Starting phenix.real_space_refine on Sun Aug 9 05:49:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x3s_66508/08_2026/9x3s_66508.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x3s_66508/08_2026/9x3s_66508.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 { model { file = "/net/cci-nas-00/data/ceres_data/9x3s_66508/08_2026/9x3s_66508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x3s_66508/08_2026/9x3s_66508.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x3s_66508/08_2026/9x3s_66508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x3s_66508/08_2026/9x3s_66508.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 20532 2.51 5 N 5514 2.21 5 O 6306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32490 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "B" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "C" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "D" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 4 Chain: "E" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "G" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "H" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 4 Chain: "I" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "J" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "K" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "L" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 4 Chain: "M" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "N" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "O" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "P" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 4 Chain: "Q" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "R" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "S" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "T" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 4 Chain: "U" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "V" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "W" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "X" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 4 Time building chain proxies: 6.72, per 1000 atoms: 0.21 Number of scatterers: 32490 At special positions: 0 Unit cell: (119.574, 119.574, 181.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 6306 8.00 N 5514 7.00 C 20532 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.4 seconds 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 78 sheets defined 19.4% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.647A pdb=" N THR A 33 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.779A pdb=" N TYR A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE B 10 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 34 Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.586A pdb=" N ALA B 92 " --> pdb=" O TRP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL C 181 " --> pdb=" O TRP C 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.621A pdb=" N VAL C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 83 removed outlier: 3.502A pdb=" N LEU D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.691A pdb=" N TYR D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 removed outlier: 4.664A pdb=" N TYR D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.647A pdb=" N THR E 33 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 93 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.779A pdb=" N TYR E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE F 10 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 79 through 94 removed outlier: 3.587A pdb=" N ALA F 92 " --> pdb=" O TRP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL G 181 " --> pdb=" O TRP G 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN G 182 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.622A pdb=" N VAL G 195 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.502A pdb=" N LEU H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 234 removed outlier: 3.690A pdb=" N TYR H 234 " --> pdb=" O ASN H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 360 removed outlier: 4.664A pdb=" N TYR H 360 " --> pdb=" O ARG H 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 29 through 34 removed outlier: 3.647A pdb=" N THR I 33 " --> pdb=" O GLN I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 93 Processing helix chain 'I' and resid 103 through 108 removed outlier: 3.779A pdb=" N TYR I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE J 10 " --> pdb=" O VAL J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 34 Processing helix chain 'J' and resid 79 through 94 removed outlier: 3.586A pdb=" N ALA J 92 " --> pdb=" O TRP J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 11 Processing helix chain 'K' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL K 181 " --> pdb=" O TRP K 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN K 182 " --> pdb=" O VAL K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.621A pdb=" N VAL K 195 " --> pdb=" O LEU K 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 83 removed outlier: 3.501A pdb=" N LEU L 77 " --> pdb=" O ASP L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 234 removed outlier: 3.690A pdb=" N TYR L 234 " --> pdb=" O ASN L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 360 removed outlier: 4.665A pdb=" N TYR L 360 " --> pdb=" O ARG L 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 9 Processing helix chain 'M' and resid 29 through 34 removed outlier: 3.647A pdb=" N THR M 33 " --> pdb=" O GLN M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 93 Processing helix chain 'M' and resid 103 through 108 removed outlier: 3.779A pdb=" N TYR M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE N 10 " --> pdb=" O VAL N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 34 Processing helix chain 'N' and resid 79 through 94 removed outlier: 3.587A pdb=" N ALA N 92 " --> pdb=" O TRP N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR N 107 " --> pdb=" O LYS N 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 11 Processing helix chain 'O' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL O 181 " --> pdb=" O TRP O 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN O 182 " --> pdb=" O VAL O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 196 removed outlier: 3.621A pdb=" N VAL O 195 " --> pdb=" O LEU O 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 83 removed outlier: 3.502A pdb=" N LEU P 77 " --> pdb=" O ASP P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 234 removed outlier: 3.691A pdb=" N TYR P 234 " --> pdb=" O ASN P 230 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 360 removed outlier: 4.664A pdb=" N TYR P 360 " --> pdb=" O ARG P 356 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 9 Processing helix chain 'Q' and resid 29 through 34 removed outlier: 3.647A pdb=" N THR Q 33 " --> pdb=" O GLN Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 93 Processing helix chain 'Q' and resid 103 through 108 removed outlier: 3.779A pdb=" N TYR Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE R 10 " --> pdb=" O VAL R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 34 Processing helix chain 'R' and resid 79 through 94 removed outlier: 3.586A pdb=" N ALA R 92 " --> pdb=" O TRP R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 11 Processing helix chain 'S' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL S 181 " --> pdb=" O TRP S 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN S 182 " --> pdb=" O VAL S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 196 removed outlier: 3.622A pdb=" N VAL S 195 " --> pdb=" O LEU S 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 83 removed outlier: 3.502A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 234 removed outlier: 3.691A pdb=" N TYR T 234 " --> pdb=" O ASN T 230 " (cutoff:3.500A) Processing helix chain 'T' and resid 355 through 360 removed outlier: 4.664A pdb=" N TYR T 360 " --> pdb=" O ARG T 356 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 9 Processing helix chain 'U' and resid 29 through 34 removed outlier: 3.647A pdb=" N THR U 33 " --> pdb=" O GLN U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 93 Processing helix chain 'U' and resid 103 through 108 removed outlier: 3.779A pdb=" N TYR U 107 " --> pdb=" O LYS U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 10 removed outlier: 3.801A pdb=" N PHE V 10 " --> pdb=" O VAL V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 34 Processing helix chain 'V' and resid 79 through 94 removed outlier: 3.586A pdb=" N ALA V 92 " --> pdb=" O TRP V 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR V 107 " --> pdb=" O LYS V 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 11 Processing helix chain 'W' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL W 181 " --> pdb=" O TRP W 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN W 182 " --> pdb=" O VAL W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 191 through 196 removed outlier: 3.621A pdb=" N VAL W 195 " --> pdb=" O LEU W 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 83 removed outlier: 3.502A pdb=" N LEU X 77 " --> pdb=" O ASP X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 215 through 234 removed outlier: 3.691A pdb=" N TYR X 234 " --> pdb=" O ASN X 230 " (cutoff:3.500A) Processing helix chain 'X' and resid 355 through 360 removed outlier: 4.665A pdb=" N TYR X 360 " --> pdb=" O ARG X 356 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 21 through 25 removed outlier: 3.828A pdb=" N GLN A 22 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 111 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 161 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 36 through 39 removed outlier: 7.906A pdb=" N GLU A 154 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL A 137 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A 156 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 45 through 52 removed outlier: 7.409A pdb=" N ILE A 45 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG A 64 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU A 47 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG B 114 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS B 109 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 131 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 115 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS B 125 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR B 156 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 38 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET B 74 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS B 36 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG B 114 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS B 109 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 131 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 115 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS B 125 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 161 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 48 through 52 Processing sheet with id=7, first strand: chain 'C' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE C 199 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR C 217 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL C 201 " --> pdb=" O MET C 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET C 215 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU C 203 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA C 213 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA C 245 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 159 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 127 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE C 199 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR C 217 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL C 201 " --> pdb=" O MET C 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET C 215 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU C 203 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA C 213 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 134 through 140 removed outlier: 7.801A pdb=" N ARG C 134 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG C 153 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER C 136 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.160A pdb=" N TYR D 34 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU D 128 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA D 36 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 125 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=12, first strand: chain 'D' and resid 141 through 144 removed outlier: 5.357A pdb=" N ARG D 142 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'D' and resid 204 through 208 removed outlier: 6.065A pdb=" N ARG D 349 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE D 316 " --> pdb=" O ARG D 349 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'E' and resid 21 through 25 removed outlier: 3.828A pdb=" N GLN E 22 " --> pdb=" O ARG E 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA E 111 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'E' and resid 36 through 39 removed outlier: 7.907A pdb=" N GLU E 154 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL E 137 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR E 156 " --> pdb=" O THR E 135 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'E' and resid 45 through 52 removed outlier: 7.410A pdb=" N ILE E 45 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG E 64 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU E 47 " --> pdb=" O GLY E 62 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'F' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG F 114 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS F 109 " --> pdb=" O GLY F 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY F 131 " --> pdb=" O LYS F 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN F 115 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS F 125 " --> pdb=" O GLN F 115 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR F 156 " --> pdb=" O THR F 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 38 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET F 74 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS F 36 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'F' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG F 114 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS F 109 " --> pdb=" O GLY F 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY F 131 " --> pdb=" O LYS F 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN F 115 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS F 125 " --> pdb=" O GLN F 115 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR F 161 " --> pdb=" O LYS F 130 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'F' and resid 48 through 52 Processing sheet with id=20, first strand: chain 'G' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE G 199 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR G 217 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL G 201 " --> pdb=" O MET G 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET G 215 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU G 203 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA G 213 " --> pdb=" O LEU G 203 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA G 245 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL G 159 " --> pdb=" O LYS G 129 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER G 127 " --> pdb=" O SER G 161 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'G' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE G 199 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR G 217 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL G 201 " --> pdb=" O MET G 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET G 215 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU G 203 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA G 213 " --> pdb=" O LEU G 203 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'G' and resid 134 through 140 removed outlier: 7.800A pdb=" N ARG G 134 " --> pdb=" O ARG G 153 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG G 153 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER G 136 " --> pdb=" O THR G 151 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'H' and resid 34 through 37 removed outlier: 6.160A pdb=" N TYR H 34 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU H 128 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA H 36 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA H 125 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=25, first strand: chain 'H' and resid 141 through 144 removed outlier: 5.358A pdb=" N ARG H 142 " --> pdb=" O GLY H 198 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'H' and resid 204 through 208 removed outlier: 6.064A pdb=" N ARG H 349 " --> pdb=" O ILE H 316 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE H 316 " --> pdb=" O ARG H 349 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'I' and resid 21 through 25 removed outlier: 3.829A pdb=" N GLN I 22 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA I 111 " --> pdb=" O ILE I 129 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR I 161 " --> pdb=" O LYS I 130 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'I' and resid 36 through 39 removed outlier: 7.906A pdb=" N GLU I 154 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL I 137 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR I 156 " --> pdb=" O THR I 135 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'I' and resid 45 through 52 removed outlier: 7.409A pdb=" N ILE I 45 " --> pdb=" O ARG I 64 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG I 64 " --> pdb=" O ILE I 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU I 47 " --> pdb=" O GLY I 62 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'J' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG J 114 " --> pdb=" O GLN J 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS J 109 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY J 131 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN J 115 " --> pdb=" O LYS J 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS J 125 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR J 156 " --> pdb=" O THR J 135 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA J 38 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET J 74 " --> pdb=" O CYS J 36 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS J 36 " --> pdb=" O MET J 74 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'J' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG J 114 " --> pdb=" O GLN J 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS J 109 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY J 131 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN J 115 " --> pdb=" O LYS J 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS J 125 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR J 161 " --> pdb=" O LYS J 130 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'J' and resid 48 through 52 Processing sheet with id=33, first strand: chain 'K' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE K 199 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR K 217 " --> pdb=" O ILE K 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL K 201 " --> pdb=" O MET K 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET K 215 " --> pdb=" O VAL K 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU K 203 " --> pdb=" O ALA K 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA K 213 " --> pdb=" O LEU K 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA K 245 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL K 159 " --> pdb=" O LYS K 129 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER K 127 " --> pdb=" O SER K 161 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'K' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE K 199 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR K 217 " --> pdb=" O ILE K 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL K 201 " --> pdb=" O MET K 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET K 215 " --> pdb=" O VAL K 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU K 203 " --> pdb=" O ALA K 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA K 213 " --> pdb=" O LEU K 203 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'K' and resid 134 through 140 removed outlier: 7.802A pdb=" N ARG K 134 " --> pdb=" O ARG K 153 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG K 153 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER K 136 " --> pdb=" O THR K 151 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'L' and resid 34 through 37 removed outlier: 6.160A pdb=" N TYR L 34 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU L 128 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA L 36 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA L 125 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'L' and resid 43 through 44 Processing sheet with id=38, first strand: chain 'L' and resid 141 through 144 removed outlier: 5.357A pdb=" N ARG L 142 " --> pdb=" O GLY L 198 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'L' and resid 204 through 208 removed outlier: 6.065A pdb=" N ARG L 349 " --> pdb=" O ILE L 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE L 316 " --> pdb=" O ARG L 349 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'M' and resid 21 through 25 removed outlier: 3.829A pdb=" N GLN M 22 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA M 111 " --> pdb=" O ILE M 129 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR M 161 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'M' and resid 36 through 39 removed outlier: 7.907A pdb=" N GLU M 154 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL M 137 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR M 156 " --> pdb=" O THR M 135 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'M' and resid 45 through 52 removed outlier: 7.410A pdb=" N ILE M 45 " --> pdb=" O ARG M 64 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG M 64 " --> pdb=" O ILE M 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU M 47 " --> pdb=" O GLY M 62 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'N' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG N 114 " --> pdb=" O GLN N 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS N 109 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY N 131 " --> pdb=" O LYS N 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN N 115 " --> pdb=" O LYS N 125 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS N 125 " --> pdb=" O GLN N 115 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR N 156 " --> pdb=" O THR N 135 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA N 38 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET N 74 " --> pdb=" O CYS N 36 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N CYS N 36 " --> pdb=" O MET N 74 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'N' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG N 114 " --> pdb=" O GLN N 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS N 109 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY N 131 " --> pdb=" O LYS N 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN N 115 " --> pdb=" O LYS N 125 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS N 125 " --> pdb=" O GLN N 115 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR N 161 " --> pdb=" O LYS N 130 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'N' and resid 48 through 52 Processing sheet with id=46, first strand: chain 'O' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE O 199 " --> pdb=" O THR O 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR O 217 " --> pdb=" O ILE O 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL O 201 " --> pdb=" O MET O 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET O 215 " --> pdb=" O VAL O 201 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU O 203 " --> pdb=" O ALA O 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA O 213 " --> pdb=" O LEU O 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA O 245 " --> pdb=" O PRO O 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL O 159 " --> pdb=" O LYS O 129 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER O 127 " --> pdb=" O SER O 161 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE O 199 " --> pdb=" O THR O 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR O 217 " --> pdb=" O ILE O 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL O 201 " --> pdb=" O MET O 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET O 215 " --> pdb=" O VAL O 201 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU O 203 " --> pdb=" O ALA O 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA O 213 " --> pdb=" O LEU O 203 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'O' and resid 134 through 140 removed outlier: 7.800A pdb=" N ARG O 134 " --> pdb=" O ARG O 153 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG O 153 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER O 136 " --> pdb=" O THR O 151 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'P' and resid 34 through 37 removed outlier: 6.160A pdb=" N TYR P 34 " --> pdb=" O ASN P 126 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU P 128 " --> pdb=" O TYR P 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA P 36 " --> pdb=" O LEU P 128 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA P 125 " --> pdb=" O ALA P 66 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'P' and resid 43 through 44 Processing sheet with id=51, first strand: chain 'P' and resid 141 through 144 removed outlier: 5.357A pdb=" N ARG P 142 " --> pdb=" O GLY P 198 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'P' and resid 204 through 208 removed outlier: 6.066A pdb=" N ARG P 349 " --> pdb=" O ILE P 316 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE P 316 " --> pdb=" O ARG P 349 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'Q' and resid 21 through 25 removed outlier: 3.828A pdb=" N GLN Q 22 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA Q 111 " --> pdb=" O ILE Q 129 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR Q 161 " --> pdb=" O LYS Q 130 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'Q' and resid 36 through 39 removed outlier: 7.905A pdb=" N GLU Q 154 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL Q 137 " --> pdb=" O GLU Q 154 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR Q 156 " --> pdb=" O THR Q 135 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'Q' and resid 45 through 52 removed outlier: 7.409A pdb=" N ILE Q 45 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG Q 64 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU Q 47 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'R' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG R 114 " --> pdb=" O GLN R 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS R 109 " --> pdb=" O GLY R 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY R 131 " --> pdb=" O LYS R 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN R 115 " --> pdb=" O LYS R 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS R 125 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR R 156 " --> pdb=" O THR R 135 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA R 38 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET R 74 " --> pdb=" O CYS R 36 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS R 36 " --> pdb=" O MET R 74 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'R' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG R 114 " --> pdb=" O GLN R 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS R 109 " --> pdb=" O GLY R 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY R 131 " --> pdb=" O LYS R 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN R 115 " --> pdb=" O LYS R 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS R 125 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR R 161 " --> pdb=" O LYS R 130 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'R' and resid 48 through 52 Processing sheet with id=59, first strand: chain 'S' and resid 23 through 26 removed outlier: 5.015A pdb=" N ILE S 199 " --> pdb=" O THR S 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR S 217 " --> pdb=" O ILE S 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL S 201 " --> pdb=" O MET S 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET S 215 " --> pdb=" O VAL S 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU S 203 " --> pdb=" O ALA S 213 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA S 213 " --> pdb=" O LEU S 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA S 245 " --> pdb=" O PRO S 221 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL S 159 " --> pdb=" O LYS S 129 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER S 127 " --> pdb=" O SER S 161 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 23 through 26 removed outlier: 5.015A pdb=" N ILE S 199 " --> pdb=" O THR S 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR S 217 " --> pdb=" O ILE S 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL S 201 " --> pdb=" O MET S 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET S 215 " --> pdb=" O VAL S 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU S 203 " --> pdb=" O ALA S 213 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA S 213 " --> pdb=" O LEU S 203 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 134 through 140 removed outlier: 7.801A pdb=" N ARG S 134 " --> pdb=" O ARG S 153 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG S 153 " --> pdb=" O ARG S 134 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER S 136 " --> pdb=" O THR S 151 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'T' and resid 34 through 37 removed outlier: 6.160A pdb=" N TYR T 34 " --> pdb=" O ASN T 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU T 128 " --> pdb=" O TYR T 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA T 36 " --> pdb=" O LEU T 128 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA T 125 " --> pdb=" O ALA T 66 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'T' and resid 43 through 44 Processing sheet with id=64, first strand: chain 'T' and resid 141 through 144 removed outlier: 5.357A pdb=" N ARG T 142 " --> pdb=" O GLY T 198 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'T' and resid 204 through 208 removed outlier: 6.065A pdb=" N ARG T 349 " --> pdb=" O ILE T 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE T 316 " --> pdb=" O ARG T 349 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'U' and resid 21 through 25 removed outlier: 3.828A pdb=" N GLN U 22 " --> pdb=" O ARG U 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA U 111 " --> pdb=" O ILE U 129 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR U 161 " --> pdb=" O LYS U 130 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'U' and resid 36 through 39 removed outlier: 7.906A pdb=" N GLU U 154 " --> pdb=" O VAL U 137 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL U 137 " --> pdb=" O GLU U 154 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR U 156 " --> pdb=" O THR U 135 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'U' and resid 45 through 52 removed outlier: 7.409A pdb=" N ILE U 45 " --> pdb=" O ARG U 64 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG U 64 " --> pdb=" O ILE U 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU U 47 " --> pdb=" O GLY U 62 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'V' and resid 21 through 25 removed outlier: 3.508A pdb=" N ARG V 114 " --> pdb=" O GLN V 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS V 109 " --> pdb=" O GLY V 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY V 131 " --> pdb=" O LYS V 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN V 115 " --> pdb=" O LYS V 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS V 125 " --> pdb=" O GLN V 115 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR V 156 " --> pdb=" O THR V 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA V 38 " --> pdb=" O THR V 72 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET V 74 " --> pdb=" O CYS V 36 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS V 36 " --> pdb=" O MET V 74 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'V' and resid 21 through 25 removed outlier: 3.508A pdb=" N ARG V 114 " --> pdb=" O GLN V 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS V 109 " --> pdb=" O GLY V 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY V 131 " --> pdb=" O LYS V 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN V 115 " --> pdb=" O LYS V 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS V 125 " --> pdb=" O GLN V 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR V 161 " --> pdb=" O LYS V 130 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'V' and resid 48 through 52 Processing sheet with id=72, first strand: chain 'W' and resid 23 through 26 removed outlier: 5.013A pdb=" N ILE W 199 " --> pdb=" O THR W 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR W 217 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL W 201 " --> pdb=" O MET W 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET W 215 " --> pdb=" O VAL W 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU W 203 " --> pdb=" O ALA W 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA W 213 " --> pdb=" O LEU W 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA W 245 " --> pdb=" O PRO W 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL W 159 " --> pdb=" O LYS W 129 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER W 127 " --> pdb=" O SER W 161 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'W' and resid 23 through 26 removed outlier: 5.013A pdb=" N ILE W 199 " --> pdb=" O THR W 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR W 217 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL W 201 " --> pdb=" O MET W 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET W 215 " --> pdb=" O VAL W 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU W 203 " --> pdb=" O ALA W 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA W 213 " --> pdb=" O LEU W 203 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'W' and resid 134 through 140 removed outlier: 7.801A pdb=" N ARG W 134 " --> pdb=" O ARG W 153 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG W 153 " --> pdb=" O ARG W 134 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER W 136 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'X' and resid 34 through 37 removed outlier: 6.160A pdb=" N TYR X 34 " --> pdb=" O ASN X 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU X 128 " --> pdb=" O TYR X 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA X 36 " --> pdb=" O LEU X 128 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA X 125 " --> pdb=" O ALA X 66 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'X' and resid 43 through 44 Processing sheet with id=77, first strand: chain 'X' and resid 141 through 144 removed outlier: 5.357A pdb=" N ARG X 142 " --> pdb=" O GLY X 198 " (cutoff:3.500A) Processing sheet with id=78, first strand: chain 'X' and resid 204 through 208 removed outlier: 6.065A pdb=" N ARG X 349 " --> pdb=" O ILE X 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE X 316 " --> pdb=" O ARG X 349 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2898 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: 7.49 Time building geometry restraints manager: 3.63 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: 10776 1.34 - 1.46: 5911 1.46 - 1.57: 16265 1.57 - 1.69: 0 1.69 - 1.80: 240 Bond restraints: 33192 Sorted by residual: bond pdb=" CA LYS V 48 " pdb=" C LYS V 48 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.25e-02 6.40e+03 4.66e+00 bond pdb=" CA LYS R 48 " pdb=" C LYS R 48 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.25e-02 6.40e+03 4.53e+00 bond pdb=" CA LYS N 48 " pdb=" C LYS N 48 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.25e-02 6.40e+03 4.37e+00 bond pdb=" CA LYS B 48 " pdb=" C LYS B 48 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.25e-02 6.40e+03 4.37e+00 bond pdb=" CA LYS J 48 " pdb=" C LYS J 48 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.25e-02 6.40e+03 4.27e+00 ... (remaining 33187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 43303 1.30 - 2.60: 1310 2.60 - 3.90: 333 3.90 - 5.20: 54 5.20 - 6.50: 18 Bond angle restraints: 45018 Sorted by residual: angle pdb=" C PHE N 53 " pdb=" N MET N 54 " pdb=" CA MET N 54 " ideal model delta sigma weight residual 122.08 126.67 -4.59 1.84e+00 2.95e-01 6.22e+00 angle pdb=" C PHE B 53 " pdb=" N MET B 54 " pdb=" CA MET B 54 " ideal model delta sigma weight residual 122.08 126.66 -4.58 1.84e+00 2.95e-01 6.19e+00 angle pdb=" C PHE J 53 " pdb=" N MET J 54 " pdb=" CA MET J 54 " ideal model delta sigma weight residual 122.08 126.65 -4.57 1.84e+00 2.95e-01 6.18e+00 angle pdb=" C PHE V 53 " pdb=" N MET V 54 " pdb=" CA MET V 54 " ideal model delta sigma weight residual 122.08 126.65 -4.57 1.84e+00 2.95e-01 6.18e+00 angle pdb=" C PHE F 53 " pdb=" N MET F 54 " pdb=" CA MET F 54 " ideal model delta sigma weight residual 122.08 126.64 -4.56 1.84e+00 2.95e-01 6.14e+00 ... (remaining 45013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17813 17.95 - 35.89: 1509 35.89 - 53.84: 274 53.84 - 71.78: 54 71.78 - 89.73: 30 Dihedral angle restraints: 19680 sinusoidal: 7824 harmonic: 11856 Sorted by residual: dihedral pdb=" CB GLU N 163 " pdb=" CG GLU N 163 " pdb=" CD GLU N 163 " pdb=" OE1 GLU N 163 " ideal model delta sinusoidal sigma weight residual 0.00 -89.73 89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU J 163 " pdb=" CG GLU J 163 " pdb=" CD GLU J 163 " pdb=" OE1 GLU J 163 " ideal model delta sinusoidal sigma weight residual 0.00 -89.73 89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 163 " pdb=" CG GLU B 163 " pdb=" CD GLU B 163 " pdb=" OE1 GLU B 163 " ideal model delta sinusoidal sigma weight residual 0.00 -89.71 89.71 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 19677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3063 0.033 - 0.066: 1257 0.066 - 0.099: 367 0.099 - 0.132: 209 0.132 - 0.166: 18 Chirality restraints: 4914 Sorted by residual: chirality pdb=" CB ILE N 127 " pdb=" CA ILE N 127 " pdb=" CG1 ILE N 127 " pdb=" CG2 ILE N 127 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CB ILE F 127 " pdb=" CA ILE F 127 " pdb=" CG1 ILE F 127 " pdb=" CG2 ILE F 127 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CB ILE R 127 " pdb=" CA ILE R 127 " pdb=" CG1 ILE R 127 " pdb=" CG2 ILE R 127 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 4911 not shown) Planarity restraints: 5898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 53 " 0.016 2.00e-02 2.50e+03 1.77e-02 5.46e+00 pdb=" CG PHE R 53 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE R 53 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 53 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE R 53 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE R 53 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 53 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 53 " -0.016 2.00e-02 2.50e+03 1.76e-02 5.45e+00 pdb=" CG PHE N 53 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE N 53 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE N 53 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE N 53 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE N 53 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE N 53 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 53 " -0.015 2.00e-02 2.50e+03 1.76e-02 5.39e+00 pdb=" CG PHE B 53 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 53 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 53 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 53 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 53 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 53 " 0.000 2.00e-02 2.50e+03 ... (remaining 5895 not shown) Histogram of nonbonded interaction distances: 0.50 - 1.38: 24 1.38 - 2.26: 211 2.26 - 3.14: 27416 3.14 - 4.02: 80994 4.02 - 4.90: 151655 Warning: very small nonbonded interaction distances. Nonbonded interactions: 260300 Sorted by model distance: nonbonded pdb=" OE1 GLU M 47 " pdb=" ND2 ASN S 235 " model vdw 0.504 3.120 nonbonded pdb=" OE1 GLU I 47 " pdb=" ND2 ASN O 235 " model vdw 0.512 3.120 nonbonded pdb=" OE1 GLU Q 47 " pdb=" ND2 ASN W 235 " model vdw 0.513 3.120 nonbonded pdb=" ND2 ASN C 235 " pdb=" OE1 GLU U 47 " model vdw 0.513 3.120 nonbonded pdb=" OE1 GLU E 47 " pdb=" ND2 ASN K 235 " model vdw 0.518 3.120 ... (remaining 260295 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'T' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.020 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 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 : 0.006 0.308 33198 Z= 0.441 Angle : 0.585 6.496 45018 Z= 0.318 Chirality : 0.043 0.166 4914 Planarity : 0.003 0.035 5898 Dihedral : 14.209 89.726 12000 Min Nonbonded Distance : 0.504 Molprobity Statistics. All-atom Clashscore : 34.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.13), residues: 3978 helix: 1.25 (0.21), residues: 594 sheet: -0.42 (0.14), residues: 1476 loop : -1.55 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 56 TYR 0.010 0.001 TYR P 34 PHE 0.041 0.002 PHE R 53 TRP 0.039 0.001 TRP X 209 HIS 0.003 0.001 HIS U 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (33192) covalent geometry : angle 0.58480 / 0.32 (45018) hydrogen bonds : bond 0.21598 / 14.39 ( 978) hydrogen bonds : angle 9.34520 / 6.55 ( 2898) Misc. bond : bond 0.29340 / 16.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1143 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 ARG cc_start: 0.8650 (mmm160) cc_final: 0.6506 (ttp-170) REVERT: B 121 LYS cc_start: 0.8333 (pttm) cc_final: 0.8111 (mppt) REVERT: B 145 ASP cc_start: 0.7183 (m-30) cc_final: 0.6695 (m-30) REVERT: B 149 GLU cc_start: 0.7802 (pt0) cc_final: 0.7539 (pm20) REVERT: B 163 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7918 (mm-30) REVERT: C 198 ASP cc_start: 0.8045 (t0) cc_final: 0.7607 (t0) REVERT: C 238 THR cc_start: 0.9485 (t) cc_final: 0.9272 (m) REVERT: C 241 ASP cc_start: 0.8812 (p0) cc_final: 0.8568 (p0) REVERT: C 246 TYR cc_start: 0.8853 (p90) cc_final: 0.8386 (p90) REVERT: D 343 THR cc_start: 0.8796 (p) cc_final: 0.8536 (p) REVERT: D 348 MET cc_start: 0.8144 (ttm) cc_final: 0.7778 (ttm) REVERT: E 68 ASP cc_start: 0.8390 (m-30) cc_final: 0.8039 (m-30) REVERT: E 115 GLN cc_start: 0.9232 (tp40) cc_final: 0.8973 (tp-100) REVERT: E 143 ASP cc_start: 0.8620 (t70) cc_final: 0.8039 (t0) REVERT: E 146 SER cc_start: 0.8696 (p) cc_final: 0.8085 (p) REVERT: E 151 GLN cc_start: 0.7763 (tt0) cc_final: 0.7468 (tt0) REVERT: F 15 PHE cc_start: 0.9148 (m-80) cc_final: 0.8922 (m-80) REVERT: F 30 GLN cc_start: 0.7758 (mm110) cc_final: 0.7365 (tp40) REVERT: F 103 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8377 (mtpt) REVERT: F 118 ARG cc_start: 0.8686 (mmm160) cc_final: 0.7054 (tmm160) REVERT: F 145 ASP cc_start: 0.7120 (m-30) cc_final: 0.6617 (m-30) REVERT: F 163 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8127 (mm-30) REVERT: G 125 ILE cc_start: 0.9358 (mp) cc_final: 0.9103 (mt) REVERT: G 130 MET cc_start: 0.9140 (tpp) cc_final: 0.8921 (tpp) REVERT: G 139 THR cc_start: 0.8992 (m) cc_final: 0.8768 (m) REVERT: G 156 ASP cc_start: 0.8737 (m-30) cc_final: 0.8444 (m-30) REVERT: G 159 VAL cc_start: 0.9287 (t) cc_final: 0.8908 (m) REVERT: G 198 ASP cc_start: 0.8362 (t0) cc_final: 0.8083 (t0) REVERT: G 215 MET cc_start: 0.8040 (ttm) cc_final: 0.7669 (ttm) REVERT: H 294 MET cc_start: 0.7629 (ttm) cc_final: 0.7416 (mtp) REVERT: H 317 GLN cc_start: 0.9462 (tt0) cc_final: 0.9188 (tt0) REVERT: H 322 ASP cc_start: 0.8996 (t70) cc_final: 0.8738 (t0) REVERT: H 348 MET cc_start: 0.8462 (ttm) cc_final: 0.8183 (ttm) REVERT: I 54 MET cc_start: 0.7232 (mtt) cc_final: 0.6873 (mtt) REVERT: I 130 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8681 (mmmt) REVERT: J 68 ASP cc_start: 0.8227 (m-30) cc_final: 0.7687 (m-30) REVERT: J 118 ARG cc_start: 0.8469 (mmm160) cc_final: 0.6349 (tmm160) REVERT: K 183 ASP cc_start: 0.8899 (t0) cc_final: 0.8698 (t0) REVERT: K 196 GLU cc_start: 0.8340 (tp30) cc_final: 0.7906 (tp30) REVERT: K 238 THR cc_start: 0.9339 (t) cc_final: 0.9127 (m) REVERT: K 241 ASP cc_start: 0.8819 (p0) cc_final: 0.8591 (p0) REVERT: L 59 LYS cc_start: 0.9352 (mttt) cc_final: 0.9069 (mttm) REVERT: L 142 ARG cc_start: 0.8572 (ptp90) cc_final: 0.8315 (mtm110) REVERT: L 196 MET cc_start: 0.7445 (mmm) cc_final: 0.6988 (mpp) REVERT: L 228 TYR cc_start: 0.7886 (m-10) cc_final: 0.7653 (m-10) REVERT: N 118 ARG cc_start: 0.8681 (mmm160) cc_final: 0.6570 (ttp-170) REVERT: N 121 LYS cc_start: 0.8345 (pttm) cc_final: 0.8126 (mppt) REVERT: N 130 LYS cc_start: 0.8817 (mttm) cc_final: 0.8437 (mttm) REVERT: N 145 ASP cc_start: 0.6940 (m-30) cc_final: 0.6525 (m-30) REVERT: N 163 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7916 (mm-30) REVERT: O 165 ASP cc_start: 0.8286 (t70) cc_final: 0.8052 (t70) REVERT: O 198 ASP cc_start: 0.8056 (t0) cc_final: 0.7620 (t0) REVERT: O 238 THR cc_start: 0.9482 (t) cc_final: 0.9255 (m) REVERT: O 241 ASP cc_start: 0.8833 (p0) cc_final: 0.8573 (p0) REVERT: O 246 TYR cc_start: 0.8844 (p90) cc_final: 0.8398 (p90) REVERT: P 292 VAL cc_start: 0.9046 (p) cc_final: 0.8698 (m) REVERT: P 343 THR cc_start: 0.8816 (p) cc_final: 0.8563 (p) REVERT: Q 56 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.8252 (mtp-110) REVERT: Q 75 ASN cc_start: 0.9113 (t0) cc_final: 0.8781 (t0) REVERT: Q 115 GLN cc_start: 0.9247 (tp40) cc_final: 0.8994 (tp-100) REVERT: Q 151 GLN cc_start: 0.7910 (tt0) cc_final: 0.7482 (tt0) REVERT: R 30 GLN cc_start: 0.7720 (mm110) cc_final: 0.7419 (tp40) REVERT: R 103 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8395 (mtpt) REVERT: R 118 ARG cc_start: 0.8698 (mmm160) cc_final: 0.7055 (tmm160) REVERT: R 129 ILE cc_start: 0.8914 (mp) cc_final: 0.8621 (mt) REVERT: R 145 ASP cc_start: 0.7089 (m-30) cc_final: 0.6617 (m-30) REVERT: R 163 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8070 (mm-30) REVERT: S 125 ILE cc_start: 0.9377 (mp) cc_final: 0.9113 (mt) REVERT: S 130 MET cc_start: 0.9139 (tpp) cc_final: 0.8908 (tpp) REVERT: S 156 ASP cc_start: 0.8729 (m-30) cc_final: 0.8412 (m-30) REVERT: S 159 VAL cc_start: 0.9286 (t) cc_final: 0.8906 (m) REVERT: S 198 ASP cc_start: 0.8178 (t0) cc_final: 0.7928 (t0) REVERT: S 215 MET cc_start: 0.8026 (ttm) cc_final: 0.7657 (ttm) REVERT: T 294 MET cc_start: 0.7649 (ttm) cc_final: 0.7424 (mtp) REVERT: T 317 GLN cc_start: 0.9453 (tt0) cc_final: 0.9179 (tt0) REVERT: T 322 ASP cc_start: 0.8986 (t70) cc_final: 0.8740 (t0) REVERT: T 348 MET cc_start: 0.8465 (ttm) cc_final: 0.8183 (ttm) REVERT: U 54 MET cc_start: 0.7240 (mtt) cc_final: 0.6875 (mtt) REVERT: U 130 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8688 (mmmt) REVERT: V 15 PHE cc_start: 0.9180 (m-80) cc_final: 0.8839 (m-80) REVERT: V 68 ASP cc_start: 0.8246 (m-30) cc_final: 0.7739 (m-30) REVERT: V 118 ARG cc_start: 0.8448 (mmm160) cc_final: 0.6233 (tmm160) REVERT: W 17 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8612 (tm-30) REVERT: W 196 GLU cc_start: 0.8316 (tp30) cc_final: 0.7867 (tp30) REVERT: W 241 ASP cc_start: 0.8810 (p0) cc_final: 0.8569 (p0) REVERT: X 59 LYS cc_start: 0.9357 (mttt) cc_final: 0.9066 (mttm) REVERT: X 142 ARG cc_start: 0.8588 (ptp90) cc_final: 0.8352 (mtm110) REVERT: X 196 MET cc_start: 0.7462 (mmm) cc_final: 0.7071 (mpp) REVERT: X 228 TYR cc_start: 0.7856 (m-10) cc_final: 0.7634 (m-10) outliers start: 0 outliers final: 0 residues processed: 1143 average time/residue: 0.2336 time to fit residues: 416.6351 Evaluate side-chains 908 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 908 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 204 HIS D 227 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN F 31 ASN F 35 GLN F 89 GLN G 204 HIS H 227 GLN H 315 GLN I 59 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN K 10 GLN K 193 GLN K 204 HIS L 315 GLN M 59 ASN ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN O 204 HIS P 227 GLN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN R 31 ASN R 35 GLN R 89 GLN ** R 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 HIS T 227 GLN ** T 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 GLN V 89 GLN ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 10 GLN W 193 GLN W 204 HIS X 315 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092597 restraints weight = 52317.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.095588 restraints weight = 25481.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097488 restraints weight = 15084.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098748 restraints weight = 10153.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099535 restraints weight = 7494.141| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 33198 Z= 0.234 Angle : 0.667 10.206 45018 Z= 0.350 Chirality : 0.047 0.308 4914 Planarity : 0.004 0.037 5898 Dihedral : 4.875 19.820 4386 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.81 % Allowed : 13.12 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 3978 helix: 0.91 (0.20), residues: 594 sheet: -0.43 (0.14), residues: 1482 loop : -1.59 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 189 TYR 0.014 0.002 TYR U 107 PHE 0.020 0.002 PHE M 21 TRP 0.013 0.002 TRP R 69 HIS 0.004 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (33192) covalent geometry : angle 0.66704 / 0.35 (45018) hydrogen bonds : bond 0.04567 / 3.00 ( 978) hydrogen bonds : angle 6.34654 / 4.48 ( 2898) Misc. bond : bond 0.00080 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 945 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8413 (t) REVERT: A 14 ASP cc_start: 0.7640 (m-30) cc_final: 0.7355 (m-30) REVERT: A 54 MET cc_start: 0.7890 (mtt) cc_final: 0.7610 (mtt) REVERT: B 54 MET cc_start: 0.8826 (mmm) cc_final: 0.8563 (mmm) REVERT: B 118 ARG cc_start: 0.8710 (mmm160) cc_final: 0.6439 (tmm160) REVERT: B 126 GLU cc_start: 0.8249 (tt0) cc_final: 0.8040 (tt0) REVERT: C 198 ASP cc_start: 0.8227 (t0) cc_final: 0.7843 (t0) REVERT: C 204 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.5222 (p-80) REVERT: C 241 ASP cc_start: 0.8761 (p0) cc_final: 0.8431 (p0) REVERT: D 292 VAL cc_start: 0.9196 (p) cc_final: 0.8887 (m) REVERT: D 348 MET cc_start: 0.8261 (ttm) cc_final: 0.7898 (ttp) REVERT: F 30 GLN cc_start: 0.7826 (mm110) cc_final: 0.7525 (tp40) REVERT: F 118 ARG cc_start: 0.8842 (mmm160) cc_final: 0.6752 (tmm160) REVERT: F 145 ASP cc_start: 0.8021 (m-30) cc_final: 0.7817 (m-30) REVERT: G 125 ILE cc_start: 0.9451 (mp) cc_final: 0.9238 (mt) REVERT: G 196 GLU cc_start: 0.8347 (tp30) cc_final: 0.8085 (tp30) REVERT: H 315 GLN cc_start: 0.8822 (mt0) cc_final: 0.8537 (mt0) REVERT: I 8 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7555 (tmm160) REVERT: I 54 MET cc_start: 0.8223 (mtt) cc_final: 0.7975 (mtt) REVERT: I 129 ILE cc_start: 0.9159 (pt) cc_final: 0.8889 (pt) REVERT: I 130 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8917 (mmmt) REVERT: I 151 GLN cc_start: 0.8196 (tt0) cc_final: 0.7872 (tt0) REVERT: J 47 GLU cc_start: 0.8246 (tp30) cc_final: 0.7928 (tp30) REVERT: J 59 ASN cc_start: 0.8838 (m110) cc_final: 0.8541 (m-40) REVERT: J 115 GLN cc_start: 0.8811 (tm-30) cc_final: 0.7780 (tm-30) REVERT: J 118 ARG cc_start: 0.8564 (mmm160) cc_final: 0.6702 (tmm160) REVERT: K 165 ASP cc_start: 0.8423 (t70) cc_final: 0.8086 (t70) REVERT: K 193 GLN cc_start: 0.8820 (tt0) cc_final: 0.8523 (tt0) REVERT: K 229 LEU cc_start: 0.8804 (pp) cc_final: 0.8529 (pp) REVERT: K 241 ASP cc_start: 0.8620 (p0) cc_final: 0.8327 (p0) REVERT: L 59 LYS cc_start: 0.9370 (mttt) cc_final: 0.9133 (mttm) REVERT: L 220 MET cc_start: 0.8054 (mmm) cc_final: 0.7622 (ttm) REVERT: M 54 MET cc_start: 0.7898 (mtt) cc_final: 0.7630 (mtt) REVERT: M 151 GLN cc_start: 0.8638 (tt0) cc_final: 0.8402 (tt0) REVERT: N 47 GLU cc_start: 0.8351 (tp30) cc_final: 0.7899 (tp30) REVERT: N 54 MET cc_start: 0.8803 (mmm) cc_final: 0.8552 (mmm) REVERT: N 118 ARG cc_start: 0.8721 (mmm160) cc_final: 0.6439 (tmm160) REVERT: N 126 GLU cc_start: 0.8261 (tt0) cc_final: 0.8055 (tt0) REVERT: N 149 GLU cc_start: 0.7736 (pt0) cc_final: 0.7490 (pt0) REVERT: O 198 ASP cc_start: 0.8227 (t0) cc_final: 0.7856 (t0) REVERT: O 204 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.5293 (p-80) REVERT: O 241 ASP cc_start: 0.8783 (p0) cc_final: 0.8435 (p0) REVERT: P 292 VAL cc_start: 0.9177 (p) cc_final: 0.8916 (m) REVERT: P 348 MET cc_start: 0.8200 (ttm) cc_final: 0.7797 (ttp) REVERT: Q 74 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.9245 (ptp) REVERT: R 30 GLN cc_start: 0.7787 (mm110) cc_final: 0.7523 (tp40) REVERT: R 68 ASP cc_start: 0.8618 (m-30) cc_final: 0.8356 (m-30) REVERT: R 118 ARG cc_start: 0.8846 (mmm160) cc_final: 0.6766 (tmm160) REVERT: R 145 ASP cc_start: 0.7954 (m-30) cc_final: 0.7749 (m-30) REVERT: S 125 ILE cc_start: 0.9461 (mp) cc_final: 0.9240 (mt) REVERT: S 196 GLU cc_start: 0.8328 (tp30) cc_final: 0.8078 (tp30) REVERT: T 304 PHE cc_start: 0.8572 (m-10) cc_final: 0.8358 (m-10) REVERT: U 8 ARG cc_start: 0.7994 (ttp-110) cc_final: 0.7562 (tmm160) REVERT: U 54 MET cc_start: 0.8176 (mtt) cc_final: 0.7930 (mtt) REVERT: U 129 ILE cc_start: 0.9064 (pt) cc_final: 0.8801 (pt) REVERT: U 130 LYS cc_start: 0.9135 (mmtt) cc_final: 0.8850 (mmmt) REVERT: U 151 GLN cc_start: 0.8297 (tt0) cc_final: 0.7987 (tt0) REVERT: V 37 LYS cc_start: 0.8203 (tttp) cc_final: 0.7985 (tppt) REVERT: V 47 GLU cc_start: 0.8293 (tp30) cc_final: 0.7971 (tp30) REVERT: V 59 ASN cc_start: 0.8923 (m110) cc_final: 0.8655 (m-40) REVERT: V 68 ASP cc_start: 0.8189 (m-30) cc_final: 0.7969 (m-30) REVERT: V 115 GLN cc_start: 0.8847 (tm-30) cc_final: 0.7836 (tm-30) REVERT: V 118 ARG cc_start: 0.8381 (mmm160) cc_final: 0.6697 (tmm160) REVERT: V 130 LYS cc_start: 0.9044 (mttm) cc_final: 0.8785 (mttm) REVERT: W 143 TYR cc_start: 0.8653 (m-80) cc_final: 0.8422 (m-80) REVERT: W 165 ASP cc_start: 0.8265 (t70) cc_final: 0.7876 (t70) REVERT: W 193 GLN cc_start: 0.8790 (tt0) cc_final: 0.8439 (tt0) REVERT: W 229 LEU cc_start: 0.8837 (pp) cc_final: 0.8571 (pp) REVERT: W 241 ASP cc_start: 0.8868 (p0) cc_final: 0.8589 (p0) REVERT: X 220 MET cc_start: 0.8058 (mmm) cc_final: 0.7643 (ttm) outliers start: 99 outliers final: 74 residues processed: 996 average time/residue: 0.2200 time to fit residues: 347.2477 Evaluate side-chains 940 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 862 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 2 TYR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 215 MET Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 220 MET Chi-restraints excluded: chain Q residue 74 MET Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 223 SER Chi-restraints excluded: chain T residue 133 LYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 89 GLN Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 143 ASP Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 343 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 346 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 400 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 193 GLN C 204 HIS ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 HIS I 148 ASN J 59 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 GLN M 141 GLN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN O 193 GLN O 204 HIS ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 148 ASN V 59 ASN ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 10 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.091685 restraints weight = 52093.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094657 restraints weight = 25251.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096558 restraints weight = 14916.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097788 restraints weight = 10022.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098601 restraints weight = 7429.297| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33198 Z= 0.220 Angle : 0.628 8.350 45018 Z= 0.329 Chirality : 0.045 0.171 4914 Planarity : 0.004 0.037 5898 Dihedral : 4.871 19.099 4386 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.40 % Allowed : 16.61 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 3978 helix: 0.70 (0.20), residues: 594 sheet: -0.49 (0.14), residues: 1500 loop : -1.62 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 56 TYR 0.016 0.001 TYR L 228 PHE 0.016 0.002 PHE X 64 TRP 0.010 0.001 TRP H 209 HIS 0.014 0.002 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (33192) covalent geometry : angle 0.62841 / 0.33 (45018) hydrogen bonds : bond 0.04247 / 2.81 ( 978) hydrogen bonds : angle 5.94278 / 4.20 ( 2898) Misc. bond : bond 0.00116 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 913 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7823 (tm-30) cc_final: 0.6853 (mp0) REVERT: A 54 MET cc_start: 0.7782 (mtt) cc_final: 0.7401 (mtt) REVERT: A 148 ASN cc_start: 0.8491 (m110) cc_final: 0.8021 (m-40) REVERT: B 24 GLU cc_start: 0.8182 (pt0) cc_final: 0.7669 (pt0) REVERT: B 118 ARG cc_start: 0.8770 (mmm160) cc_final: 0.6410 (tmm160) REVERT: B 126 GLU cc_start: 0.8505 (tt0) cc_final: 0.8193 (tt0) REVERT: C 196 GLU cc_start: 0.7783 (tp30) cc_final: 0.7583 (tp30) REVERT: C 198 ASP cc_start: 0.8125 (t0) cc_final: 0.7782 (t0) REVERT: C 204 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.5479 (p-80) REVERT: C 241 ASP cc_start: 0.8746 (p0) cc_final: 0.8444 (p0) REVERT: D 292 VAL cc_start: 0.9153 (p) cc_final: 0.8885 (m) REVERT: E 151 GLN cc_start: 0.8640 (tt0) cc_final: 0.8262 (mt0) REVERT: F 8 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7791 (ttm-80) REVERT: F 30 GLN cc_start: 0.7777 (mm110) cc_final: 0.7529 (tp40) REVERT: F 37 LYS cc_start: 0.8487 (ttpt) cc_final: 0.8254 (ttpt) REVERT: F 68 ASP cc_start: 0.8606 (m-30) cc_final: 0.8356 (m-30) REVERT: F 118 ARG cc_start: 0.8832 (mmm160) cc_final: 0.6975 (tmm160) REVERT: F 145 ASP cc_start: 0.8018 (m-30) cc_final: 0.7632 (m-30) REVERT: G 125 ILE cc_start: 0.9468 (mp) cc_final: 0.9228 (mt) REVERT: G 128 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8686 (p) REVERT: G 156 ASP cc_start: 0.8656 (m-30) cc_final: 0.8429 (m-30) REVERT: G 196 GLU cc_start: 0.8399 (tp30) cc_final: 0.7806 (mm-30) REVERT: H 80 MET cc_start: 0.8389 (ttp) cc_final: 0.8175 (mtp) REVERT: I 8 ARG cc_start: 0.7639 (ttp-110) cc_final: 0.7143 (tmm160) REVERT: I 54 MET cc_start: 0.7820 (mtt) cc_final: 0.7399 (mtt) REVERT: I 130 LYS cc_start: 0.9200 (mmtt) cc_final: 0.8950 (mmmt) REVERT: I 151 GLN cc_start: 0.8241 (tt0) cc_final: 0.7748 (tt0) REVERT: I 154 GLU cc_start: 0.7563 (tt0) cc_final: 0.7133 (mm-30) REVERT: J 47 GLU cc_start: 0.8279 (tp30) cc_final: 0.7696 (tp30) REVERT: J 68 ASP cc_start: 0.8227 (m-30) cc_final: 0.7906 (m-30) REVERT: J 115 GLN cc_start: 0.8932 (tm-30) cc_final: 0.7655 (tm-30) REVERT: J 118 ARG cc_start: 0.8559 (mmm160) cc_final: 0.6564 (tmm160) REVERT: J 128 GLU cc_start: 0.7650 (pt0) cc_final: 0.7440 (pt0) REVERT: J 160 ASP cc_start: 0.8896 (m-30) cc_final: 0.8644 (m-30) REVERT: K 193 GLN cc_start: 0.8855 (tt0) cc_final: 0.8532 (tt0) REVERT: K 241 ASP cc_start: 0.8637 (p0) cc_final: 0.8333 (p0) REVERT: L 59 LYS cc_start: 0.9432 (mttt) cc_final: 0.9160 (mttm) REVERT: L 196 MET cc_start: 0.7800 (mmm) cc_final: 0.7574 (mmm) REVERT: L 220 MET cc_start: 0.8007 (mmm) cc_final: 0.7648 (ttm) REVERT: M 11 GLU cc_start: 0.7788 (tm-30) cc_final: 0.6697 (mp0) REVERT: N 47 GLU cc_start: 0.8301 (tp30) cc_final: 0.7808 (tp30) REVERT: N 118 ARG cc_start: 0.8780 (mmm160) cc_final: 0.6417 (tmm160) REVERT: N 126 GLU cc_start: 0.8515 (tt0) cc_final: 0.8209 (tt0) REVERT: O 196 GLU cc_start: 0.7791 (tp30) cc_final: 0.7585 (tp30) REVERT: O 198 ASP cc_start: 0.8153 (t0) cc_final: 0.7807 (t0) REVERT: O 204 HIS cc_start: 0.9049 (OUTLIER) cc_final: 0.5557 (p-80) REVERT: O 241 ASP cc_start: 0.8735 (p0) cc_final: 0.8434 (p0) REVERT: P 292 VAL cc_start: 0.9141 (p) cc_final: 0.8866 (m) REVERT: Q 151 GLN cc_start: 0.8637 (tt0) cc_final: 0.8403 (mt0) REVERT: R 8 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7852 (ttm-80) REVERT: R 30 GLN cc_start: 0.7660 (mm110) cc_final: 0.7449 (tp40) REVERT: R 109 LYS cc_start: 0.9309 (mttt) cc_final: 0.9105 (mttm) REVERT: R 118 ARG cc_start: 0.8842 (mmm160) cc_final: 0.6983 (tmm160) REVERT: R 145 ASP cc_start: 0.8033 (m-30) cc_final: 0.7643 (m-30) REVERT: S 125 ILE cc_start: 0.9472 (mp) cc_final: 0.9221 (mt) REVERT: S 128 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8650 (p) REVERT: S 196 GLU cc_start: 0.8414 (tp30) cc_final: 0.7831 (mm-30) REVERT: U 8 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7144 (tmm160) REVERT: U 54 MET cc_start: 0.7741 (mtt) cc_final: 0.7384 (mtt) REVERT: U 125 LYS cc_start: 0.9581 (tppt) cc_final: 0.9267 (tptm) REVERT: U 130 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8791 (mmmt) REVERT: U 151 GLN cc_start: 0.8227 (tt0) cc_final: 0.7860 (tt0) REVERT: U 154 GLU cc_start: 0.7577 (tt0) cc_final: 0.7152 (mm-30) REVERT: V 8 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8348 (tpp80) REVERT: V 68 ASP cc_start: 0.8242 (m-30) cc_final: 0.7948 (m-30) REVERT: V 115 GLN cc_start: 0.8953 (tm-30) cc_final: 0.7659 (tm-30) REVERT: V 118 ARG cc_start: 0.8456 (mmm160) cc_final: 0.6709 (tmm160) REVERT: V 119 ASP cc_start: 0.8111 (t70) cc_final: 0.7713 (t70) REVERT: V 132 LEU cc_start: 0.9438 (mt) cc_final: 0.9230 (mt) REVERT: V 160 ASP cc_start: 0.8866 (m-30) cc_final: 0.8610 (m-30) REVERT: W 165 ASP cc_start: 0.8298 (t70) cc_final: 0.8013 (t0) REVERT: W 193 GLN cc_start: 0.8854 (tt0) cc_final: 0.8522 (tt0) REVERT: W 241 ASP cc_start: 0.8705 (p0) cc_final: 0.8443 (p0) REVERT: X 196 MET cc_start: 0.7802 (mmm) cc_final: 0.7563 (mmm) outliers start: 155 outliers final: 116 residues processed: 1008 average time/residue: 0.2093 time to fit residues: 337.4526 Evaluate side-chains 956 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 836 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 172 ARG Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 2 TYR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 232 ASP Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 223 SER Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 89 GLN Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 143 ASP Chi-restraints excluded: chain V residue 15 PHE Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 239 THR Chi-restraints excluded: chain W residue 248 VAL Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain X residue 346 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 265 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 378 optimal weight: 3.9990 chunk 314 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN A 151 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 193 GLN C 204 HIS ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 HIS ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN M 75 ASN M 151 GLN N 31 ASN N 75 ASN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN O 193 GLN O 204 HIS ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN X 317 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094560 restraints weight = 51473.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097625 restraints weight = 24511.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099556 restraints weight = 14285.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100805 restraints weight = 9514.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101567 restraints weight = 6978.449| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33198 Z= 0.136 Angle : 0.576 8.000 45018 Z= 0.300 Chirality : 0.043 0.184 4914 Planarity : 0.004 0.037 5898 Dihedral : 4.655 18.269 4386 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.23 % Allowed : 18.31 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 3978 helix: 0.75 (0.20), residues: 618 sheet: -0.43 (0.14), residues: 1494 loop : -1.70 (0.12), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 56 TYR 0.025 0.001 TYR L 228 PHE 0.013 0.001 PHE X 64 TRP 0.010 0.001 TRP U 162 HIS 0.007 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (33192) covalent geometry : angle 0.57630 / 0.30 (45018) hydrogen bonds : bond 0.03659 / 2.43 ( 978) hydrogen bonds : angle 5.61075 / 3.96 ( 2898) Misc. bond : bond 0.00063 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 880 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7726 (tm-30) cc_final: 0.6858 (mp0) REVERT: A 54 MET cc_start: 0.7675 (mtt) cc_final: 0.7120 (mtt) REVERT: B 24 GLU cc_start: 0.8124 (pt0) cc_final: 0.7657 (pt0) REVERT: B 28 LEU cc_start: 0.9427 (mm) cc_final: 0.9190 (mp) REVERT: B 118 ARG cc_start: 0.8674 (mmm160) cc_final: 0.6489 (tmm160) REVERT: C 196 GLU cc_start: 0.7842 (tp30) cc_final: 0.7529 (tp30) REVERT: C 198 ASP cc_start: 0.8007 (t0) cc_final: 0.7618 (t0) REVERT: C 229 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8654 (pp) REVERT: C 235 ASN cc_start: 0.8452 (m110) cc_final: 0.8213 (m-40) REVERT: C 241 ASP cc_start: 0.8682 (p0) cc_final: 0.8438 (p0) REVERT: C 246 TYR cc_start: 0.8921 (p90) cc_final: 0.8247 (p90) REVERT: D 292 VAL cc_start: 0.9149 (p) cc_final: 0.8828 (m) REVERT: D 348 MET cc_start: 0.8135 (ttm) cc_final: 0.7643 (ttm) REVERT: E 64 ARG cc_start: 0.8760 (ttm170) cc_final: 0.8335 (ttm170) REVERT: E 151 GLN cc_start: 0.8466 (tt0) cc_final: 0.8094 (mt0) REVERT: F 8 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7916 (ttm-80) REVERT: F 30 GLN cc_start: 0.7655 (mm110) cc_final: 0.7426 (tp40) REVERT: F 109 LYS cc_start: 0.9186 (mttt) cc_final: 0.8980 (mttm) REVERT: F 118 ARG cc_start: 0.8782 (mmm160) cc_final: 0.6975 (tmm160) REVERT: F 145 ASP cc_start: 0.8208 (m-30) cc_final: 0.7827 (m-30) REVERT: G 6 GLU cc_start: 0.7128 (mp0) cc_final: 0.6897 (mp0) REVERT: G 125 ILE cc_start: 0.9457 (mp) cc_final: 0.9222 (mt) REVERT: G 148 ILE cc_start: 0.8774 (pt) cc_final: 0.8523 (pt) REVERT: G 196 GLU cc_start: 0.8357 (tp30) cc_final: 0.7666 (mm-30) REVERT: H 80 MET cc_start: 0.8426 (ttp) cc_final: 0.8092 (mtp) REVERT: H 317 GLN cc_start: 0.9285 (tt0) cc_final: 0.8923 (tt0) REVERT: I 8 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.7111 (tmm160) REVERT: I 54 MET cc_start: 0.7632 (mtt) cc_final: 0.7078 (mtt) REVERT: I 130 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8894 (mmmt) REVERT: J 30 GLN cc_start: 0.7580 (mm110) cc_final: 0.7258 (tp40) REVERT: J 106 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8357 (mt-10) REVERT: J 114 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.7574 (mtt-85) REVERT: J 115 GLN cc_start: 0.8937 (tm-30) cc_final: 0.7636 (tm-30) REVERT: J 118 ARG cc_start: 0.8458 (mmm160) cc_final: 0.6712 (tmm160) REVERT: K 193 GLN cc_start: 0.8877 (tt0) cc_final: 0.8525 (tt0) REVERT: K 198 ASP cc_start: 0.7476 (t70) cc_final: 0.7044 (m-30) REVERT: K 241 ASP cc_start: 0.8608 (p0) cc_final: 0.8375 (p0) REVERT: L 59 LYS cc_start: 0.9355 (mttt) cc_final: 0.9043 (mttm) REVERT: L 220 MET cc_start: 0.7885 (mmm) cc_final: 0.7601 (ttm) REVERT: N 24 GLU cc_start: 0.7937 (pt0) cc_final: 0.7566 (pt0) REVERT: N 47 GLU cc_start: 0.8304 (tp30) cc_final: 0.7717 (tp30) REVERT: N 118 ARG cc_start: 0.8680 (mmm160) cc_final: 0.6487 (tmm160) REVERT: O 196 GLU cc_start: 0.7867 (tp30) cc_final: 0.7522 (tp30) REVERT: O 198 ASP cc_start: 0.8024 (t0) cc_final: 0.7641 (t0) REVERT: O 229 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8610 (pp) REVERT: O 241 ASP cc_start: 0.8699 (p0) cc_final: 0.8440 (p0) REVERT: O 246 TYR cc_start: 0.8914 (p90) cc_final: 0.8283 (p90) REVERT: P 81 ARG cc_start: 0.7504 (tpt90) cc_final: 0.7257 (tpt90) REVERT: P 196 MET cc_start: 0.8451 (tpp) cc_final: 0.7709 (mpp) REVERT: P 292 VAL cc_start: 0.9104 (p) cc_final: 0.8780 (m) REVERT: Q 64 ARG cc_start: 0.8741 (ttm170) cc_final: 0.8312 (ttm170) REVERT: Q 151 GLN cc_start: 0.8490 (tt0) cc_final: 0.8114 (mt0) REVERT: R 8 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7914 (ttm-80) REVERT: R 30 GLN cc_start: 0.7635 (mm110) cc_final: 0.7428 (tp40) REVERT: R 109 LYS cc_start: 0.9277 (mttt) cc_final: 0.9008 (mttm) REVERT: R 118 ARG cc_start: 0.8797 (mmm160) cc_final: 0.7017 (tmm160) REVERT: R 145 ASP cc_start: 0.8055 (m-30) cc_final: 0.7635 (m-30) REVERT: S 125 ILE cc_start: 0.9465 (mp) cc_final: 0.9217 (mt) REVERT: S 148 ILE cc_start: 0.8729 (pt) cc_final: 0.8458 (pt) REVERT: S 196 GLU cc_start: 0.8359 (tp30) cc_final: 0.7711 (mm-30) REVERT: T 317 GLN cc_start: 0.9274 (tt0) cc_final: 0.8964 (tt0) REVERT: U 8 ARG cc_start: 0.7639 (ttp-110) cc_final: 0.7075 (tmm160) REVERT: U 54 MET cc_start: 0.7592 (mtt) cc_final: 0.7024 (mtt) REVERT: U 125 LYS cc_start: 0.9564 (tppt) cc_final: 0.9276 (tptm) REVERT: U 129 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8659 (mt) REVERT: U 130 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8716 (mmmt) REVERT: U 154 GLU cc_start: 0.7579 (tt0) cc_final: 0.7117 (mm-30) REVERT: V 30 GLN cc_start: 0.7616 (mm110) cc_final: 0.7288 (tp40) REVERT: V 47 GLU cc_start: 0.8240 (tp30) cc_final: 0.7716 (tp30) REVERT: V 114 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.7703 (mtt-85) REVERT: V 115 GLN cc_start: 0.8966 (tm-30) cc_final: 0.7680 (tm-30) REVERT: V 121 LYS cc_start: 0.8082 (mtmm) cc_final: 0.7824 (ptmm) REVERT: V 132 LEU cc_start: 0.9423 (mt) cc_final: 0.9215 (mt) REVERT: W 165 ASP cc_start: 0.8211 (t70) cc_final: 0.7872 (t0) REVERT: W 193 GLN cc_start: 0.8874 (tt0) cc_final: 0.8533 (tt0) REVERT: W 224 VAL cc_start: 0.8878 (p) cc_final: 0.8501 (m) REVERT: W 241 ASP cc_start: 0.8843 (p0) cc_final: 0.8620 (p0) REVERT: X 220 MET cc_start: 0.7902 (mmm) cc_final: 0.7616 (ttm) outliers start: 149 outliers final: 106 residues processed: 985 average time/residue: 0.2054 time to fit residues: 323.7748 Evaluate side-chains 964 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 855 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 346 ILE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 2 TYR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 223 SER Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain U residue 143 ASP Chi-restraints excluded: chain V residue 15 PHE Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 248 VAL Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain X residue 346 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 26 optimal weight: 2.9990 chunk 361 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 318 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 371 optimal weight: 0.0270 chunk 388 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 193 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 HIS I 148 ASN ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN O 193 GLN O 235 ASN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095118 restraints weight = 51438.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098146 restraints weight = 24837.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100091 restraints weight = 14574.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101330 restraints weight = 9694.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102167 restraints weight = 7121.321| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33198 Z= 0.137 Angle : 0.565 9.266 45018 Z= 0.294 Chirality : 0.043 0.197 4914 Planarity : 0.004 0.049 5898 Dihedral : 4.565 20.036 4386 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.49 % Allowed : 19.36 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 3978 helix: 0.77 (0.21), residues: 618 sheet: -0.32 (0.14), residues: 1464 loop : -1.75 (0.12), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 56 TYR 0.028 0.001 TYR X 228 PHE 0.013 0.001 PHE X 64 TRP 0.008 0.001 TRP U 162 HIS 0.018 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (33192) covalent geometry : angle 0.56502 / 0.29 (45018) hydrogen bonds : bond 0.03492 / 2.33 ( 978) hydrogen bonds : angle 5.45250 / 3.84 ( 2898) Misc. bond : bond 0.00051 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 890 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7681 (tm-30) cc_final: 0.6951 (mp0) REVERT: A 54 MET cc_start: 0.7677 (mtt) cc_final: 0.7042 (mtt) REVERT: B 24 GLU cc_start: 0.7994 (pt0) cc_final: 0.7452 (pt0) REVERT: B 28 LEU cc_start: 0.9426 (mm) cc_final: 0.9193 (mp) REVERT: B 118 ARG cc_start: 0.8650 (mmm160) cc_final: 0.6488 (tmm160) REVERT: B 126 GLU cc_start: 0.8414 (tt0) cc_final: 0.8027 (tt0) REVERT: C 196 GLU cc_start: 0.7694 (tp30) cc_final: 0.6921 (mm-30) REVERT: C 198 ASP cc_start: 0.7967 (t0) cc_final: 0.7571 (t0) REVERT: C 204 HIS cc_start: 0.8933 (OUTLIER) cc_final: 0.5664 (p-80) REVERT: C 229 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8491 (pp) REVERT: C 241 ASP cc_start: 0.8676 (p0) cc_final: 0.8427 (p0) REVERT: D 122 SER cc_start: 0.7988 (m) cc_final: 0.7535 (t) REVERT: E 28 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9041 (mm) REVERT: E 47 GLU cc_start: 0.7379 (tt0) cc_final: 0.7150 (tt0) REVERT: E 151 GLN cc_start: 0.8445 (tt0) cc_final: 0.8094 (mt0) REVERT: F 8 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7905 (ttm-80) REVERT: F 114 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7885 (mtm180) REVERT: F 118 ARG cc_start: 0.8782 (mmm160) cc_final: 0.6989 (tmm160) REVERT: F 145 ASP cc_start: 0.8209 (m-30) cc_final: 0.7837 (m-30) REVERT: G 125 ILE cc_start: 0.9483 (mp) cc_final: 0.9214 (mt) REVERT: G 128 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8456 (p) REVERT: G 164 MET cc_start: 0.8694 (mtp) cc_final: 0.8216 (mmm) REVERT: G 196 GLU cc_start: 0.8327 (tp30) cc_final: 0.7807 (mm-30) REVERT: H 80 MET cc_start: 0.8418 (ttp) cc_final: 0.8053 (mtp) REVERT: H 317 GLN cc_start: 0.9235 (tt0) cc_final: 0.8888 (tt0) REVERT: I 54 MET cc_start: 0.7579 (mtt) cc_final: 0.6987 (mtt) REVERT: I 130 LYS cc_start: 0.9242 (mmtt) cc_final: 0.9035 (mmmt) REVERT: J 30 GLN cc_start: 0.7572 (mm110) cc_final: 0.7283 (tp40) REVERT: J 106 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8424 (mt-10) REVERT: J 114 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.7391 (mtt-85) REVERT: J 115 GLN cc_start: 0.9018 (tm-30) cc_final: 0.7699 (tm-30) REVERT: K 193 GLN cc_start: 0.8831 (tt0) cc_final: 0.8506 (tt0) REVERT: K 198 ASP cc_start: 0.7453 (t70) cc_final: 0.7063 (m-30) REVERT: K 224 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8624 (p) REVERT: K 241 ASP cc_start: 0.8544 (p0) cc_final: 0.8329 (p0) REVERT: L 59 LYS cc_start: 0.9379 (mttt) cc_final: 0.9040 (mttm) REVERT: L 196 MET cc_start: 0.7934 (mmm) cc_final: 0.7643 (mpp) REVERT: M 8 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.8049 (ttp-110) REVERT: M 11 GLU cc_start: 0.7930 (tm-30) cc_final: 0.6631 (mp0) REVERT: M 75 ASN cc_start: 0.9381 (t0) cc_final: 0.9026 (t0) REVERT: N 24 GLU cc_start: 0.7932 (pt0) cc_final: 0.7581 (pt0) REVERT: N 47 GLU cc_start: 0.8323 (tp30) cc_final: 0.7698 (tp30) REVERT: N 118 ARG cc_start: 0.8660 (mmm160) cc_final: 0.6500 (tmm160) REVERT: N 126 GLU cc_start: 0.8536 (tt0) cc_final: 0.8192 (tt0) REVERT: O 196 GLU cc_start: 0.7726 (tp30) cc_final: 0.6944 (mm-30) REVERT: O 198 ASP cc_start: 0.7982 (t0) cc_final: 0.7610 (t0) REVERT: O 204 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.5678 (p-80) REVERT: O 229 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8598 (pp) REVERT: O 241 ASP cc_start: 0.8700 (p0) cc_final: 0.8426 (p0) REVERT: P 196 MET cc_start: 0.8415 (tpp) cc_final: 0.7699 (mpp) REVERT: P 228 TYR cc_start: 0.7598 (m-80) cc_final: 0.7278 (m-10) REVERT: P 292 VAL cc_start: 0.9107 (p) cc_final: 0.8827 (m) REVERT: Q 28 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9025 (mm) REVERT: Q 151 GLN cc_start: 0.8492 (tt0) cc_final: 0.8158 (mt0) REVERT: R 8 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7908 (ttm-80) REVERT: R 114 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.7882 (mtm180) REVERT: R 118 ARG cc_start: 0.8808 (mmm160) cc_final: 0.6991 (tmm160) REVERT: R 145 ASP cc_start: 0.8052 (m-30) cc_final: 0.7655 (m-30) REVERT: S 125 ILE cc_start: 0.9493 (mp) cc_final: 0.9234 (mt) REVERT: S 164 MET cc_start: 0.8745 (mtp) cc_final: 0.8240 (mmm) REVERT: S 196 GLU cc_start: 0.8300 (tp30) cc_final: 0.7817 (mm-30) REVERT: S 241 ASP cc_start: 0.8753 (p0) cc_final: 0.8523 (p0) REVERT: T 317 GLN cc_start: 0.9113 (tt0) cc_final: 0.8690 (tt0) REVERT: U 11 GLU cc_start: 0.7015 (mp0) cc_final: 0.6783 (mp0) REVERT: U 54 MET cc_start: 0.7498 (mtt) cc_final: 0.6899 (mtt) REVERT: U 106 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8109 (mt-10) REVERT: U 125 LYS cc_start: 0.9539 (tppt) cc_final: 0.9306 (tptp) REVERT: U 130 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8722 (mmmt) REVERT: V 30 GLN cc_start: 0.7610 (mm110) cc_final: 0.7323 (tp40) REVERT: V 47 GLU cc_start: 0.8254 (tp30) cc_final: 0.7703 (tp30) REVERT: V 106 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8413 (mt-10) REVERT: V 114 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8071 (mtt90) REVERT: V 115 GLN cc_start: 0.9038 (tm-30) cc_final: 0.7749 (tm-30) REVERT: V 121 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7913 (ptmm) REVERT: W 130 MET cc_start: 0.9216 (tpp) cc_final: 0.8972 (mmm) REVERT: W 165 ASP cc_start: 0.8115 (t70) cc_final: 0.7848 (t0) REVERT: W 193 GLN cc_start: 0.8824 (tt0) cc_final: 0.8507 (tt0) REVERT: W 224 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8653 (p) REVERT: W 241 ASP cc_start: 0.8815 (p0) cc_final: 0.8606 (p0) REVERT: X 196 MET cc_start: 0.7880 (mmm) cc_final: 0.7549 (mpp) REVERT: X 220 MET cc_start: 0.7865 (mmm) cc_final: 0.7603 (ttm) outliers start: 158 outliers final: 121 residues processed: 1003 average time/residue: 0.2115 time to fit residues: 339.1806 Evaluate side-chains 961 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 831 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 346 ILE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 136 ASN Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 2 TYR Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 143 ASP Chi-restraints excluded: chain V residue 15 PHE Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 248 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain X residue 346 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 271 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 274 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 230 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 366 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN A 75 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 HIS I 22 GLN I 89 GLN I 148 ASN K 235 ASN M 59 ASN ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN O 10 GLN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 315 GLN U 22 GLN U 89 GLN U 148 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096915 restraints weight = 51195.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099942 restraints weight = 24598.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101854 restraints weight = 14393.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103100 restraints weight = 9564.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103907 restraints weight = 6996.450| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33198 Z= 0.118 Angle : 0.554 8.335 45018 Z= 0.288 Chirality : 0.043 0.205 4914 Planarity : 0.003 0.039 5898 Dihedral : 4.440 19.942 4386 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.37 % Allowed : 21.58 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 3978 helix: 0.84 (0.21), residues: 618 sheet: -0.40 (0.14), residues: 1494 loop : -1.68 (0.12), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 56 TYR 0.025 0.001 TYR X 228 PHE 0.013 0.001 PHE L 64 TRP 0.009 0.001 TRP U 162 HIS 0.012 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (33192) covalent geometry : angle 0.55402 / 0.29 (45018) hydrogen bonds : bond 0.03313 / 2.22 ( 978) hydrogen bonds : angle 5.33237 / 3.75 ( 2898) Misc. bond : bond 0.00047 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 901 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6938 (mp0) REVERT: A 54 MET cc_start: 0.7758 (mtt) cc_final: 0.7412 (mtt) REVERT: B 24 GLU cc_start: 0.7984 (pt0) cc_final: 0.7429 (pt0) REVERT: B 28 LEU cc_start: 0.9394 (mm) cc_final: 0.9182 (mp) REVERT: B 118 ARG cc_start: 0.8633 (mmm160) cc_final: 0.6401 (tmm160) REVERT: B 126 GLU cc_start: 0.8451 (tt0) cc_final: 0.8072 (tt0) REVERT: C 196 GLU cc_start: 0.7769 (tp30) cc_final: 0.7541 (tp30) REVERT: C 204 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.4826 (p-80) REVERT: C 229 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8449 (pp) REVERT: C 241 ASP cc_start: 0.8710 (p0) cc_final: 0.8415 (p0) REVERT: C 246 TYR cc_start: 0.8842 (p90) cc_final: 0.8167 (p90) REVERT: D 122 SER cc_start: 0.7873 (m) cc_final: 0.7449 (t) REVERT: E 28 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9047 (mm) REVERT: E 151 GLN cc_start: 0.8364 (tt0) cc_final: 0.8023 (mt0) REVERT: F 8 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7827 (ttm-80) REVERT: F 114 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7803 (mtm-85) REVERT: F 118 ARG cc_start: 0.8787 (mmm160) cc_final: 0.6999 (tmm160) REVERT: F 145 ASP cc_start: 0.8135 (m-30) cc_final: 0.7785 (m-30) REVERT: F 149 GLU cc_start: 0.7787 (pt0) cc_final: 0.7486 (pt0) REVERT: G 125 ILE cc_start: 0.9460 (mp) cc_final: 0.9189 (mt) REVERT: G 164 MET cc_start: 0.8679 (mtp) cc_final: 0.8176 (mmm) REVERT: G 196 GLU cc_start: 0.8342 (tp30) cc_final: 0.7878 (mm-30) REVERT: H 80 MET cc_start: 0.8379 (ttp) cc_final: 0.7998 (mtp) REVERT: H 317 GLN cc_start: 0.9111 (tt0) cc_final: 0.8681 (tt0) REVERT: H 350 GLU cc_start: 0.8408 (pt0) cc_final: 0.8131 (pt0) REVERT: I 54 MET cc_start: 0.7393 (mtt) cc_final: 0.6713 (mtt) REVERT: J 30 GLN cc_start: 0.7568 (mm110) cc_final: 0.7269 (tp40) REVERT: J 47 GLU cc_start: 0.8269 (tp30) cc_final: 0.7676 (tp30) REVERT: J 106 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8463 (mt-10) REVERT: J 114 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.7405 (mtt-85) REVERT: J 115 GLN cc_start: 0.9051 (tm-30) cc_final: 0.7726 (tm-30) REVERT: J 126 GLU cc_start: 0.8569 (tt0) cc_final: 0.7996 (tt0) REVERT: K 130 MET cc_start: 0.9207 (tpp) cc_final: 0.8998 (tpp) REVERT: K 193 GLN cc_start: 0.8722 (tt0) cc_final: 0.8431 (tt0) REVERT: K 198 ASP cc_start: 0.7359 (t70) cc_final: 0.6997 (m-30) REVERT: K 224 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8610 (p) REVERT: K 235 ASN cc_start: 0.8043 (m-40) cc_final: 0.7639 (m110) REVERT: L 59 LYS cc_start: 0.9351 (mttt) cc_final: 0.8919 (mttm) REVERT: L 350 GLU cc_start: 0.7638 (pt0) cc_final: 0.7405 (pt0) REVERT: M 8 ARG cc_start: 0.8259 (ttp-110) cc_final: 0.8027 (ttp-110) REVERT: M 11 GLU cc_start: 0.7836 (tm-30) cc_final: 0.6655 (mp0) REVERT: M 75 ASN cc_start: 0.9384 (t0) cc_final: 0.9022 (t0) REVERT: N 24 GLU cc_start: 0.7912 (pt0) cc_final: 0.7484 (pt0) REVERT: N 47 GLU cc_start: 0.8334 (tp30) cc_final: 0.7703 (tp30) REVERT: N 118 ARG cc_start: 0.8717 (mmm160) cc_final: 0.6511 (tmm160) REVERT: N 126 GLU cc_start: 0.8573 (tt0) cc_final: 0.8227 (tt0) REVERT: N 149 GLU cc_start: 0.7699 (pt0) cc_final: 0.7442 (pt0) REVERT: O 196 GLU cc_start: 0.7794 (tp30) cc_final: 0.7311 (mm-30) REVERT: O 204 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.4847 (p-80) REVERT: O 229 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8451 (pp) REVERT: O 241 ASP cc_start: 0.8722 (p0) cc_final: 0.8417 (p0) REVERT: O 246 TYR cc_start: 0.8846 (p90) cc_final: 0.8187 (p90) REVERT: P 228 TYR cc_start: 0.7536 (m-80) cc_final: 0.7252 (m-10) REVERT: P 292 VAL cc_start: 0.9079 (p) cc_final: 0.8782 (m) REVERT: Q 28 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9021 (mm) REVERT: Q 151 GLN cc_start: 0.8468 (tt0) cc_final: 0.8136 (mt0) REVERT: R 8 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7806 (ttm-80) REVERT: R 114 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.7745 (mtm-85) REVERT: R 118 ARG cc_start: 0.8795 (mmm160) cc_final: 0.6991 (tmm160) REVERT: R 145 ASP cc_start: 0.8164 (m-30) cc_final: 0.7800 (m-30) REVERT: R 149 GLU cc_start: 0.7594 (pt0) cc_final: 0.7282 (pt0) REVERT: S 125 ILE cc_start: 0.9470 (mp) cc_final: 0.9183 (mt) REVERT: S 164 MET cc_start: 0.8714 (mtp) cc_final: 0.8194 (mmm) REVERT: S 196 GLU cc_start: 0.8312 (tp30) cc_final: 0.7907 (mm-30) REVERT: T 317 GLN cc_start: 0.9099 (tt0) cc_final: 0.8691 (tt0) REVERT: U 54 MET cc_start: 0.7262 (mtt) cc_final: 0.6570 (mtt) REVERT: U 75 ASN cc_start: 0.8874 (t0) cc_final: 0.8647 (t0) REVERT: U 106 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8048 (mt-10) REVERT: U 125 LYS cc_start: 0.9520 (tppt) cc_final: 0.9251 (tptm) REVERT: U 130 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8745 (mmmt) REVERT: U 154 GLU cc_start: 0.7538 (tt0) cc_final: 0.7278 (mm-30) REVERT: V 30 GLN cc_start: 0.7573 (mm110) cc_final: 0.7331 (tp40) REVERT: V 47 GLU cc_start: 0.8227 (tp30) cc_final: 0.7657 (tp30) REVERT: V 114 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8015 (mtt90) REVERT: V 115 GLN cc_start: 0.9063 (tm-30) cc_final: 0.7752 (tm-30) REVERT: V 121 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7954 (ptmm) REVERT: V 139 GLU cc_start: 0.7369 (pm20) cc_final: 0.7082 (mp0) REVERT: W 130 MET cc_start: 0.9200 (tpp) cc_final: 0.8952 (mmm) REVERT: W 165 ASP cc_start: 0.8049 (t70) cc_final: 0.7818 (t0) REVERT: W 193 GLN cc_start: 0.8770 (tt0) cc_final: 0.8445 (tt0) outliers start: 154 outliers final: 115 residues processed: 1012 average time/residue: 0.2115 time to fit residues: 342.2921 Evaluate side-chains 936 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 814 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 346 ILE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 223 SER Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 172 ARG Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 343 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 61 optimal weight: 0.0020 chunk 310 optimal weight: 0.8980 chunk 382 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 294 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN A 151 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN I 148 ASN M 59 ASN ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN O 235 ASN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 HIS U 148 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098779 restraints weight = 51164.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101843 restraints weight = 24492.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103773 restraints weight = 14211.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105001 restraints weight = 9376.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105820 restraints weight = 6847.736| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33198 Z= 0.108 Angle : 0.564 11.086 45018 Z= 0.290 Chirality : 0.043 0.213 4914 Planarity : 0.003 0.038 5898 Dihedral : 4.362 19.284 4386 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.06 % Allowed : 23.11 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 3978 helix: 0.91 (0.21), residues: 618 sheet: -0.27 (0.14), residues: 1452 loop : -1.78 (0.12), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 56 TYR 0.022 0.001 TYR X 228 PHE 0.019 0.001 PHE C 244 TRP 0.009 0.001 TRP U 162 HIS 0.020 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (33192) covalent geometry : angle 0.56405 / 0.29 (45018) hydrogen bonds : bond 0.03150 / 2.11 ( 978) hydrogen bonds : angle 5.22129 / 3.67 ( 2898) Misc. bond : bond 0.00041 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 838 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6989 (mp0) REVERT: A 125 LYS cc_start: 0.9433 (tppt) cc_final: 0.9202 (tptm) REVERT: B 24 GLU cc_start: 0.7935 (pt0) cc_final: 0.7424 (pt0) REVERT: B 27 TYR cc_start: 0.8800 (t80) cc_final: 0.8589 (t80) REVERT: B 28 LEU cc_start: 0.9334 (mm) cc_final: 0.9103 (mp) REVERT: B 118 ARG cc_start: 0.8632 (mmm160) cc_final: 0.6384 (tmm160) REVERT: B 126 GLU cc_start: 0.8442 (tt0) cc_final: 0.7957 (tt0) REVERT: B 129 ILE cc_start: 0.9309 (mp) cc_final: 0.9083 (mp) REVERT: C 196 GLU cc_start: 0.7540 (tp30) cc_final: 0.7186 (mm-30) REVERT: C 229 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8496 (pp) REVERT: C 241 ASP cc_start: 0.8673 (p0) cc_final: 0.8433 (p0) REVERT: D 122 SER cc_start: 0.7807 (m) cc_final: 0.7359 (t) REVERT: D 342 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7345 (p90) REVERT: E 28 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9023 (mm) REVERT: F 114 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7816 (mtm180) REVERT: F 118 ARG cc_start: 0.8902 (mmm160) cc_final: 0.7082 (tmm160) REVERT: F 145 ASP cc_start: 0.8104 (m-30) cc_final: 0.7777 (m-30) REVERT: G 21 MET cc_start: 0.8226 (mmm) cc_final: 0.7631 (mmm) REVERT: G 125 ILE cc_start: 0.9424 (mp) cc_final: 0.9182 (mt) REVERT: G 130 MET cc_start: 0.8675 (mtp) cc_final: 0.8448 (mtm) REVERT: G 164 MET cc_start: 0.8657 (mtp) cc_final: 0.8194 (mmm) REVERT: G 167 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8008 (mm-30) REVERT: G 196 GLU cc_start: 0.8282 (tp30) cc_final: 0.7692 (mm-30) REVERT: H 80 MET cc_start: 0.8356 (ttp) cc_final: 0.7970 (mtp) REVERT: H 317 GLN cc_start: 0.9098 (tt0) cc_final: 0.8635 (tt0) REVERT: I 54 MET cc_start: 0.7101 (mtt) cc_final: 0.6446 (mtt) REVERT: I 106 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8043 (mt-10) REVERT: J 24 GLU cc_start: 0.7671 (pt0) cc_final: 0.7450 (pt0) REVERT: J 30 GLN cc_start: 0.7531 (mm110) cc_final: 0.7245 (tp40) REVERT: J 47 GLU cc_start: 0.8274 (tp30) cc_final: 0.7637 (tp30) REVERT: J 106 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8451 (mt-10) REVERT: J 114 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.7610 (mtt-85) REVERT: J 115 GLN cc_start: 0.9051 (tm-30) cc_final: 0.7635 (tm-30) REVERT: K 193 GLN cc_start: 0.8760 (tt0) cc_final: 0.8443 (tt0) REVERT: K 198 ASP cc_start: 0.7081 (t70) cc_final: 0.6802 (m-30) REVERT: K 224 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8509 (p) REVERT: L 59 LYS cc_start: 0.9347 (mttt) cc_final: 0.8899 (mttm) REVERT: M 8 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7981 (ttp-170) REVERT: M 11 GLU cc_start: 0.7801 (tm-30) cc_final: 0.6676 (mp0) REVERT: M 89 GLN cc_start: 0.8699 (tt0) cc_final: 0.8361 (tt0) REVERT: N 24 GLU cc_start: 0.7889 (pt0) cc_final: 0.7455 (pt0) REVERT: N 47 GLU cc_start: 0.8328 (tp30) cc_final: 0.7692 (tp30) REVERT: N 118 ARG cc_start: 0.8653 (mmm160) cc_final: 0.6389 (tmm160) REVERT: N 126 GLU cc_start: 0.8446 (tt0) cc_final: 0.7960 (tt0) REVERT: O 196 GLU cc_start: 0.7540 (tp30) cc_final: 0.7105 (mm-30) REVERT: O 204 HIS cc_start: 0.8531 (OUTLIER) cc_final: 0.4982 (p-80) REVERT: O 229 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8516 (pp) REVERT: O 238 THR cc_start: 0.9398 (t) cc_final: 0.9128 (m) REVERT: O 241 ASP cc_start: 0.8457 (p0) cc_final: 0.8210 (p0) REVERT: P 122 SER cc_start: 0.7832 (m) cc_final: 0.7423 (t) REVERT: P 196 MET cc_start: 0.8415 (tpp) cc_final: 0.8123 (mmm) REVERT: P 228 TYR cc_start: 0.7375 (m-80) cc_final: 0.7144 (m-10) REVERT: P 292 VAL cc_start: 0.9059 (p) cc_final: 0.8753 (m) REVERT: P 342 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7236 (p90) REVERT: Q 28 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9002 (mm) REVERT: Q 151 GLN cc_start: 0.8434 (tt0) cc_final: 0.8060 (mt0) REVERT: R 114 ARG cc_start: 0.8187 (mtm-85) cc_final: 0.7827 (mtm180) REVERT: R 118 ARG cc_start: 0.8894 (mmm160) cc_final: 0.7085 (tmm160) REVERT: R 145 ASP cc_start: 0.8189 (m-30) cc_final: 0.7915 (m-30) REVERT: S 125 ILE cc_start: 0.9430 (mp) cc_final: 0.9175 (mt) REVERT: S 130 MET cc_start: 0.8723 (mtp) cc_final: 0.8469 (mtm) REVERT: S 164 MET cc_start: 0.8679 (mtp) cc_final: 0.8188 (mmm) REVERT: S 196 GLU cc_start: 0.8255 (tp30) cc_final: 0.7705 (mm-30) REVERT: T 317 GLN cc_start: 0.9086 (tt0) cc_final: 0.8667 (tt0) REVERT: U 11 GLU cc_start: 0.6880 (mp0) cc_final: 0.6652 (mp0) REVERT: U 54 MET cc_start: 0.7110 (mtt) cc_final: 0.6491 (mtt) REVERT: U 130 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8792 (mmmt) REVERT: U 154 GLU cc_start: 0.7536 (tt0) cc_final: 0.7278 (mm-30) REVERT: V 30 GLN cc_start: 0.7548 (mm110) cc_final: 0.7322 (tp40) REVERT: V 47 GLU cc_start: 0.8220 (tp30) cc_final: 0.7625 (tp30) REVERT: V 114 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8000 (mtt90) REVERT: V 115 GLN cc_start: 0.9085 (tm-30) cc_final: 0.7565 (tm-30) REVERT: W 165 ASP cc_start: 0.8043 (t70) cc_final: 0.7836 (t0) REVERT: W 193 GLN cc_start: 0.8758 (tt0) cc_final: 0.8435 (tt0) outliers start: 143 outliers final: 108 residues processed: 948 average time/residue: 0.2065 time to fit residues: 312.9037 Evaluate side-chains 928 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 812 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 342 PHE Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 310 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 257 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 355 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 272 optimal weight: 0.0070 chunk 25 optimal weight: 0.9980 chunk 329 optimal weight: 5.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 151 GLN B 75 ASN C 10 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN G 204 HIS I 148 ASN M 75 ASN N 75 ASN O 10 GLN O 235 ASN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN S 204 HIS U 148 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096280 restraints weight = 51416.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099302 restraints weight = 24725.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101213 restraints weight = 14428.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102449 restraints weight = 9574.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103239 restraints weight = 7005.353| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33198 Z= 0.148 Angle : 0.578 10.409 45018 Z= 0.300 Chirality : 0.043 0.213 4914 Planarity : 0.004 0.037 5898 Dihedral : 4.473 18.886 4386 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.32 % Allowed : 23.08 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 3978 helix: 0.86 (0.21), residues: 618 sheet: -0.35 (0.14), residues: 1506 loop : -1.72 (0.12), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 56 TYR 0.022 0.001 TYR X 228 PHE 0.017 0.001 PHE C 244 TRP 0.009 0.001 TRP I 162 HIS 0.011 0.001 HIS S 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (33192) covalent geometry : angle 0.57778 / 0.30 (45018) hydrogen bonds : bond 0.03313 / 2.21 ( 978) hydrogen bonds : angle 5.22398 / 3.68 ( 2898) Misc. bond : bond 0.00058 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 856 time to evaluate : 0.945 Fit side-chains REVERT: A 125 LYS cc_start: 0.9411 (tppt) cc_final: 0.9204 (tptm) REVERT: A 151 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8391 (mt0) REVERT: B 24 GLU cc_start: 0.7983 (pt0) cc_final: 0.7472 (pt0) REVERT: B 27 TYR cc_start: 0.8814 (t80) cc_final: 0.8588 (t80) REVERT: B 28 LEU cc_start: 0.9425 (mm) cc_final: 0.9194 (mp) REVERT: B 118 ARG cc_start: 0.8626 (mmm160) cc_final: 0.6399 (tmm160) REVERT: C 196 GLU cc_start: 0.7652 (tp30) cc_final: 0.7104 (mm-30) REVERT: C 198 ASP cc_start: 0.7831 (t0) cc_final: 0.7626 (t0) REVERT: C 204 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.4766 (p-80) REVERT: C 241 ASP cc_start: 0.8476 (p0) cc_final: 0.8253 (p0) REVERT: D 122 SER cc_start: 0.7821 (m) cc_final: 0.7383 (t) REVERT: D 342 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7555 (p90) REVERT: F 114 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7760 (mtm-85) REVERT: F 118 ARG cc_start: 0.8887 (mmm160) cc_final: 0.7078 (tmm160) REVERT: F 145 ASP cc_start: 0.8254 (m-30) cc_final: 0.7983 (m-30) REVERT: G 21 MET cc_start: 0.8434 (mmm) cc_final: 0.7756 (mmm) REVERT: G 125 ILE cc_start: 0.9425 (mp) cc_final: 0.9203 (mt) REVERT: G 130 MET cc_start: 0.8837 (mtp) cc_final: 0.8585 (mtm) REVERT: G 164 MET cc_start: 0.8790 (mtp) cc_final: 0.8110 (mmm) REVERT: G 196 GLU cc_start: 0.8308 (tp30) cc_final: 0.7724 (mm-30) REVERT: H 80 MET cc_start: 0.8386 (ttp) cc_final: 0.7970 (mtp) REVERT: H 317 GLN cc_start: 0.9107 (tt0) cc_final: 0.8652 (tt0) REVERT: I 54 MET cc_start: 0.7303 (mtt) cc_final: 0.6693 (mtt) REVERT: I 106 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7999 (mt-10) REVERT: J 24 GLU cc_start: 0.7706 (pt0) cc_final: 0.7466 (pt0) REVERT: J 30 GLN cc_start: 0.7548 (mm110) cc_final: 0.7274 (tp40) REVERT: J 47 GLU cc_start: 0.8279 (tp30) cc_final: 0.7640 (tp30) REVERT: J 106 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8442 (mt-10) REVERT: J 114 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.7389 (mtt-85) REVERT: J 115 GLN cc_start: 0.9168 (tm-30) cc_final: 0.7561 (tm-30) REVERT: J 126 GLU cc_start: 0.8554 (tt0) cc_final: 0.8234 (tt0) REVERT: K 193 GLN cc_start: 0.8778 (tt0) cc_final: 0.8451 (tt0) REVERT: K 224 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8481 (p) REVERT: K 250 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7287 (mm-40) REVERT: L 59 LYS cc_start: 0.9366 (mttt) cc_final: 0.8900 (mttm) REVERT: M 8 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.8015 (ttp-170) REVERT: M 11 GLU cc_start: 0.7814 (tm-30) cc_final: 0.6811 (mp0) REVERT: M 75 ASN cc_start: 0.9327 (t0) cc_final: 0.9016 (t0) REVERT: N 47 GLU cc_start: 0.8324 (tp30) cc_final: 0.7713 (tp30) REVERT: N 118 ARG cc_start: 0.8649 (mmm160) cc_final: 0.6390 (tmm160) REVERT: N 126 GLU cc_start: 0.8575 (tt0) cc_final: 0.8170 (tt0) REVERT: O 196 GLU cc_start: 0.7686 (tp30) cc_final: 0.7108 (mm-30) REVERT: O 198 ASP cc_start: 0.7859 (t0) cc_final: 0.7636 (t0) REVERT: O 204 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.4701 (p-80) REVERT: O 229 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8408 (pp) REVERT: O 241 ASP cc_start: 0.8493 (p0) cc_final: 0.8227 (p0) REVERT: P 122 SER cc_start: 0.7884 (m) cc_final: 0.7447 (t) REVERT: P 228 TYR cc_start: 0.7392 (m-80) cc_final: 0.7183 (m-10) REVERT: P 292 VAL cc_start: 0.9069 (p) cc_final: 0.8717 (m) REVERT: P 342 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7447 (p90) REVERT: Q 151 GLN cc_start: 0.8482 (tt0) cc_final: 0.8139 (mt0) REVERT: R 114 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7813 (mtm-85) REVERT: R 118 ARG cc_start: 0.8896 (mmm160) cc_final: 0.7070 (tmm160) REVERT: R 145 ASP cc_start: 0.8273 (m-30) cc_final: 0.7994 (m-30) REVERT: S 125 ILE cc_start: 0.9442 (mp) cc_final: 0.9212 (mt) REVERT: S 130 MET cc_start: 0.8878 (mtp) cc_final: 0.8639 (mtm) REVERT: S 164 MET cc_start: 0.8802 (mtp) cc_final: 0.8110 (mmm) REVERT: S 196 GLU cc_start: 0.8306 (tp30) cc_final: 0.7750 (mm-30) REVERT: T 317 GLN cc_start: 0.9097 (tt0) cc_final: 0.8678 (tt0) REVERT: U 11 GLU cc_start: 0.6953 (mp0) cc_final: 0.6728 (mp0) REVERT: U 54 MET cc_start: 0.7302 (mtt) cc_final: 0.6700 (mtt) REVERT: V 30 GLN cc_start: 0.7577 (mm110) cc_final: 0.7337 (tp40) REVERT: V 114 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8039 (mtt90) REVERT: V 115 GLN cc_start: 0.9087 (tm-30) cc_final: 0.7535 (tm-30) REVERT: V 121 LYS cc_start: 0.8361 (mtmm) cc_final: 0.7923 (ptmm) REVERT: V 139 GLU cc_start: 0.7516 (mp0) cc_final: 0.7176 (mp0) REVERT: W 165 ASP cc_start: 0.8112 (t70) cc_final: 0.7814 (t0) REVERT: W 193 GLN cc_start: 0.8779 (tt0) cc_final: 0.8445 (tt0) REVERT: X 81 ARG cc_start: 0.7770 (tpt-90) cc_final: 0.7373 (ttt180) outliers start: 152 outliers final: 128 residues processed: 966 average time/residue: 0.1951 time to fit residues: 301.6586 Evaluate side-chains 941 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 806 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 303 LYS Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 2 TYR Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 342 PHE Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 223 SER Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 172 ARG Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain X residue 54 VAL Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 343 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 326 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 333 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 344 optimal weight: 8.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN B 75 ASN C 10 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN O 10 GLN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 HIS U 148 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094105 restraints weight = 51513.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097099 restraints weight = 25034.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099010 restraints weight = 14747.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100238 restraints weight = 9848.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101049 restraints weight = 7251.106| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33198 Z= 0.188 Angle : 0.609 8.331 45018 Z= 0.316 Chirality : 0.045 0.213 4914 Planarity : 0.004 0.042 5898 Dihedral : 4.642 18.464 4386 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.34 % Allowed : 23.23 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.13), residues: 3978 helix: 0.74 (0.21), residues: 618 sheet: -0.33 (0.14), residues: 1482 loop : -1.77 (0.12), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 56 TYR 0.024 0.001 TYR X 228 PHE 0.016 0.001 PHE C 244 TRP 0.009 0.001 TRP A 69 HIS 0.017 0.001 HIS S 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (33192) covalent geometry : angle 0.60904 / 0.32 (45018) hydrogen bonds : bond 0.03501 / 2.33 ( 978) hydrogen bonds : angle 5.29333 / 3.73 ( 2898) Misc. bond : bond 0.00077 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 816 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9405 (tppt) cc_final: 0.9205 (tptm) REVERT: B 24 GLU cc_start: 0.8016 (pt0) cc_final: 0.7407 (pt0) REVERT: B 28 LEU cc_start: 0.9478 (mm) cc_final: 0.9243 (mp) REVERT: B 114 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8087 (mtm110) REVERT: B 118 ARG cc_start: 0.8644 (mmm160) cc_final: 0.6401 (tmm160) REVERT: B 126 GLU cc_start: 0.8473 (tt0) cc_final: 0.8195 (tt0) REVERT: C 196 GLU cc_start: 0.7776 (tp30) cc_final: 0.7157 (mm-30) REVERT: C 198 ASP cc_start: 0.7959 (t0) cc_final: 0.7749 (t0) REVERT: C 204 HIS cc_start: 0.8854 (OUTLIER) cc_final: 0.5421 (p-80) REVERT: C 241 ASP cc_start: 0.8521 (p0) cc_final: 0.8263 (p0) REVERT: D 122 SER cc_start: 0.7825 (m) cc_final: 0.7387 (t) REVERT: D 342 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7596 (p90) REVERT: F 114 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7910 (mtm-85) REVERT: F 118 ARG cc_start: 0.8843 (mmm160) cc_final: 0.7083 (tmm160) REVERT: F 145 ASP cc_start: 0.8288 (m-30) cc_final: 0.7998 (m-30) REVERT: G 125 ILE cc_start: 0.9414 (mp) cc_final: 0.9214 (mt) REVERT: G 164 MET cc_start: 0.8851 (mtp) cc_final: 0.8084 (mmm) REVERT: G 196 GLU cc_start: 0.8325 (tp30) cc_final: 0.7759 (mm-30) REVERT: H 80 MET cc_start: 0.8422 (ttp) cc_final: 0.7807 (mtm) REVERT: H 317 GLN cc_start: 0.9129 (tt0) cc_final: 0.8693 (tt0) REVERT: I 46 VAL cc_start: 0.8402 (t) cc_final: 0.8192 (t) REVERT: I 54 MET cc_start: 0.7476 (mtt) cc_final: 0.6818 (mtt) REVERT: J 24 GLU cc_start: 0.7712 (pt0) cc_final: 0.7394 (pt0) REVERT: J 30 GLN cc_start: 0.7573 (mm110) cc_final: 0.7327 (tp40) REVERT: J 47 GLU cc_start: 0.8221 (tp30) cc_final: 0.7675 (tp30) REVERT: J 114 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7852 (mtt90) REVERT: J 115 GLN cc_start: 0.9160 (tm-30) cc_final: 0.7572 (tm-30) REVERT: K 193 GLN cc_start: 0.8803 (tt0) cc_final: 0.8456 (tt0) REVERT: K 224 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8443 (p) REVERT: L 59 LYS cc_start: 0.9379 (mttt) cc_final: 0.8913 (mttm) REVERT: M 11 GLU cc_start: 0.7722 (tm-30) cc_final: 0.6913 (mp0) REVERT: M 75 ASN cc_start: 0.9238 (t0) cc_final: 0.8899 (t0) REVERT: N 47 GLU cc_start: 0.8334 (tp30) cc_final: 0.7720 (tp30) REVERT: N 118 ARG cc_start: 0.8659 (mmm160) cc_final: 0.6401 (tmm160) REVERT: O 196 GLU cc_start: 0.7810 (tp30) cc_final: 0.7167 (mm-30) REVERT: O 198 ASP cc_start: 0.7964 (t0) cc_final: 0.7744 (t0) REVERT: O 204 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.5224 (p-80) REVERT: O 238 THR cc_start: 0.9437 (t) cc_final: 0.9144 (m) REVERT: O 241 ASP cc_start: 0.8533 (p0) cc_final: 0.8235 (p0) REVERT: P 122 SER cc_start: 0.7900 (m) cc_final: 0.7456 (t) REVERT: P 292 VAL cc_start: 0.9173 (p) cc_final: 0.8738 (m) REVERT: P 342 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7560 (p90) REVERT: Q 151 GLN cc_start: 0.8539 (tt0) cc_final: 0.8196 (mt0) REVERT: R 114 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7942 (mtm-85) REVERT: R 118 ARG cc_start: 0.8826 (mmm160) cc_final: 0.7075 (tmm160) REVERT: R 145 ASP cc_start: 0.8167 (m-30) cc_final: 0.7847 (m-30) REVERT: S 125 ILE cc_start: 0.9447 (mp) cc_final: 0.9232 (mt) REVERT: S 164 MET cc_start: 0.8887 (mtp) cc_final: 0.8087 (mmm) REVERT: S 196 GLU cc_start: 0.8376 (tp30) cc_final: 0.7840 (mm-30) REVERT: T 317 GLN cc_start: 0.9121 (tt0) cc_final: 0.8707 (tt0) REVERT: U 11 GLU cc_start: 0.7051 (mp0) cc_final: 0.6820 (mp0) REVERT: U 54 MET cc_start: 0.7521 (mtt) cc_final: 0.6883 (mtt) REVERT: U 154 GLU cc_start: 0.7558 (tt0) cc_final: 0.7257 (mm-30) REVERT: V 30 GLN cc_start: 0.7597 (mm110) cc_final: 0.7375 (tp40) REVERT: V 114 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.7953 (mtt90) REVERT: V 115 GLN cc_start: 0.9072 (tm-30) cc_final: 0.7540 (tm-30) REVERT: V 121 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7966 (ptmm) REVERT: V 139 GLU cc_start: 0.7554 (mp0) cc_final: 0.7347 (mp0) REVERT: W 165 ASP cc_start: 0.8284 (t70) cc_final: 0.8074 (t0) REVERT: W 193 GLN cc_start: 0.8842 (tt0) cc_final: 0.8531 (tt0) REVERT: X 225 ILE cc_start: 0.8711 (mt) cc_final: 0.8442 (mm) outliers start: 153 outliers final: 136 residues processed: 928 average time/residue: 0.1987 time to fit residues: 294.5303 Evaluate side-chains 934 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 793 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 303 LYS Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 2 TYR Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 342 PHE Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 149 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 223 SER Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 172 ARG Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain X residue 54 VAL Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 303 LYS Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 284 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 378 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 304 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 ASN C 10 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 HIS I 148 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 HIS U 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.093898 restraints weight = 51856.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096915 restraints weight = 24979.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098818 restraints weight = 14580.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100056 restraints weight = 9665.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100871 restraints weight = 7050.155| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33198 Z= 0.155 Angle : 0.600 9.565 45018 Z= 0.311 Chirality : 0.044 0.213 4914 Planarity : 0.004 0.055 5898 Dihedral : 4.637 23.208 4386 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.09 % Allowed : 23.65 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 3978 helix: 0.71 (0.21), residues: 618 sheet: -0.31 (0.14), residues: 1446 loop : -1.77 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 56 TYR 0.023 0.001 TYR X 228 PHE 0.017 0.001 PHE O 244 TRP 0.009 0.001 TRP I 162 HIS 0.013 0.001 HIS S 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (33192) covalent geometry : angle 0.60023 / 0.31 (45018) hydrogen bonds : bond 0.03407 / 2.27 ( 978) hydrogen bonds : angle 5.28860 / 3.72 ( 2898) Misc. bond : bond 0.00063 / 0.03 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 796 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: B 24 GLU cc_start: 0.7999 (pt0) cc_final: 0.7385 (pt0) REVERT: B 28 LEU cc_start: 0.9493 (mm) cc_final: 0.9272 (mp) REVERT: B 114 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.8052 (mtm110) REVERT: B 118 ARG cc_start: 0.8660 (mmm160) cc_final: 0.6382 (tmm160) REVERT: B 126 GLU cc_start: 0.8514 (tt0) cc_final: 0.8050 (tt0) REVERT: C 196 GLU cc_start: 0.7675 (tp30) cc_final: 0.7105 (mm-30) REVERT: C 198 ASP cc_start: 0.7951 (t0) cc_final: 0.7747 (t0) REVERT: C 204 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.5380 (p-80) REVERT: C 235 ASN cc_start: 0.7229 (m-40) cc_final: 0.6634 (t0) REVERT: C 236 GLN cc_start: 0.7860 (mt0) cc_final: 0.7640 (mt0) REVERT: C 241 ASP cc_start: 0.8496 (p0) cc_final: 0.8234 (p0) REVERT: D 122 SER cc_start: 0.7641 (m) cc_final: 0.7202 (t) REVERT: D 342 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7563 (p90) REVERT: F 114 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7791 (mtm-85) REVERT: F 118 ARG cc_start: 0.8842 (mmm160) cc_final: 0.7083 (tmm160) REVERT: F 145 ASP cc_start: 0.8292 (m-30) cc_final: 0.7993 (m-30) REVERT: G 21 MET cc_start: 0.8576 (mmm) cc_final: 0.7592 (mmm) REVERT: G 125 ILE cc_start: 0.9397 (mp) cc_final: 0.9191 (mt) REVERT: G 164 MET cc_start: 0.8822 (mtp) cc_final: 0.8057 (mmm) REVERT: G 196 GLU cc_start: 0.8321 (tp30) cc_final: 0.7798 (mm-30) REVERT: H 80 MET cc_start: 0.8396 (ttp) cc_final: 0.8015 (mtp) REVERT: H 317 GLN cc_start: 0.9115 (tt0) cc_final: 0.8679 (tt0) REVERT: I 46 VAL cc_start: 0.8312 (t) cc_final: 0.8052 (p) REVERT: I 54 MET cc_start: 0.7282 (mtt) cc_final: 0.6609 (mtt) REVERT: J 24 GLU cc_start: 0.7694 (pt0) cc_final: 0.7492 (pt0) REVERT: J 30 GLN cc_start: 0.7554 (mm110) cc_final: 0.7308 (tp40) REVERT: J 41 LEU cc_start: 0.9020 (mt) cc_final: 0.8757 (mp) REVERT: J 47 GLU cc_start: 0.8229 (tp30) cc_final: 0.7682 (tp30) REVERT: J 106 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8259 (mt-10) REVERT: J 114 ARG cc_start: 0.8489 (mtm-85) cc_final: 0.7495 (mtt-85) REVERT: J 115 GLN cc_start: 0.9110 (tm-30) cc_final: 0.7511 (tm-30) REVERT: K 193 GLN cc_start: 0.8874 (tt0) cc_final: 0.8556 (tt0) REVERT: K 224 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8419 (p) REVERT: L 59 LYS cc_start: 0.9377 (mttt) cc_final: 0.8905 (mttm) REVERT: L 67 TYR cc_start: 0.8769 (m-10) cc_final: 0.8524 (m-10) REVERT: M 11 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6982 (mp0) REVERT: M 75 ASN cc_start: 0.9181 (t0) cc_final: 0.8847 (t0) REVERT: N 47 GLU cc_start: 0.8332 (tp30) cc_final: 0.7762 (tp30) REVERT: N 54 MET cc_start: 0.8726 (mmm) cc_final: 0.8393 (mmm) REVERT: N 114 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.8038 (mtm110) REVERT: N 118 ARG cc_start: 0.8671 (mmm160) cc_final: 0.6373 (tmm160) REVERT: N 126 GLU cc_start: 0.8466 (tt0) cc_final: 0.8044 (tt0) REVERT: O 5 GLU cc_start: 0.7885 (tp30) cc_final: 0.7571 (tp30) REVERT: O 196 GLU cc_start: 0.7697 (tp30) cc_final: 0.7103 (mm-30) REVERT: O 198 ASP cc_start: 0.7962 (t0) cc_final: 0.7740 (t0) REVERT: O 204 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.5341 (p-80) REVERT: O 236 GLN cc_start: 0.8225 (mt0) cc_final: 0.8003 (mt0) REVERT: O 238 THR cc_start: 0.9425 (t) cc_final: 0.9132 (m) REVERT: O 241 ASP cc_start: 0.8527 (p0) cc_final: 0.8186 (p0) REVERT: P 122 SER cc_start: 0.7713 (m) cc_final: 0.7239 (t) REVERT: P 196 MET cc_start: 0.8347 (tpp) cc_final: 0.8031 (mmm) REVERT: P 342 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7454 (p90) REVERT: Q 151 GLN cc_start: 0.8505 (tt0) cc_final: 0.8160 (mt0) REVERT: R 8 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7920 (ttp80) REVERT: R 114 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7919 (mtm-85) REVERT: R 118 ARG cc_start: 0.8838 (mmm160) cc_final: 0.7099 (tmm160) REVERT: R 145 ASP cc_start: 0.8157 (m-30) cc_final: 0.7834 (m-30) REVERT: S 125 ILE cc_start: 0.9426 (mp) cc_final: 0.9205 (mt) REVERT: S 164 MET cc_start: 0.8854 (mtp) cc_final: 0.8062 (mmm) REVERT: S 196 GLU cc_start: 0.8328 (tp30) cc_final: 0.7816 (mm-30) REVERT: T 317 GLN cc_start: 0.9100 (tt0) cc_final: 0.8688 (tt0) REVERT: U 11 GLU cc_start: 0.7066 (mp0) cc_final: 0.6831 (mp0) REVERT: U 54 MET cc_start: 0.7293 (mtt) cc_final: 0.6633 (mtt) REVERT: U 154 GLU cc_start: 0.7580 (tt0) cc_final: 0.7275 (mm-30) REVERT: V 41 LEU cc_start: 0.9030 (mt) cc_final: 0.8756 (mp) REVERT: V 114 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.7937 (mtt90) REVERT: V 115 GLN cc_start: 0.9048 (tm-30) cc_final: 0.7518 (tm-30) REVERT: V 121 LYS cc_start: 0.8350 (mtmm) cc_final: 0.7976 (ptmm) REVERT: W 193 GLN cc_start: 0.8847 (tt0) cc_final: 0.8541 (tt0) outliers start: 144 outliers final: 135 residues processed: 903 average time/residue: 0.1981 time to fit residues: 284.8820 Evaluate side-chains 936 residues out of total 3522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 796 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 303 LYS Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 342 PHE Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 149 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 223 SER Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain X residue 54 VAL Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 303 LYS Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 241 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 10 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 HIS H 53 GLN I 148 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 HIS U 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094017 restraints weight = 51932.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097040 restraints weight = 25073.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098954 restraints weight = 14676.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.100192 restraints weight = 9756.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101009 restraints weight = 7137.680| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33198 Z= 0.150 Angle : 0.601 10.860 45018 Z= 0.311 Chirality : 0.044 0.215 4914 Planarity : 0.004 0.054 5898 Dihedral : 4.628 21.680 4386 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.15 % Allowed : 23.59 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 3978 helix: 0.72 (0.21), residues: 618 sheet: -0.32 (0.14), residues: 1416 loop : -1.69 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 56 TYR 0.022 0.001 TYR X 67 PHE 0.016 0.001 PHE C 244 TRP 0.009 0.001 TRP I 162 HIS 0.010 0.001 HIS S 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (33192) covalent geometry : angle 0.60105 / 0.31 (45018) hydrogen bonds : bond 0.03367 / 2.25 ( 978) hydrogen bonds : angle 5.27972 / 3.72 ( 2898) Misc. bond : bond 0.00060 / 0.03 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6333.23 seconds wall clock time: 109 minutes 53.74 seconds (6593.74 seconds total)