) REVERT: X 436 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6699 (tp) REVERT: X 468 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7219 (t80) REVERT: X 557 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.5866 (tp) REVERT: U 1 MET cc_start: 0.1754 (tpt) cc_final: 0.0735 (mmm) outliers start: 151 outliers final: 112 residues processed: 631 average time/residue: 0.5514 time to fit residues: 624.3419 Evaluate side-chains 617 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 483 time to evaluate : 5.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 58 ASP Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 204 MET Chi-restraints excluded: chain 0 residue 207 LEU Chi-restraints excluded: chain 0 residue 214 VAL Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 295 THR Chi-restraints excluded: chain 0 residue 301 THR Chi-restraints excluded: chain 1 residue 96 LEU Chi-restraints excluded: chain 1 residue 131 LYS Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 108 GLU Chi-restraints excluded: chain 3 residue 49 MET Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 4 residue 106 GLN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain N residue 201 HIS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 300 CYS Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 500 LEU Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 780 VAL Chi-restraints excluded: chain N residue 815 THR Chi-restraints excluded: chain N residue 833 ILE Chi-restraints excluded: chain N residue 847 CYS Chi-restraints excluded: chain O residue 622 LEU Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 678 LEU Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 171 PHE Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 452 LEU Chi-restraints excluded: chain P residue 515 THR Chi-restraints excluded: chain P residue 589 ASP Chi-restraints excluded: chain P residue 599 LEU Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 814 THR Chi-restraints excluded: chain P residue 827 CYS Chi-restraints excluded: chain Q residue 140 ASN Chi-restraints excluded: chain Q residue 263 LYS Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain Q residue 405 MET Chi-restraints excluded: chain Q residue 427 LEU Chi-restraints excluded: chain Q residue 472 GLU Chi-restraints excluded: chain Q residue 499 VAL Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 604 LEU Chi-restraints excluded: chain Q residue 625 VAL Chi-restraints excluded: chain Q residue 637 TYR Chi-restraints excluded: chain R residue 30 HIS Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 99 HIS Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain V residue 12 GLU Chi-restraints excluded: chain V residue 19 ASN Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 474 ILE Chi-restraints excluded: chain W residue 612 MET Chi-restraints excluded: chain W residue 618 HIS Chi-restraints excluded: chain W residue 707 ILE Chi-restraints excluded: chain W residue 798 LEU Chi-restraints excluded: chain W residue 820 VAL Chi-restraints excluded: chain W residue 830 LEU Chi-restraints excluded: chain W residue 844 ASN Chi-restraints excluded: chain W residue 1074 ARG Chi-restraints excluded: chain W residue 1113 MET Chi-restraints excluded: chain W residue 1129 VAL Chi-restraints excluded: chain W residue 1142 ILE Chi-restraints excluded: chain W residue 1314 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 20 ASP Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 214 GLN Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 239 THR Chi-restraints excluded: chain X residue 342 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 436 LEU Chi-restraints excluded: chain X residue 442 MET Chi-restraints excluded: chain X residue 458 THR Chi-restraints excluded: chain X residue 468 PHE Chi-restraints excluded: chain X residue 488 VAL Chi-restraints excluded: chain X residue 557 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 601 SER Chi-restraints excluded: chain X residue 695 MET Chi-restraints excluded: chain X residue 714 ILE Chi-restraints excluded: chain X residue 741 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 770 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 442 optimal weight: 0.2980 chunk 712 optimal weight: 0.7980 chunk 434 optimal weight: 0.9980 chunk 337 optimal weight: 2.9990 chunk 495 optimal weight: 2.9990 chunk 747 optimal weight: 2.9990 chunk 687 optimal weight: 0.9990 chunk 594 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 459 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN I 124 GLN ** N 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 HIS ** V 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 874 HIS X 214 GLN X 737 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 61133 Z= 0.211 Angle : 0.618 13.336 82795 Z= 0.313 Chirality : 0.042 0.213 9521 Planarity : 0.005 0.113 10565 Dihedral : 4.536 63.256 8111 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.30 % Favored : 94.69 % Rotamer: Outliers : 2.37 % Allowed : 18.94 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.10), residues: 7453 helix: 1.67 (0.08), residues: 4117 sheet: 0.46 (0.19), residues: 731 loop : -2.00 (0.11), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP X 592 HIS 0.020 0.001 HIS V 62 PHE 0.025 0.002 PHE G 89 TYR 0.019 0.001 TYR F 145 ARG 0.007 0.000 ARG I 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14906 Ramachandran restraints generated. 7453 Oldfield, 0 Emsley, 7453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 510 time to evaluate : 5.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 131 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6596 (tptm) REVERT: 2 108 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: 3 58 MET cc_start: 0.8409 (tmm) cc_final: 0.7072 (tmm) REVERT: 3 80 ASP cc_start: 0.6545 (t0) cc_final: 0.6203 (t0) REVERT: 3 137 GLU cc_start: 0.4923 (mm-30) cc_final: 0.4460 (pm20) REVERT: 4 106 GLN cc_start: 0.2404 (OUTLIER) cc_final: 0.1086 (pt0) REVERT: 4 113 MET cc_start: 0.2698 (ptp) cc_final: 0.1851 (mmt) REVERT: A 181 GLU cc_start: 0.4479 (OUTLIER) cc_final: 0.2776 (mm-30) REVERT: D 94 GLN cc_start: 0.4355 (OUTLIER) cc_final: 0.3930 (mm-40) REVERT: D 190 MET cc_start: 0.3280 (OUTLIER) cc_final: 0.2726 (pmm) REVERT: F 23 ILE cc_start: -0.1340 (OUTLIER) cc_final: -0.1574 (mm) REVERT: F 134 MET cc_start: 0.3459 (tmm) cc_final: 0.3118 (tmm) REVERT: F 146 TRP cc_start: 0.3502 (p90) cc_final: 0.2931 (p90) REVERT: G 15 MET cc_start: 0.2697 (ppp) cc_final: 0.1319 (ppp) REVERT: G 54 LEU cc_start: 0.3788 (tp) cc_final: 0.2874 (mt) REVERT: G 83 MET cc_start: -0.0095 (tmm) cc_final: -0.0377 (mtt) REVERT: G 114 LEU cc_start: 0.0925 (tt) cc_final: 0.0621 (mt) REVERT: G 138 MET cc_start: 0.2367 (ppp) cc_final: 0.0499 (mmt) REVERT: G 139 MET cc_start: 0.2625 (mtp) cc_final: 0.1011 (tpt) REVERT: H 30 ILE cc_start: 0.1914 (OUTLIER) cc_final: 0.1705 (mp) REVERT: I 130 GLU cc_start: 0.2814 (OUTLIER) cc_final: 0.2429 (mm-30) REVERT: J 69 GLU cc_start: 0.4887 (OUTLIER) cc_final: 0.4635 (mp0) REVERT: K 71 THR cc_start: 0.6022 (p) cc_final: 0.5821 (t) REVERT: N 240 ASP cc_start: 0.5396 (t0) cc_final: 0.5099 (p0) REVERT: N 584 MET cc_start: 0.6337 (ttm) cc_final: 0.5873 (mtp) REVERT: N 749 TYR cc_start: 0.7080 (m-80) cc_final: 0.6797 (m-80) REVERT: O 622 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7756 (mm) REVERT: O 700 ASN cc_start: 0.4291 (p0) cc_final: 0.3582 (m110) REVERT: O 743 TYR cc_start: 0.6621 (m-80) cc_final: 0.6346 (m-10) REVERT: P 49 MET cc_start: 0.7086 (ttp) cc_final: 0.6862 (ttm) REVERT: P 131 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8427 (mp) REVERT: P 187 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8277 (mp) REVERT: P 578 ASP cc_start: 0.6759 (m-30) cc_final: 0.6333 (m-30) REVERT: Q 36 MET cc_start: 0.2962 (tpp) cc_final: -0.0884 (mtm) REVERT: Q 378 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8703 (mm) REVERT: Q 592 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8802 (mm) REVERT: R 19 MET cc_start: 0.6557 (ptm) cc_final: 0.5686 (ttm) REVERT: R 93 MET cc_start: 0.4624 (mpp) cc_final: 0.3805 (mpp) REVERT: R 142 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6227 (mtpt) REVERT: V 38 LYS cc_start: 0.6001 (mmtt) cc_final: 0.5453 (mmmt) REVERT: V 87 ILE cc_start: 0.6378 (OUTLIER) cc_final: 0.5686 (pt) REVERT: W 339 ILE cc_start: 0.8705 (mm) cc_final: 0.8334 (mm) REVERT: W 396 MET cc_start: 0.7122 (mmp) cc_final: 0.6819 (mtm) REVERT: W 515 MET cc_start: 0.4480 (pmm) cc_final: 0.4172 (mmp) REVERT: W 607 MET cc_start: 0.6753 (ttm) cc_final: 0.6283 (ttp) REVERT: W 720 MET cc_start: 0.4742 (tmm) cc_final: 0.4378 (tmm) REVERT: W 782 MET cc_start: 0.4140 (tmm) cc_final: 0.3532 (tpt) REVERT: W 903 PHE cc_start: 0.6157 (t80) cc_final: 0.5751 (t80) REVERT: W 976 GLU cc_start: 0.5998 (mm-30) cc_final: 0.5671 (mm-30) REVERT: X 103 MET cc_start: 0.7436 (ttm) cc_final: 0.7195 (ttm) REVERT: X 221 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5677 (tp) REVERT: X 254 MET cc_start: 0.6917 (ttm) cc_final: 0.6628 (tpt) REVERT: X 436 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6533 (tp) REVERT: X 468 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7348 (t80) REVERT: X 557 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.5829 (tp) REVERT: U 1 MET cc_start: 0.1548 (tpt) cc_final: 0.0783 (mmm) outliers start: 156 outliers final: 118 residues processed: 626 average time/residue: 0.5492 time to fit residues: 605.0158 Evaluate side-chains 623 residues out of total 6820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 484 time to evaluate : 5.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 58 ASP Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 204 MET Chi-restraints excluded: chain 0 residue 214 VAL Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 295 THR Chi-restraints excluded: chain 0 residue 301 THR Chi-restraints excluded: chain 1 residue 45 VAL Chi-restraints excluded: chain 1 residue 73 ILE Chi-restraints excluded: chain 1 residue 96 LEU Chi-restraints excluded: chain 1 residue 131 LYS Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 108 GLU Chi-restraints excluded: chain 3 residue 49 MET Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 167 ILE Chi-restraints excluded: chain 4 residue 106 GLN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 300 CYS Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 500 LEU Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 780 VAL Chi-restraints excluded: chain N residue 815 THR Chi-restraints excluded: chain N residue 833 ILE Chi-restraints excluded: chain N residue 847 CYS Chi-restraints excluded: chain O residue 622 LEU Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 452 LEU Chi-restraints excluded: chain P residue 515 THR Chi-restraints excluded: chain P residue 589 ASP Chi-restraints excluded: chain P residue 599 LEU Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 739 VAL Chi-restraints excluded: chain P residue 814 THR Chi-restraints excluded: chain P residue 827 CYS Chi-restraints excluded: chain Q residue 140 ASN Chi-restraints excluded: chain Q residue 263 LYS Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain Q residue 405 MET Chi-restraints excluded: chain Q residue 427 LEU Chi-restraints excluded: chain Q residue 472 GLU Chi-restraints excluded: chain Q residue 499 VAL Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 604 LEU Chi-restraints excluded: chain Q residue 609 VAL Chi-restraints excluded: chain Q residue 625 VAL Chi-restraints excluded: chain Q residue 637 TYR Chi-restraints excluded: chain R residue 30 HIS Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 99 HIS Chi-restraints excluded: chain R residue 142 LYS Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 186 MET Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain V residue 12 GLU Chi-restraints excluded: chain V residue 19 ASN Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 474 ILE Chi-restraints excluded: chain W residue 612 MET Chi-restraints excluded: chain W residue 618 HIS Chi-restraints excluded: chain W residue 707 ILE Chi-restraints excluded: chain W residue 820 VAL Chi-restraints excluded: chain W residue 830 LEU Chi-restraints excluded: chain W residue 844 ASN Chi-restraints excluded: chain W residue 1074 ARG Chi-restraints excluded: chain W residue 1129 VAL Chi-restraints excluded: chain W residue 1142 ILE Chi-restraints excluded: chain W residue 1314 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 20 ASP Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 239 THR Chi-restraints excluded: chain X residue 253 THR Chi-restraints excluded: chain X residue 342 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 436 LEU Chi-restraints excluded: chain X residue 442 MET Chi-restraints excluded: chain X residue 458 THR Chi-restraints excluded: chain X residue 468 PHE Chi-restraints excluded: chain X residue 488 VAL Chi-restraints excluded: chain X residue 557 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 710 VAL Chi-restraints excluded: chain X residue 714 ILE Chi-restraints excluded: chain X residue 741 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 770 SER Chi-restraints excluded: chain U residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 472 optimal weight: 0.1980 chunk 633 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 548 optimal weight: 0.0980 chunk 87 optimal weight: 0.0060 chunk 165 optimal weight: 0.0570 chunk 595 optimal weight: 0.9980 chunk 249 optimal weight: 0.6980 chunk 611 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN G 50 GLN ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 290 GLN ** O 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 GLN X 737 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.159207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.138550 restraints weight = 147077.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.134967 restraints weight = 253295.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.132751 restraints weight = 214598.734| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 61133 Z= 0.149 Angle : 0.587 13.245 82795 Z= 0.295 Chirality : 0.040 0.197 9521 Planarity : 0.004 0.110 10565 Dihedral : 4.305 60.561 8111 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 1.64 % Allowed : 19.57 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.10), residues: 7453 helix: 1.84 (0.08), residues: 4110 sheet: 0.63 (0.20), residues: 723 loop : -1.87 (0.11), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 192 HIS 0.015 0.001 HIS V 62 PHE 0.024 0.001 PHE U 19 TYR 0.022 0.001 TYR O 729 ARG 0.006 0.000 ARG X 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11541.29 seconds wall clock time: 203 minutes 57.46 seconds (12237.46 seconds total)