Starting phenix.real_space_refine on Fri Mar 6 20:19:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ptj_20471/03_2026/6ptj_20471.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ptj_20471/03_2026/6ptj_20471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ptj_20471/03_2026/6ptj_20471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ptj_20471/03_2026/6ptj_20471.map" model { file = "/net/cci-nas-00/data/ceres_data/6ptj_20471/03_2026/6ptj_20471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ptj_20471/03_2026/6ptj_20471.cif" } resolution = 3.8 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= 0.001 sd= 0.007 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 146 5.16 5 C 21918 2.51 5 N 5844 2.21 5 O 6453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 211 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34361 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1696 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1557 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "C" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1288 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 148} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1891 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 3 Chain: "c" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4482 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 15, 'TRANS': 537} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "2" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2025 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 247} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "3" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2139 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain breaks: 3 Chain: "4" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2299 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2006 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 12, 'TRANS': 239} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2081 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 13, 'TRANS': 259} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 4, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "7" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2615 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 3 Chain: "E" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3408 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 400} Chain breaks: 2 Chain: "F" Number of atoms: 3472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 431, 3464 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 431, 3464 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 bond proxies already assigned to first conformer: 3541 Chain: "G" Number of atoms: 3402 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 423, 3394 Classifications: {'peptide': 423} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 399} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 423, 3394 Classifications: {'peptide': 423} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 399} Chain breaks: 2 bond proxies already assigned to first conformer: 3470 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AASN F 753 " occ=0.35 ... (14 atoms not shown) pdb=" ND2BASN F 753 " occ=0.65 residue: pdb=" N AASN G 753 " occ=0.38 ... (14 atoms not shown) pdb=" ND2BASN G 753 " occ=0.62 Time building chain proxies: 9.00, per 1000 atoms: 0.26 Number of scatterers: 34361 At special positions: 0 Unit cell: (221.244, 182.58, 200.838, 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 146 16.00 O 6453 8.00 N 5844 7.00 C 21918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 7 265 " - pdb=" SG CYS 7 289 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.7 seconds 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8178 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 48 sheets defined 30.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 removed outlier: 4.102A pdb=" N LEU A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 52 removed outlier: 3.551A pdb=" N ASN A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.693A pdb=" N GLU A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 57 " --> pdb=" O TYR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 removed outlier: 4.040A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 104 removed outlier: 3.785A pdb=" N TYR A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 94 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 142 removed outlier: 3.789A pdb=" N LEU A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.512A pdb=" N GLU B 23 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 3.715A pdb=" N GLN B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 82' Processing helix chain 'B' and resid 99 through 107 removed outlier: 4.362A pdb=" N GLU B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 130 removed outlier: 3.885A pdb=" N LYS B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.815A pdb=" N GLN B 146 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU B 157 " --> pdb=" O GLN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 4.172A pdb=" N GLU B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 11 through 13 No H-bonds generated for 'chain 'C' and resid 11 through 13' Processing helix chain 'C' and resid 81 through 91 removed outlier: 4.361A pdb=" N LYS C 89 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.551A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 133 removed outlier: 4.133A pdb=" N LEU C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 189 removed outlier: 3.638A pdb=" N LYS C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 185 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 11 Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.768A pdb=" N PHE D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 68 " --> pdb=" O MET D 64 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.747A pdb=" N LYS D 85 " --> pdb=" O GLN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 105 removed outlier: 3.989A pdb=" N SER D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET D 93 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 97 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 128 through 142 removed outlier: 3.636A pdb=" N GLU D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.687A pdb=" N GLN D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 161 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 195 removed outlier: 3.548A pdb=" N ASP D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 187 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 189 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU D 193 " --> pdb=" O ILE D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.928A pdb=" N MET D 202 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 17 removed outlier: 3.673A pdb=" N LYS c 14 " --> pdb=" O GLU c 10 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE c 15 " --> pdb=" O ALA c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 36 through 48 removed outlier: 3.517A pdb=" N ALA c 41 " --> pdb=" O ASP c 37 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR c 42 " --> pdb=" O ALA c 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU c 45 " --> pdb=" O ALA c 41 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU c 47 " --> pdb=" O LYS c 43 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU c 48 " --> pdb=" O MET c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 65 through 72 removed outlier: 3.554A pdb=" N ARG c 69 " --> pdb=" O SER c 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 91 through 97 Processing helix chain 'c' and resid 130 through 135 removed outlier: 3.939A pdb=" N ILE c 134 " --> pdb=" O ASN c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 145 through 150 removed outlier: 3.607A pdb=" N ASP c 149 " --> pdb=" O ASP c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 153 through 161 removed outlier: 3.633A pdb=" N ALA c 158 " --> pdb=" O GLU c 154 " (cutoff:3.500A) Processing helix chain 'c' and resid 219 through 237 removed outlier: 3.524A pdb=" N GLU c 234 " --> pdb=" O ILE c 230 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY c 235 " --> pdb=" O HIS c 231 " (cutoff:3.500A) Processing helix chain 'c' and resid 250 through 263 removed outlier: 3.794A pdb=" N GLN c 254 " --> pdb=" O SER c 250 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR c 256 " --> pdb=" O SER c 252 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA c 261 " --> pdb=" O SER c 257 " (cutoff:3.500A) Processing helix chain 'c' and resid 267 through 275 removed outlier: 4.862A pdb=" N ASN c 273 " --> pdb=" O ASN c 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE c 274 " --> pdb=" O LEU c 270 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU c 275 " --> pdb=" O TRP c 271 " (cutoff:3.500A) Processing helix chain 'c' and resid 278 through 283 removed outlier: 4.170A pdb=" N ILE c 282 " --> pdb=" O THR c 278 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA c 283 " --> pdb=" O SER c 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 278 through 283' Processing helix chain 'c' and resid 297 through 302 removed outlier: 3.955A pdb=" N LEU c 302 " --> pdb=" O GLU c 298 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 340 removed outlier: 4.092A pdb=" N TYR c 340 " --> pdb=" O ASP c 336 " (cutoff:3.500A) Processing helix chain 'c' and resid 344 through 349 Processing helix chain 'c' and resid 355 through 367 removed outlier: 3.933A pdb=" N HIS c 360 " --> pdb=" O LYS c 356 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS c 361 " --> pdb=" O LYS c 357 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE c 363 " --> pdb=" O LEU c 359 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG c 365 " --> pdb=" O LYS c 361 " (cutoff:3.500A) Processing helix chain 'c' and resid 371 through 375 Processing helix chain 'c' and resid 376 through 380 removed outlier: 4.071A pdb=" N MET c 380 " --> pdb=" O TRP c 377 " (cutoff:3.500A) Processing helix chain 'c' and resid 381 through 386 removed outlier: 3.733A pdb=" N LYS c 385 " --> pdb=" O ASP c 381 " (cutoff:3.500A) Processing helix chain 'c' and resid 387 through 395 removed outlier: 3.516A pdb=" N ILE c 391 " --> pdb=" O GLU c 387 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP c 393 " --> pdb=" O GLY c 389 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS c 394 " --> pdb=" O ILE c 390 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN c 395 " --> pdb=" O ILE c 391 " (cutoff:3.500A) Processing helix chain 'c' and resid 421 through 430 removed outlier: 3.536A pdb=" N VAL c 425 " --> pdb=" O ALA c 421 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA c 427 " --> pdb=" O GLU c 423 " (cutoff:3.500A) Processing helix chain 'c' and resid 463 through 482 removed outlier: 3.637A pdb=" N THR c 467 " --> pdb=" O ALA c 463 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN c 468 " --> pdb=" O GLN c 464 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU c 469 " --> pdb=" O LYS c 465 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG c 472 " --> pdb=" O ASN c 468 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN c 476 " --> pdb=" O ARG c 472 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP c 478 " --> pdb=" O VAL c 474 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU c 479 " --> pdb=" O SER c 475 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER c 480 " --> pdb=" O ASN c 476 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP c 482 " --> pdb=" O TRP c 478 " (cutoff:3.500A) Processing helix chain 'c' and resid 492 through 497 removed outlier: 4.092A pdb=" N GLN c 497 " --> pdb=" O ASN c 493 " (cutoff:3.500A) Processing helix chain 'c' and resid 509 through 517 removed outlier: 3.857A pdb=" N LEU c 514 " --> pdb=" O GLY c 510 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS c 516 " --> pdb=" O ALA c 512 " (cutoff:3.500A) Processing helix chain 'c' and resid 537 through 540 removed outlier: 3.916A pdb=" N ARG c 540 " --> pdb=" O ASP c 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 537 through 540' Processing helix chain 'c' and resid 541 through 557 removed outlier: 3.544A pdb=" N LEU c 545 " --> pdb=" O ASN c 541 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU c 546 " --> pdb=" O PRO c 542 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG c 547 " --> pdb=" O LEU c 543 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU c 554 " --> pdb=" O ASN c 550 " (cutoff:3.500A) Processing helix chain 'c' and resid 606 through 614 removed outlier: 4.327A pdb=" N ILE c 612 " --> pdb=" O ALA c 608 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR c 613 " --> pdb=" O PHE c 609 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA c 614 " --> pdb=" O GLN c 610 " (cutoff:3.500A) Processing helix chain 'c' and resid 636 through 646 removed outlier: 3.655A pdb=" N PHE c 640 " --> pdb=" O ASP c 636 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU c 642 " --> pdb=" O SER c 638 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS c 643 " --> pdb=" O PRO c 639 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU c 644 " --> pdb=" O PHE c 640 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR c 645 " --> pdb=" O LEU c 641 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU c 646 " --> pdb=" O GLU c 642 " (cutoff:3.500A) Processing helix chain '2' and resid 203 through 212 removed outlier: 3.716A pdb=" N ARG 2 209 " --> pdb=" O ARG 2 205 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU 2 210 " --> pdb=" O THR 2 206 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS 2 212 " --> pdb=" O ALA 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 217 removed outlier: 3.524A pdb=" N LEU 2 216 " --> pdb=" O LYS 2 212 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 251 removed outlier: 3.546A pdb=" N GLU 2 251 " --> pdb=" O ARG 2 247 " (cutoff:3.500A) Processing helix chain '2' and resid 253 through 262 removed outlier: 3.826A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU 2 258 " --> pdb=" O ALA 2 254 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA 2 261 " --> pdb=" O ALA 2 257 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 280 removed outlier: 4.781A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA 2 275 " --> pdb=" O PHE 2 271 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU 2 277 " --> pdb=" O LEU 2 273 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 Processing helix chain '3' and resid 18 through 27 removed outlier: 3.536A pdb=" N GLY 3 22 " --> pdb=" O ASP 3 18 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG 3 24 " --> pdb=" O VAL 3 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG 3 26 " --> pdb=" O GLY 3 22 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 52 removed outlier: 3.508A pdb=" N SER 3 41 " --> pdb=" O SER 3 37 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL 3 42 " --> pdb=" O TYR 3 38 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER 3 50 " --> pdb=" O GLN 3 46 " (cutoff:3.500A) Processing helix chain '3' and resid 52 through 57 Processing helix chain '3' and resid 102 through 107 Processing helix chain '3' and resid 107 through 115 removed outlier: 3.510A pdb=" N SER 3 112 " --> pdb=" O ARG 3 108 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 136 removed outlier: 3.716A pdb=" N LYS 3 127 " --> pdb=" O PRO 3 123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU 3 129 " --> pdb=" O ALA 3 125 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR 3 130 " --> pdb=" O GLU 3 126 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP 3 131 " --> pdb=" O LYS 3 127 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU 3 132 " --> pdb=" O ALA 3 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET 3 136 " --> pdb=" O LEU 3 132 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 200 Processing helix chain '4' and resid 204 through 208 removed outlier: 3.812A pdb=" N ILE 4 208 " --> pdb=" O PHE 4 205 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 237 removed outlier: 4.257A pdb=" N LYS 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN 4 229 " --> pdb=" O TYR 4 225 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU 4 230 " --> pdb=" O TYR 4 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU 4 232 " --> pdb=" O LYS 4 228 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG 4 234 " --> pdb=" O LEU 4 230 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU 4 236 " --> pdb=" O GLU 4 232 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.733A pdb=" N LEU 4 262 " --> pdb=" O TYR 4 258 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN 4 263 " --> pdb=" O HIS 4 259 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR 4 264 " --> pdb=" O GLN 4 260 " (cutoff:3.500A) Processing helix chain '4' and resid 266 through 279 removed outlier: 3.770A pdb=" N GLN 4 274 " --> pdb=" O SER 4 270 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR 4 275 " --> pdb=" O ILE 4 271 " (cutoff:3.500A) Processing helix chain '4' and resid 280 through 285 removed outlier: 3.856A pdb=" N ILE 4 284 " --> pdb=" O MET 4 280 " (cutoff:3.500A) Processing helix chain '4' and resid 420 through 424 removed outlier: 3.788A pdb=" N VAL 4 424 " --> pdb=" O ASP 4 421 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 38 removed outlier: 4.275A pdb=" N PHE 5 34 " --> pdb=" O SER 5 30 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU 5 36 " --> pdb=" O LYS 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 48 removed outlier: 4.141A pdb=" N ARG 5 47 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) Processing helix chain '5' and resid 51 through 56 removed outlier: 3.640A pdb=" N LEU 5 55 " --> pdb=" O ARG 5 51 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 51 through 56' Processing helix chain '5' and resid 65 through 72 removed outlier: 4.230A pdb=" N ILE 5 69 " --> pdb=" O MET 5 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR 5 71 " --> pdb=" O HIS 5 67 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 82 removed outlier: 4.468A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS 5 78 " --> pdb=" O ASP 5 74 " (cutoff:3.500A) Processing helix chain '5' and resid 86 through 95 removed outlier: 4.272A pdb=" N THR 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR 5 95 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) Processing helix chain '6' and resid 104 through 120 removed outlier: 3.739A pdb=" N GLU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 147 removed outlier: 3.558A pdb=" N GLU 6 141 " --> pdb=" O ARG 6 137 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE 6 142 " --> pdb=" O ALA 6 138 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET 6 143 " --> pdb=" O GLN 6 139 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 160 Processing helix chain '6' and resid 166 through 173 Processing helix chain '6' and resid 177 through 190 removed outlier: 3.623A pdb=" N VAL 6 188 " --> pdb=" O GLY 6 184 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG 6 190 " --> pdb=" O ARG 6 186 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 284 removed outlier: 4.036A pdb=" N ILE 6 284 " --> pdb=" O SER 6 281 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 368 removed outlier: 3.871A pdb=" N GLU 6 367 " --> pdb=" O ASN 6 364 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE 6 368 " --> pdb=" O ALA 6 365 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 364 through 368' Processing helix chain '7' and resid 15 through 17 No H-bonds generated for 'chain '7' and resid 15 through 17' Processing helix chain '7' and resid 18 through 23 Processing helix chain '7' and resid 61 through 72 removed outlier: 3.910A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET 7 66 " --> pdb=" O LYS 7 62 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 92 removed outlier: 3.754A pdb=" N LYS 7 92 " --> pdb=" O TYR 7 88 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 110 removed outlier: 3.827A pdb=" N GLN 7 108 " --> pdb=" O SER 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 116 removed outlier: 4.140A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU 7 116 " --> pdb=" O HIS 7 112 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 111 through 116' Processing helix chain '7' and resid 140 through 154 removed outlier: 3.704A pdb=" N ASN 7 144 " --> pdb=" O ASP 7 140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN 7 150 " --> pdb=" O ARG 7 146 " (cutoff:3.500A) Processing helix chain '7' and resid 210 through 215 removed outlier: 3.639A pdb=" N ARG 7 214 " --> pdb=" O ASN 7 210 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 210 through 215' Processing helix chain '7' and resid 231 through 235 removed outlier: 3.914A pdb=" N PHE 7 234 " --> pdb=" O LYS 7 231 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU 7 235 " --> pdb=" O GLY 7 232 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 231 through 235' Processing helix chain 'E' and resid 673 through 680 removed outlier: 3.746A pdb=" N TYR E 677 " --> pdb=" O ASN E 673 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN E 678 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE E 679 " --> pdb=" O ASP E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 732 Processing helix chain 'E' and resid 786 through 790 Processing helix chain 'E' and resid 818 through 844 removed outlier: 5.320A pdb=" N GLU E 824 " --> pdb=" O SER E 820 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU E 825 " --> pdb=" O MET E 821 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU E 826 " --> pdb=" O ALA E 822 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER E 830 " --> pdb=" O GLU E 826 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU E 835 " --> pdb=" O LYS E 831 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 836 " --> pdb=" O VAL E 832 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP E 839 " --> pdb=" O GLU E 835 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR E 840 " --> pdb=" O LEU E 836 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 841 " --> pdb=" O LEU E 837 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU E 842 " --> pdb=" O THR E 838 " (cutoff:3.500A) Processing helix chain 'E' and resid 850 through 876 removed outlier: 3.809A pdb=" N VAL E 854 " --> pdb=" O ASN E 850 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 864 " --> pdb=" O GLY E 860 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 866 " --> pdb=" O TYR E 862 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG E 868 " --> pdb=" O LYS E 864 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU E 869 " --> pdb=" O ALA E 865 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 872 " --> pdb=" O ARG E 868 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP E 876 " --> pdb=" O SER E 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 879 through 885 removed outlier: 3.526A pdb=" N SER E 884 " --> pdb=" O GLU E 880 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU E 885 " --> pdb=" O LYS E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 888 No H-bonds generated for 'chain 'E' and resid 886 through 888' Processing helix chain 'E' and resid 894 through 906 removed outlier: 3.650A pdb=" N VAL E 899 " --> pdb=" O LEU E 895 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS E 900 " --> pdb=" O THR E 896 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 901 " --> pdb=" O ALA E 897 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG E 904 " --> pdb=" O LYS E 900 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA E 905 " --> pdb=" O ILE E 901 " (cutoff:3.500A) Processing helix chain 'E' and resid 907 through 927 removed outlier: 3.601A pdb=" N VAL E 911 " --> pdb=" O LEU E 907 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS E 912 " --> pdb=" O PRO E 908 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS E 913 " --> pdb=" O SER E 909 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 914 " --> pdb=" O LEU E 910 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN E 915 " --> pdb=" O VAL E 911 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 919 " --> pdb=" O ASN E 915 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 920 " --> pdb=" O ASN E 916 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN E 925 " --> pdb=" O ARG E 921 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU E 926 " --> pdb=" O TYR E 922 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS E 927 " --> pdb=" O GLU E 923 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 670 Processing helix chain 'F' and resid 673 through 680 Processing helix chain 'F' and resid 723 through 732 removed outlier: 3.720A pdb=" N GLU F 727 " --> pdb=" O ASP F 723 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP F 729 " --> pdb=" O ASN F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 788 removed outlier: 3.636A pdb=" N LEU F 786 " --> pdb=" O VAL F 782 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 787 " --> pdb=" O LYS F 783 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU F 788 " --> pdb=" O SER F 784 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 782 through 788' Processing helix chain 'F' and resid 818 through 842 removed outlier: 3.824A pdb=" N ALA F 823 " --> pdb=" O VAL F 819 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU F 824 " --> pdb=" O SER F 820 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU F 825 " --> pdb=" O MET F 821 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU F 833 " --> pdb=" O ARG F 829 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU F 835 " --> pdb=" O LYS F 831 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 837 " --> pdb=" O LEU F 833 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR F 838 " --> pdb=" O SER F 834 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP F 839 " --> pdb=" O GLU F 835 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR F 840 " --> pdb=" O LEU F 836 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 841 " --> pdb=" O LEU F 837 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 876 removed outlier: 3.617A pdb=" N VAL F 854 " --> pdb=" O ASN F 850 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY F 860 " --> pdb=" O ALA F 856 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA F 861 " --> pdb=" O ALA F 857 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU F 867 " --> pdb=" O ASP F 863 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG F 868 " --> pdb=" O LYS F 864 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU F 869 " --> pdb=" O ALA F 865 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE F 870 " --> pdb=" O LEU F 866 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER F 875 " --> pdb=" O ALA F 871 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP F 876 " --> pdb=" O SER F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 887 removed outlier: 3.668A pdb=" N LEU F 885 " --> pdb=" O LYS F 881 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA F 886 " --> pdb=" O ALA F 882 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS F 887 " --> pdb=" O LEU F 883 " (cutoff:3.500A) Processing helix chain 'F' and resid 891 through 903 removed outlier: 3.900A pdb=" N LEU F 895 " --> pdb=" O GLN F 891 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 897 " --> pdb=" O ARG F 893 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 898 " --> pdb=" O ALA F 894 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 899 " --> pdb=" O LEU F 895 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS F 900 " --> pdb=" O THR F 896 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 901 " --> pdb=" O ALA F 897 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER F 902 " --> pdb=" O ALA F 898 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 903 " --> pdb=" O VAL F 899 " (cutoff:3.500A) Processing helix chain 'F' and resid 909 through 926 removed outlier: 4.206A pdb=" N LYS F 913 " --> pdb=" O SER F 909 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 914 " --> pdb=" O LEU F 910 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN F 916 " --> pdb=" O LYS F 912 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 917 " --> pdb=" O LYS F 913 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR F 922 " --> pdb=" O ARG F 918 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU F 923 " --> pdb=" O GLU F 919 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN F 924 " --> pdb=" O ALA F 920 " (cutoff:3.500A) Processing helix chain 'G' and resid 673 through 678 removed outlier: 3.667A pdb=" N TYR G 677 " --> pdb=" O ASN G 673 " (cutoff:3.500A) Processing helix chain 'G' and resid 724 through 733 removed outlier: 3.789A pdb=" N ILE G 728 " --> pdb=" O SER G 724 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP G 729 " --> pdb=" O ASN G 725 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY G 733 " --> pdb=" O TRP G 729 " (cutoff:3.500A) Processing helix chain 'G' and resid 782 through 790 Processing helix chain 'G' and resid 818 through 844 removed outlier: 4.586A pdb=" N GLU G 824 " --> pdb=" O SER G 820 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU G 825 " --> pdb=" O MET G 821 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 828 " --> pdb=" O GLU G 824 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER G 834 " --> pdb=" O SER G 830 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU G 835 " --> pdb=" O LYS G 831 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU G 837 " --> pdb=" O LEU G 833 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR G 838 " --> pdb=" O SER G 834 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP G 839 " --> pdb=" O GLU G 835 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR G 840 " --> pdb=" O LEU G 836 " (cutoff:3.500A) Processing helix chain 'G' and resid 850 through 875 removed outlier: 3.692A pdb=" N VAL G 854 " --> pdb=" O ASN G 850 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA G 856 " --> pdb=" O ASN G 852 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP G 863 " --> pdb=" O ASN G 859 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU G 869 " --> pdb=" O ALA G 865 " (cutoff:3.500A) Processing helix chain 'G' and resid 878 through 882 removed outlier: 3.601A pdb=" N LYS G 881 " --> pdb=" O ASN G 878 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 882 " --> pdb=" O VAL G 879 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 878 through 882' Processing helix chain 'G' and resid 884 through 889 Processing helix chain 'G' and resid 891 through 905 removed outlier: 3.884A pdb=" N LEU G 895 " --> pdb=" O GLN G 891 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS G 900 " --> pdb=" O THR G 896 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE G 901 " --> pdb=" O ALA G 897 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER G 902 " --> pdb=" O ALA G 898 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG G 904 " --> pdb=" O LYS G 900 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA G 905 " --> pdb=" O ILE G 901 " (cutoff:3.500A) Processing helix chain 'G' and resid 907 through 922 removed outlier: 3.848A pdb=" N LYS G 912 " --> pdb=" O PRO G 908 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS G 913 " --> pdb=" O SER G 909 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG G 918 " --> pdb=" O ILE G 914 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU G 919 " --> pdb=" O ASN G 915 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.673A pdb=" N GLN A 188 " --> pdb=" O ILE c 58 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU c 27 " --> pdb=" O GLN c 57 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL c 59 " --> pdb=" O LEU c 27 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE c 29 " --> pdb=" O VAL c 59 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE c 61 " --> pdb=" O ILE c 29 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL c 31 " --> pdb=" O ILE c 61 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL c 28 " --> pdb=" O LEU c 82 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL c 84 " --> pdb=" O VAL c 28 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE c 30 " --> pdb=" O VAL c 84 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU c 83 " --> pdb=" O TYR c 121 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ILE c 120 " --> pdb=" O GLN c 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'C' and resid 24 through 25 Processing sheet with id=AA5, first strand: chain 'D' and resid 274 through 278 Processing sheet with id=AA6, first strand: chain 'c' and resid 317 through 323 removed outlier: 3.735A pdb=" N THR c 412 " --> pdb=" O THR c 317 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL c 410 " --> pdb=" O ASN c 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 519 through 520 removed outlier: 4.007A pdb=" N GLU c 631 " --> pdb=" O ARG c 621 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG c 621 " --> pdb=" O GLU c 631 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 241 through 244 removed outlier: 7.337A pdb=" N LEU 2 242 " --> pdb=" O ARG 2 296 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '2' and resid 429 through 431 removed outlier: 3.588A pdb=" N ILE 2 450 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN 2 386 " --> pdb=" O LEU 2 410 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR 2 325 " --> pdb=" O THR 2 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 193 through 198 removed outlier: 3.530A pdb=" N ILE 3 197 " --> pdb=" O THR 3 249 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE 3 321 " --> pdb=" O ASP 3 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 193 through 198 removed outlier: 3.530A pdb=" N ILE 3 197 " --> pdb=" O THR 3 249 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL 3 180 " --> pdb=" O GLY 3 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 201 through 202 Processing sheet with id=AB4, first strand: chain '4' and resid 339 through 342 removed outlier: 9.222A pdb=" N SER 4 414 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N VAL 4 461 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER 4 416 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU 4 456 " --> pdb=" O ILE 4 444 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE 4 444 " --> pdb=" O LEU 4 456 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS 4 458 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR 4 460 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 339 through 342 removed outlier: 7.802A pdb=" N VAL 4 396 " --> pdb=" O SER 4 335 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER 4 335 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU 4 434 " --> pdb=" O VAL 4 466 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL 4 466 " --> pdb=" O GLU 4 434 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '4' and resid 344 through 345 removed outlier: 3.550A pdb=" N VAL 4 358 " --> pdb=" O ALA 4 345 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 60 through 64 removed outlier: 6.031A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '5' and resid 273 through 274 removed outlier: 8.647A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '5' and resid 190 through 193 removed outlier: 3.518A pdb=" N ILE 5 181 " --> pdb=" O THR 5 190 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N ALA 5 176 " --> pdb=" O SER 5 248 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N SER 5 248 " --> pdb=" O ALA 5 176 " (cutoff:3.500A) removed outlier: 11.704A pdb=" N TYR 5 178 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N GLU 5 246 " --> pdb=" O TYR 5 178 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '6' and resid 150 through 154 removed outlier: 3.641A pdb=" N ILE 6 151 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER 6 266 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '6' and resid 301 through 303 removed outlier: 3.714A pdb=" N GLY 6 292 " --> pdb=" O CYS 6 395 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS 6 395 " --> pdb=" O GLY 6 292 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '6' and resid 301 through 303 removed outlier: 3.660A pdb=" N GLN 6 357 " --> pdb=" O LEU 6 381 " (cutoff:3.500A) removed outlier: 14.186A pdb=" N THR 6 376 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ILE 6 452 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASP 6 378 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR 6 449 " --> pdb=" O ASP 6 406 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS 6 451 " --> pdb=" O VAL 6 404 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '7' and resid 78 through 79 Processing sheet with id=AC5, first strand: chain '7' and resid 376 through 377 removed outlier: 6.769A pdb=" N ASN 7 332 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE 7 244 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE 7 239 " --> pdb=" O GLY 7 353 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE 7 380 " --> pdb=" O THR 7 352 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '7' and resid 254 through 255 removed outlier: 3.770A pdb=" N SER 7 308 " --> pdb=" O ALA 7 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '7' and resid 259 through 261 removed outlier: 4.830A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 491 through 496 removed outlier: 6.815A pdb=" N VAL E 502 " --> pdb=" O LEU E 494 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N MET E 496 " --> pdb=" O GLY E 500 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY E 500 " --> pdb=" O MET E 496 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR E 511 " --> pdb=" O ASP E 530 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR E 526 " --> pdb=" O VAL E 515 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 536 through 539 removed outlier: 3.905A pdb=" N LEU E 536 " --> pdb=" O GLY E 547 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 553 through 556 removed outlier: 3.782A pdb=" N LYS E 568 " --> pdb=" O ILE E 554 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP E 566 " --> pdb=" O TYR E 556 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 578 through 582 removed outlier: 3.597A pdb=" N SER E 580 " --> pdb=" O GLY E 591 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL E 588 " --> pdb=" O PHE E 600 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 615 through 620 removed outlier: 6.775A pdb=" N VAL E 628 " --> pdb=" O VAL E 616 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU E 618 " --> pdb=" O PHE E 626 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE E 626 " --> pdb=" O LEU E 618 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA E 620 " --> pdb=" O ARG E 624 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG E 624 " --> pdb=" O ALA E 620 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR E 638 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 652 " --> pdb=" O LEU E 640 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 686 through 689 removed outlier: 4.061A pdb=" N SER E 686 " --> pdb=" O PHE E 698 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE E 698 " --> pdb=" O SER E 686 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE E 688 " --> pdb=" O CYS E 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 707 through 708 removed outlier: 3.545A pdb=" N LYS E 717 " --> pdb=" O SER E 708 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 744 through 747 removed outlier: 7.263A pdb=" N ASN E 753 " --> pdb=" O LEU E 745 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU E 747 " --> pdb=" O THR E 751 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR E 751 " --> pdb=" O LEU E 747 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 491 through 496 removed outlier: 6.813A pdb=" N VAL F 502 " --> pdb=" O LEU F 494 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE F 528 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 526 " --> pdb=" O VAL F 515 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 536 through 539 removed outlier: 3.571A pdb=" N PHE F 546 " --> pdb=" O GLN F 555 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN F 555 " --> pdb=" O PHE F 546 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN F 553 " --> pdb=" O GLN F 548 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS F 568 " --> pdb=" O ILE F 554 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 578 through 583 removed outlier: 3.933A pdb=" N SER F 580 " --> pdb=" O GLY F 591 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY F 591 " --> pdb=" O SER F 580 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE F 589 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR F 592 " --> pdb=" O TYR F 596 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR F 596 " --> pdb=" O THR F 592 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU F 610 " --> pdb=" O PHE F 597 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 615 through 620 removed outlier: 3.617A pdb=" N ALA F 617 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR F 638 " --> pdb=" O ARG F 653 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG F 653 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU F 640 " --> pdb=" O TYR F 651 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 696 through 698 removed outlier: 3.550A pdb=" N ILE F 697 " --> pdb=" O LEU F 705 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 705 " --> pdb=" O ILE F 697 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 744 through 747 removed outlier: 4.463A pdb=" N ALA F 746 " --> pdb=" O AASN F 753 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N AASN F 753 " --> pdb=" O ALA F 746 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 491 through 496 removed outlier: 6.710A pdb=" N VAL G 502 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET G 496 " --> pdb=" O GLY G 500 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY G 500 " --> pdb=" O MET G 496 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR G 511 " --> pdb=" O ASP G 530 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE G 528 " --> pdb=" O ILE G 513 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 536 through 539 Processing sheet with id=AE6, first strand: chain 'G' and resid 578 through 583 removed outlier: 3.501A pdb=" N SER G 580 " --> pdb=" O GLY G 591 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 615 through 620 removed outlier: 3.925A pdb=" N ALA G 617 " --> pdb=" O VAL G 628 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 615 through 620 removed outlier: 3.925A pdb=" N ALA G 617 " --> pdb=" O VAL G 628 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 686 through 689 removed outlier: 3.773A pdb=" N ILE G 697 " --> pdb=" O LEU G 705 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 686 through 689 removed outlier: 3.773A pdb=" N ILE G 697 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU G 722 " --> pdb=" O LEU G 704 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 740 through 741 Processing sheet with id=AF3, first strand: chain 'G' and resid 744 through 747 removed outlier: 6.822A pdb=" N AASN G 753 " --> pdb=" O LEU G 745 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU G 747 " --> pdb=" O THR G 751 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR G 751 " --> pdb=" O LEU G 747 " (cutoff:3.500A) 821 hydrogen bonds defined for protein. 2278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.77 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10830 1.34 - 1.46: 7016 1.46 - 1.58: 16970 1.58 - 1.70: 0 1.70 - 1.82: 234 Bond restraints: 35050 Sorted by residual: bond pdb=" CA ASN 6 320 " pdb=" C ASN 6 320 " ideal model delta sigma weight residual 1.519 1.539 -0.020 5.30e-03 3.56e+04 1.46e+01 bond pdb=" C LEU D 76 " pdb=" N LEU D 77 " ideal model delta sigma weight residual 1.330 1.275 0.055 1.47e-02 4.63e+03 1.40e+01 bond pdb=" CA THR 3 325 " pdb=" C THR 3 325 " ideal model delta sigma weight residual 1.525 1.480 0.044 1.35e-02 5.49e+03 1.07e+01 bond pdb=" CA GLU D 221 " pdb=" C GLU D 221 " ideal model delta sigma weight residual 1.532 1.552 -0.020 6.50e-03 2.37e+04 9.34e+00 bond pdb=" N VAL 5 265 " pdb=" CA VAL 5 265 " ideal model delta sigma weight residual 1.468 1.432 0.036 1.22e-02 6.72e+03 8.57e+00 ... (remaining 35045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 47006 4.15 - 8.30: 376 8.30 - 12.44: 35 12.44 - 16.59: 9 16.59 - 20.74: 3 Bond angle restraints: 47429 Sorted by residual: angle pdb=" N ILE 5 45 " pdb=" CA ILE 5 45 " pdb=" C ILE 5 45 " ideal model delta sigma weight residual 110.62 127.79 -17.17 1.02e+00 9.61e-01 2.83e+02 angle pdb=" N ARG 4 373 " pdb=" CA ARG 4 373 " pdb=" C ARG 4 373 " ideal model delta sigma weight residual 111.02 90.28 20.74 1.25e+00 6.40e-01 2.75e+02 angle pdb=" N GLY 6 399 " pdb=" CA GLY 6 399 " pdb=" C GLY 6 399 " ideal model delta sigma weight residual 112.73 132.16 -19.43 1.20e+00 6.94e-01 2.62e+02 angle pdb=" CA THR 3 325 " pdb=" C THR 3 325 " pdb=" O THR 3 325 " ideal model delta sigma weight residual 119.95 105.72 14.23 1.18e+00 7.18e-01 1.46e+02 angle pdb=" N VAL 5 265 " pdb=" CA VAL 5 265 " pdb=" C VAL 5 265 " ideal model delta sigma weight residual 108.95 120.20 -11.25 9.80e-01 1.04e+00 1.32e+02 ... (remaining 47424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 18825 17.73 - 35.46: 2064 35.46 - 53.19: 348 53.19 - 70.93: 62 70.93 - 88.66: 22 Dihedral angle restraints: 21321 sinusoidal: 8723 harmonic: 12598 Sorted by residual: dihedral pdb=" CA LEU 2 411 " pdb=" C LEU 2 411 " pdb=" N ALA 2 412 " pdb=" CA ALA 2 412 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLN c 286 " pdb=" C GLN c 286 " pdb=" N VAL c 287 " pdb=" CA VAL c 287 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PRO D 254 " pdb=" C PRO D 254 " pdb=" N CYS D 255 " pdb=" CA CYS D 255 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 21318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5017 0.110 - 0.221: 304 0.221 - 0.331: 17 0.331 - 0.442: 3 0.442 - 0.552: 4 Chirality restraints: 5345 Sorted by residual: chirality pdb=" CA THR 3 187 " pdb=" N THR 3 187 " pdb=" C THR 3 187 " pdb=" CB THR 3 187 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CA PHE 5 44 " pdb=" N PHE 5 44 " pdb=" C PHE 5 44 " pdb=" CB PHE 5 44 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" CA GLU D 221 " pdb=" N GLU D 221 " pdb=" C GLU D 221 " pdb=" CB GLU D 221 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 5342 not shown) Planarity restraints: 6082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG 5 39 " 0.022 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C ARG 5 39 " -0.079 2.00e-02 2.50e+03 pdb=" O ARG 5 39 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU 5 40 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 7 93 " 0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C PHE 7 93 " -0.071 2.00e-02 2.50e+03 pdb=" O PHE 7 93 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU 7 94 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE 2 331 " 0.065 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO 2 332 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO 2 332 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO 2 332 " 0.053 5.00e-02 4.00e+02 ... (remaining 6079 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 333 2.59 - 3.17: 26408 3.17 - 3.74: 48308 3.74 - 4.32: 64891 4.32 - 4.90: 105962 Nonbonded interactions: 245902 Sorted by model distance: nonbonded pdb=" OD1 ASP 4 294 " pdb=" N GLU 4 295 " model vdw 2.011 3.120 nonbonded pdb=" OE2 GLU B 105 " pdb=" OG SER B 113 " model vdw 2.011 3.040 nonbonded pdb=" C LEU 3 278 " pdb=" OD1 ASP 3 279 " model vdw 2.018 3.270 nonbonded pdb=" O GLU 4 372 " pdb=" O ARG 4 373 " model vdw 2.020 3.040 nonbonded pdb=" O ALA 6 307 " pdb=" O VAL 6 318 " model vdw 2.079 3.040 ... (remaining 245897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 474 through 752 or resid 754 through 923)) selection = (chain 'F' and (resid 474 through 663 or resid 671 through 752 or resid 754 thro \ ugh 923)) selection = (chain 'G' and (resid 474 through 752 or resid 754 through 790 or resid 814 thro \ ugh 923)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.35 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: 1.430 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: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.960 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 35051 Z= 0.363 Angle : 1.123 20.740 47431 Z= 0.671 Chirality : 0.061 0.552 5345 Planarity : 0.007 0.098 6082 Dihedral : 14.872 88.658 13140 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.63 % Favored : 89.15 % Rotamer: Outliers : 0.39 % Allowed : 10.24 % Favored : 89.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.53 % 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: -5.32 (0.10), residues: 4200 helix: -4.58 (0.06), residues: 1200 sheet: -2.73 (0.19), residues: 673 loop : -3.25 (0.10), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 3 24 TYR 0.028 0.002 TYR D 201 PHE 0.024 0.002 PHE A 189 TRP 0.021 0.002 TRP B 92 HIS 0.008 0.001 HIS 4 413 Details of bonding type rmsd covalent geometry : bond 0.00765 (35050) covalent geometry : angle 1.12303 (47429) SS BOND : bond 0.00602 ( 1) SS BOND : angle 0.76177 ( 2) hydrogen bonds : bond 0.33278 ( 800) hydrogen bonds : angle 10.64028 ( 2278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 600 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 TYR cc_start: 0.8916 (t80) cc_final: 0.8505 (t80) REVERT: C 5 ASP cc_start: 0.8392 (t0) cc_final: 0.7865 (t0) REVERT: C 8 ASP cc_start: 0.8253 (m-30) cc_final: 0.7759 (m-30) REVERT: C 82 THR cc_start: 0.9065 (m) cc_final: 0.8857 (m) REVERT: C 113 MET cc_start: 0.8042 (mmm) cc_final: 0.7747 (mtt) REVERT: C 117 GLU cc_start: 0.8354 (tt0) cc_final: 0.7973 (tt0) REVERT: C 171 GLU cc_start: 0.8688 (tp30) cc_final: 0.7997 (tp30) REVERT: D 126 LEU cc_start: 0.9180 (mt) cc_final: 0.8959 (tp) REVERT: D 207 GLN cc_start: 0.7007 (mt0) cc_final: 0.6806 (pm20) REVERT: c 127 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7615 (mmm-85) REVERT: c 267 LEU cc_start: 0.9051 (tp) cc_final: 0.8847 (tp) REVERT: 2 224 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7843 (ptp-170) REVERT: 2 276 MET cc_start: 0.8396 (tpt) cc_final: 0.8143 (tpp) REVERT: 2 293 ILE cc_start: 0.8745 (mp) cc_final: 0.8323 (mm) REVERT: 3 30 GLU cc_start: 0.8759 (mp0) cc_final: 0.8517 (mp0) REVERT: 3 205 LYS cc_start: 0.8659 (tmmt) cc_final: 0.8234 (ttpt) REVERT: 3 275 ASP cc_start: 0.8272 (p0) cc_final: 0.8067 (p0) REVERT: 3 320 LEU cc_start: 0.8958 (mt) cc_final: 0.8744 (mp) REVERT: 3 325 THR cc_start: 0.8717 (p) cc_final: 0.8429 (t) REVERT: 4 421 ASP cc_start: 0.8731 (p0) cc_final: 0.8362 (p0) REVERT: 5 287 ILE cc_start: 0.9231 (mt) cc_final: 0.8947 (pt) REVERT: 6 413 PRO cc_start: 0.5647 (Cg_endo) cc_final: 0.5412 (Cg_exo) REVERT: 7 66 MET cc_start: 0.8783 (ttp) cc_final: 0.8517 (ptm) REVERT: 7 360 TYR cc_start: 0.5507 (t80) cc_final: 0.4439 (t80) REVERT: E 661 LEU cc_start: 0.8927 (mt) cc_final: 0.8515 (mt) REVERT: E 704 LEU cc_start: 0.9240 (tp) cc_final: 0.8981 (tt) REVERT: E 726 MET cc_start: 0.8658 (tpt) cc_final: 0.8437 (tpp) REVERT: E 851 GLU cc_start: 0.7555 (mp0) cc_final: 0.6854 (mp0) REVERT: E 852 ASN cc_start: 0.8930 (m-40) cc_final: 0.8687 (p0) REVERT: F 496 MET cc_start: 0.8462 (ttm) cc_final: 0.8169 (mtt) REVERT: F 655 CYS cc_start: 0.8711 (m) cc_final: 0.8360 (m) REVERT: G 679 PHE cc_start: 0.8924 (t80) cc_final: 0.8564 (t80) outliers start: 13 outliers final: 4 residues processed: 610 average time/residue: 0.2422 time to fit residues: 230.5395 Evaluate side-chains 388 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 384 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 7 residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 90 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN c 70 HIS c 133 ASN c 254 GLN c 266 ASN ** c 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 248 HIS 2 340 ASN 2 433 ASN 4 240 ASN 4 354 HIS 5 49 GLN 5 254 GLN 5 284 ASN 6 173 GLN 6 274 HIS 6 357 GLN 7 89 GLN 7 150 ASN E 877 GLN E 916 ASN F 507 ASN F 553 GLN F 877 GLN F 915 ASN G 553 GLN ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 680 ASN ** G 753 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.116691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.086738 restraints weight = 173492.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089369 restraints weight = 78398.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.092164 restraints weight = 49410.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092041 restraints weight = 44346.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.091972 restraints weight = 34833.021| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35051 Z= 0.152 Angle : 0.694 10.734 47431 Z= 0.365 Chirality : 0.045 0.205 5345 Planarity : 0.005 0.072 6082 Dihedral : 6.231 40.947 4671 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.04 % Favored : 91.94 % Rotamer: Outliers : 1.91 % Allowed : 14.93 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (0.11), residues: 4200 helix: -3.38 (0.10), residues: 1257 sheet: -2.06 (0.19), residues: 690 loop : -2.96 (0.11), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 504 TYR 0.025 0.002 TYR A 89 PHE 0.020 0.001 PHE F 597 TRP 0.013 0.001 TRP 6 356 HIS 0.006 0.001 HIS 3 201 Details of bonding type rmsd covalent geometry : bond 0.00335 (35050) covalent geometry : angle 0.69356 (47429) SS BOND : bond 0.00037 ( 1) SS BOND : angle 1.15004 ( 2) hydrogen bonds : bond 0.05877 ( 800) hydrogen bonds : angle 6.61299 ( 2278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 445 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8659 (t80) cc_final: 0.8408 (t80) REVERT: B 26 LYS cc_start: 0.8927 (mttt) cc_final: 0.8508 (mtpp) REVERT: B 162 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.6215 (t80) REVERT: C 5 ASP cc_start: 0.8216 (t0) cc_final: 0.7595 (t0) REVERT: C 8 ASP cc_start: 0.8138 (m-30) cc_final: 0.7221 (m-30) REVERT: C 23 ASP cc_start: 0.8004 (m-30) cc_final: 0.7683 (m-30) REVERT: C 117 GLU cc_start: 0.8044 (tt0) cc_final: 0.7746 (tt0) REVERT: C 171 GLU cc_start: 0.8544 (tp30) cc_final: 0.8064 (tp30) REVERT: D 134 GLU cc_start: 0.7747 (mp0) cc_final: 0.7459 (mp0) REVERT: c 127 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: c 129 TRP cc_start: 0.5379 (OUTLIER) cc_final: 0.4650 (m-90) REVERT: c 629 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8685 (mt) REVERT: 2 267 MET cc_start: 0.8752 (tpp) cc_final: 0.8487 (tpp) REVERT: 2 272 ASP cc_start: 0.7544 (m-30) cc_final: 0.7336 (m-30) REVERT: 2 276 MET cc_start: 0.8264 (tpt) cc_final: 0.7908 (tpt) REVERT: 2 293 ILE cc_start: 0.8639 (mp) cc_final: 0.8333 (mm) REVERT: 3 261 MET cc_start: 0.8113 (ttm) cc_final: 0.7702 (mtt) REVERT: 3 320 LEU cc_start: 0.8828 (mt) cc_final: 0.8616 (mp) REVERT: 4 194 PHE cc_start: 0.8661 (t80) cc_final: 0.8356 (t80) REVERT: 4 354 HIS cc_start: 0.7493 (t-170) cc_final: 0.7232 (t70) REVERT: 4 421 ASP cc_start: 0.8627 (p0) cc_final: 0.8253 (p0) REVERT: 5 82 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7393 (pp20) REVERT: 6 347 ASN cc_start: 0.7678 (m-40) cc_final: 0.7402 (t0) REVERT: 7 1 MET cc_start: 0.1794 (ptt) cc_final: 0.0257 (ptp) REVERT: 7 360 TYR cc_start: 0.5217 (t80) cc_final: 0.4134 (t80) REVERT: E 530 ASP cc_start: 0.7651 (t0) cc_final: 0.7435 (t70) REVERT: E 661 LEU cc_start: 0.8838 (mt) cc_final: 0.8591 (mt) REVERT: E 704 LEU cc_start: 0.9336 (tp) cc_final: 0.9123 (tt) REVERT: E 852 ASN cc_start: 0.8900 (m-40) cc_final: 0.8584 (p0) REVERT: F 726 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8003 (tpt) REVERT: G 618 LEU cc_start: 0.9287 (mt) cc_final: 0.9037 (mt) REVERT: G 679 PHE cc_start: 0.8935 (t80) cc_final: 0.8555 (t80) REVERT: G 821 MET cc_start: 0.7125 (tpp) cc_final: 0.6857 (tpp) REVERT: G 824 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8098 (tm-30) outliers start: 73 outliers final: 33 residues processed: 496 average time/residue: 0.2110 time to fit residues: 175.6063 Evaluate side-chains 413 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 374 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain c residue 129 TRP Chi-restraints excluded: chain c residue 142 CYS Chi-restraints excluded: chain c residue 310 VAL Chi-restraints excluded: chain c residue 413 LEU Chi-restraints excluded: chain c residue 580 LEU Chi-restraints excluded: chain c residue 629 ILE Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 2 residue 348 LEU Chi-restraints excluded: chain 2 residue 444 PHE Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 355 THR Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 43 GLN Chi-restraints excluded: chain 5 residue 82 GLU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 173 GLN Chi-restraints excluded: chain 6 residue 273 VAL Chi-restraints excluded: chain 6 residue 395 CYS Chi-restraints excluded: chain 7 residue 83 ASP Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain E residue 686 SER Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain F residue 726 MET Chi-restraints excluded: chain G residue 824 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 235 optimal weight: 1.9990 chunk 412 optimal weight: 0.0770 chunk 407 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 394 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 69 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 overall best weight: 1.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 340 ASN ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 559 HIS ** G 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 702 ASN ** G 753 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.114846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.086939 restraints weight = 143342.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.088582 restraints weight = 73502.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.089392 restraints weight = 51807.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.089665 restraints weight = 55063.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.089842 restraints weight = 44771.760| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35051 Z= 0.133 Angle : 0.640 11.219 47431 Z= 0.330 Chirality : 0.044 0.188 5345 Planarity : 0.005 0.060 6082 Dihedral : 5.625 39.379 4667 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.80 % Favored : 91.18 % Rotamer: Outliers : 2.28 % Allowed : 16.21 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.12), residues: 4200 helix: -2.61 (0.12), residues: 1248 sheet: -1.81 (0.20), residues: 694 loop : -2.72 (0.12), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 6 360 TYR 0.024 0.001 TYR 6 305 PHE 0.017 0.001 PHE 5 44 TRP 0.025 0.001 TRP B 119 HIS 0.018 0.001 HIS 4 413 Details of bonding type rmsd covalent geometry : bond 0.00303 (35050) covalent geometry : angle 0.63973 (47429) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.88849 ( 2) hydrogen bonds : bond 0.04709 ( 800) hydrogen bonds : angle 5.85519 ( 2278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 398 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8715 (t80) cc_final: 0.8503 (t80) REVERT: A 110 MET cc_start: 0.6053 (mmm) cc_final: 0.5704 (mmp) REVERT: A 181 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7610 (m-10) REVERT: B 17 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: B 162 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.6256 (t80) REVERT: C 5 ASP cc_start: 0.8304 (t0) cc_final: 0.7676 (t0) REVERT: C 8 ASP cc_start: 0.8292 (m-30) cc_final: 0.7385 (m-30) REVERT: C 23 ASP cc_start: 0.8198 (m-30) cc_final: 0.7902 (m-30) REVERT: C 117 GLU cc_start: 0.8228 (tt0) cc_final: 0.7851 (tt0) REVERT: C 171 GLU cc_start: 0.8395 (tp30) cc_final: 0.8162 (tp30) REVERT: D 84 MET cc_start: 0.8523 (ttm) cc_final: 0.8315 (ttm) REVERT: D 207 GLN cc_start: 0.7467 (mt0) cc_final: 0.6944 (mm-40) REVERT: c 127 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7581 (mmm-85) REVERT: c 129 TRP cc_start: 0.5372 (OUTLIER) cc_final: 0.4582 (m-90) REVERT: c 465 LYS cc_start: 0.8496 (mttt) cc_final: 0.7961 (tptt) REVERT: 2 272 ASP cc_start: 0.7382 (m-30) cc_final: 0.7153 (m-30) REVERT: 2 276 MET cc_start: 0.8374 (tpt) cc_final: 0.8019 (tpt) REVERT: 2 293 ILE cc_start: 0.8615 (mp) cc_final: 0.8309 (mm) REVERT: 3 260 GLU cc_start: 0.8073 (pm20) cc_final: 0.7507 (pm20) REVERT: 4 233 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7655 (tpt) REVERT: 4 354 HIS cc_start: 0.7547 (t-170) cc_final: 0.7269 (t70) REVERT: 4 421 ASP cc_start: 0.8681 (p0) cc_final: 0.8227 (p0) REVERT: 5 82 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7395 (pp20) REVERT: 5 336 ASP cc_start: 0.7787 (p0) cc_final: 0.7400 (p0) REVERT: 7 26 VAL cc_start: 0.8079 (t) cc_final: 0.7535 (m) REVERT: 7 360 TYR cc_start: 0.5225 (t80) cc_final: 0.4253 (t80) REVERT: E 704 LEU cc_start: 0.9287 (tp) cc_final: 0.9075 (tt) REVERT: E 839 ASP cc_start: 0.8631 (p0) cc_final: 0.8097 (p0) REVERT: E 883 LEU cc_start: 0.9201 (tp) cc_final: 0.8793 (pp) REVERT: F 603 PHE cc_start: 0.7827 (m-80) cc_final: 0.6836 (m-80) REVERT: F 726 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7978 (tpt) REVERT: G 618 LEU cc_start: 0.9280 (mt) cc_final: 0.9031 (mt) REVERT: G 679 PHE cc_start: 0.8916 (t80) cc_final: 0.8587 (t80) REVERT: G 821 MET cc_start: 0.7213 (tpp) cc_final: 0.6502 (tpp) REVERT: G 880 GLU cc_start: 0.3593 (tm-30) cc_final: 0.2108 (mt-10) outliers start: 87 outliers final: 42 residues processed: 459 average time/residue: 0.2035 time to fit residues: 159.0896 Evaluate side-chains 394 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 345 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain c residue 129 TRP Chi-restraints excluded: chain c residue 142 CYS Chi-restraints excluded: chain c residue 262 ILE Chi-restraints excluded: chain c residue 310 VAL Chi-restraints excluded: chain c residue 413 LEU Chi-restraints excluded: chain c residue 536 LEU Chi-restraints excluded: chain c residue 556 CYS Chi-restraints excluded: chain c residue 580 LEU Chi-restraints excluded: chain c residue 629 ILE Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 417 VAL Chi-restraints excluded: chain 2 residue 444 PHE Chi-restraints excluded: chain 3 residue 33 ASP Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 4 residue 233 MET Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 5 residue 43 GLN Chi-restraints excluded: chain 5 residue 82 GLU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 333 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 273 VAL Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain F residue 726 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 271 optimal weight: 4.9990 chunk 335 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 263 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 69 optimal weight: 0.0010 chunk 358 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 414 optimal weight: 8.9990 overall best weight: 1.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 173 GLN 6 347 ASN F 507 ASN ** G 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.108599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.075752 restraints weight = 154352.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.079130 restraints weight = 74176.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080752 restraints weight = 47307.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081662 restraints weight = 34656.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082026 restraints weight = 31263.429| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35051 Z= 0.128 Angle : 0.622 14.171 47431 Z= 0.319 Chirality : 0.043 0.164 5345 Planarity : 0.004 0.056 6082 Dihedral : 5.361 37.963 4667 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.66 % Favored : 91.32 % Rotamer: Outliers : 2.65 % Allowed : 17.42 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.12), residues: 4200 helix: -2.17 (0.13), residues: 1254 sheet: -1.62 (0.20), residues: 670 loop : -2.58 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 587 TYR 0.026 0.001 TYR 6 305 PHE 0.025 0.001 PHE F 597 TRP 0.024 0.001 TRP B 119 HIS 0.005 0.001 HIS c 231 Details of bonding type rmsd covalent geometry : bond 0.00296 (35050) covalent geometry : angle 0.62239 (47429) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.82944 ( 2) hydrogen bonds : bond 0.03985 ( 800) hydrogen bonds : angle 5.50795 ( 2278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 368 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.5595 (mmm) cc_final: 0.5230 (mmm) REVERT: A 181 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: B 17 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: B 70 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7980 (mm-30) REVERT: B 162 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.6461 (t80) REVERT: C 5 ASP cc_start: 0.8380 (t0) cc_final: 0.7480 (t70) REVERT: C 8 ASP cc_start: 0.8332 (m-30) cc_final: 0.7614 (m-30) REVERT: C 18 CYS cc_start: 0.8895 (m) cc_final: 0.8576 (m) REVERT: C 117 GLU cc_start: 0.8401 (tt0) cc_final: 0.8001 (tt0) REVERT: D 84 MET cc_start: 0.8557 (ttm) cc_final: 0.8306 (ttm) REVERT: D 202 MET cc_start: 0.6938 (ttp) cc_final: 0.6019 (ttp) REVERT: D 207 GLN cc_start: 0.7336 (mt0) cc_final: 0.6885 (mm-40) REVERT: D 289 ASP cc_start: 0.8184 (t70) cc_final: 0.7699 (t70) REVERT: c 127 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7636 (mmm-85) REVERT: c 129 TRP cc_start: 0.5345 (OUTLIER) cc_final: 0.4560 (m-90) REVERT: c 375 GLU cc_start: 0.7999 (tt0) cc_final: 0.7749 (tt0) REVERT: c 465 LYS cc_start: 0.8438 (mttt) cc_final: 0.8004 (tptt) REVERT: 2 272 ASP cc_start: 0.7379 (m-30) cc_final: 0.7160 (m-30) REVERT: 2 276 MET cc_start: 0.8394 (tpt) cc_final: 0.8032 (tpt) REVERT: 2 293 ILE cc_start: 0.8563 (mp) cc_final: 0.8279 (mm) REVERT: 3 202 TYR cc_start: 0.8433 (t80) cc_final: 0.8129 (t80) REVERT: 3 260 GLU cc_start: 0.7951 (pm20) cc_final: 0.7321 (pm20) REVERT: 4 188 GLN cc_start: 0.8119 (mt0) cc_final: 0.7734 (pp30) REVERT: 4 233 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7857 (tpt) REVERT: 4 342 MET cc_start: 0.8574 (mmm) cc_final: 0.8286 (mmt) REVERT: 4 421 ASP cc_start: 0.8685 (p0) cc_final: 0.8420 (p0) REVERT: 5 336 ASP cc_start: 0.7697 (p0) cc_final: 0.7387 (p0) REVERT: 7 1 MET cc_start: 0.1324 (ptt) cc_final: 0.0891 (pmm) REVERT: 7 64 MET cc_start: 0.8792 (mmm) cc_final: 0.8440 (mmm) REVERT: 7 360 TYR cc_start: 0.5186 (t80) cc_final: 0.4281 (t80) REVERT: E 573 GLN cc_start: 0.8328 (mp10) cc_final: 0.8023 (mp10) REVERT: E 704 LEU cc_start: 0.9275 (tp) cc_final: 0.9034 (tt) REVERT: E 883 LEU cc_start: 0.9224 (tp) cc_final: 0.8832 (pp) REVERT: F 477 MET cc_start: 0.8428 (mmp) cc_final: 0.8162 (mmm) REVERT: F 496 MET cc_start: 0.8358 (mtm) cc_final: 0.7846 (mpp) REVERT: G 618 LEU cc_start: 0.9286 (mt) cc_final: 0.9064 (mt) REVERT: G 821 MET cc_start: 0.6885 (tpp) cc_final: 0.6386 (tpp) outliers start: 101 outliers final: 54 residues processed: 441 average time/residue: 0.1949 time to fit residues: 147.7227 Evaluate side-chains 397 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 338 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 129 TRP Chi-restraints excluded: chain c residue 142 CYS Chi-restraints excluded: chain c residue 310 VAL Chi-restraints excluded: chain c residue 392 PHE Chi-restraints excluded: chain c residue 413 LEU Chi-restraints excluded: chain c residue 536 LEU Chi-restraints excluded: chain c residue 556 CYS Chi-restraints excluded: chain c residue 580 LEU Chi-restraints excluded: chain c residue 629 ILE Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 328 THR Chi-restraints excluded: chain 2 residue 417 VAL Chi-restraints excluded: chain 2 residue 444 PHE Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 258 VAL Chi-restraints excluded: chain 4 residue 233 MET Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 333 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 173 GLN Chi-restraints excluded: chain 6 residue 273 VAL Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 659 MET Chi-restraints excluded: chain E residue 697 ILE Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain F residue 655 CYS Chi-restraints excluded: chain G residue 634 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 344 optimal weight: 5.9990 chunk 414 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 317 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 ASN G 510 GLN ** G 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 891 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.107328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.074751 restraints weight = 144318.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078507 restraints weight = 74226.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.079582 restraints weight = 43645.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080273 restraints weight = 33454.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080481 restraints weight = 33015.373| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35051 Z= 0.173 Angle : 0.647 14.424 47431 Z= 0.330 Chirality : 0.044 0.204 5345 Planarity : 0.004 0.056 6082 Dihedral : 5.338 38.726 4667 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.12 % Allowed : 18.39 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.12), residues: 4200 helix: -1.85 (0.13), residues: 1258 sheet: -1.58 (0.20), residues: 687 loop : -2.51 (0.12), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 4 388 TYR 0.027 0.001 TYR 6 305 PHE 0.022 0.001 PHE 5 44 TRP 0.025 0.001 TRP B 119 HIS 0.005 0.001 HIS c 231 Details of bonding type rmsd covalent geometry : bond 0.00399 (35050) covalent geometry : angle 0.64749 (47429) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.61012 ( 2) hydrogen bonds : bond 0.03942 ( 800) hydrogen bonds : angle 5.39934 ( 2278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 356 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7662 (m-10) REVERT: A 183 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8115 (tt) REVERT: B 17 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: B 32 THR cc_start: 0.8070 (p) cc_final: 0.7852 (p) REVERT: B 162 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.6572 (t80) REVERT: C 5 ASP cc_start: 0.8408 (t0) cc_final: 0.7484 (t70) REVERT: C 8 ASP cc_start: 0.8463 (m-30) cc_final: 0.7777 (m-30) REVERT: C 18 CYS cc_start: 0.8953 (m) cc_final: 0.8620 (m) REVERT: C 23 ASP cc_start: 0.8239 (m-30) cc_final: 0.7993 (m-30) REVERT: C 117 GLU cc_start: 0.8401 (tt0) cc_final: 0.8004 (tt0) REVERT: D 289 ASP cc_start: 0.8249 (t70) cc_final: 0.7807 (t70) REVERT: c 127 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7931 (mtp180) REVERT: c 129 TRP cc_start: 0.5379 (OUTLIER) cc_final: 0.4509 (m-90) REVERT: c 465 LYS cc_start: 0.8446 (mttt) cc_final: 0.8006 (tptt) REVERT: 2 276 MET cc_start: 0.8417 (tpt) cc_final: 0.8018 (tpt) REVERT: 2 293 ILE cc_start: 0.8545 (mp) cc_final: 0.8153 (mm) REVERT: 2 340 ASN cc_start: 0.9141 (t0) cc_final: 0.8738 (t0) REVERT: 3 260 GLU cc_start: 0.8001 (pm20) cc_final: 0.7675 (pm20) REVERT: 3 306 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8141 (mmm) REVERT: 4 188 GLN cc_start: 0.8186 (mt0) cc_final: 0.7794 (pp30) REVERT: 4 233 MET cc_start: 0.8424 (tpt) cc_final: 0.7815 (tpt) REVERT: 4 342 MET cc_start: 0.8553 (mmm) cc_final: 0.8287 (mmt) REVERT: 4 356 MET cc_start: 0.7030 (ppp) cc_final: 0.6289 (tmm) REVERT: 4 421 ASP cc_start: 0.8692 (p0) cc_final: 0.8413 (p0) REVERT: 4 442 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8599 (tp) REVERT: 5 43 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7815 (pp30) REVERT: 7 1 MET cc_start: 0.1367 (ptt) cc_final: 0.0991 (pmm) REVERT: 7 64 MET cc_start: 0.8920 (mmm) cc_final: 0.8596 (mmm) REVERT: 7 150 ASN cc_start: 0.7208 (t160) cc_final: 0.6949 (t0) REVERT: 7 331 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8522 (tt) REVERT: 7 360 TYR cc_start: 0.5250 (t80) cc_final: 0.4357 (t80) REVERT: E 573 GLN cc_start: 0.8512 (mp10) cc_final: 0.8191 (mp10) REVERT: E 704 LEU cc_start: 0.9275 (tp) cc_final: 0.9040 (tt) REVERT: F 477 MET cc_start: 0.8416 (mmp) cc_final: 0.8200 (mmm) REVERT: F 496 MET cc_start: 0.8392 (mtm) cc_final: 0.8015 (mpp) REVERT: G 618 LEU cc_start: 0.9330 (mt) cc_final: 0.9091 (mt) REVERT: G 821 MET cc_start: 0.7040 (tpp) cc_final: 0.6522 (tpp) outliers start: 119 outliers final: 81 residues processed: 437 average time/residue: 0.1830 time to fit residues: 138.7332 Evaluate side-chains 421 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 331 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 129 TRP Chi-restraints excluded: chain c residue 142 CYS Chi-restraints excluded: chain c residue 152 LEU Chi-restraints excluded: chain c residue 262 ILE Chi-restraints excluded: chain c residue 310 VAL Chi-restraints excluded: chain c residue 392 PHE Chi-restraints excluded: chain c residue 413 LEU Chi-restraints excluded: chain c residue 419 ILE Chi-restraints excluded: chain c residue 536 LEU Chi-restraints excluded: chain c residue 556 CYS Chi-restraints excluded: chain c residue 580 LEU Chi-restraints excluded: chain c residue 629 ILE Chi-restraints excluded: chain c residue 632 ILE Chi-restraints excluded: chain 2 residue 211 LEU Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 328 THR Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 417 VAL Chi-restraints excluded: chain 2 residue 444 PHE Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 161 PHE Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 258 VAL Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 280 ASP Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 306 MET Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 43 GLN Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 265 VAL Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 333 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 273 VAL Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 412 LEU Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 215 TYR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 331 LEU Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 686 SER Chi-restraints excluded: chain E residue 697 ILE Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain F residue 513 ILE Chi-restraints excluded: chain F residue 655 CYS Chi-restraints excluded: chain F residue 704 LEU Chi-restraints excluded: chain G residue 634 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 347 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 355 optimal weight: 5.9990 chunk 368 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 120 optimal weight: 0.1980 chunk 370 optimal weight: 0.2980 chunk 248 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 139 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 196 ASN 6 173 GLN 7 384 HIS E 540 ASN F 507 ASN G 510 GLN ** G 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 891 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.108431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.078106 restraints weight = 169299.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080078 restraints weight = 82338.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080907 restraints weight = 52575.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081685 restraints weight = 44612.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.081998 restraints weight = 39408.521| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35051 Z= 0.117 Angle : 0.612 13.528 47431 Z= 0.312 Chirality : 0.043 0.191 5345 Planarity : 0.004 0.054 6082 Dihedral : 5.097 35.593 4667 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.49 % Allowed : 19.70 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.96 (0.12), residues: 4200 helix: -1.57 (0.14), residues: 1264 sheet: -1.40 (0.20), residues: 685 loop : -2.42 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 587 TYR 0.029 0.001 TYR 6 305 PHE 0.031 0.001 PHE G 679 TRP 0.019 0.001 TRP B 119 HIS 0.005 0.001 HIS c 231 Details of bonding type rmsd covalent geometry : bond 0.00274 (35050) covalent geometry : angle 0.61215 (47429) SS BOND : bond 0.00014 ( 1) SS BOND : angle 0.66469 ( 2) hydrogen bonds : bond 0.03503 ( 800) hydrogen bonds : angle 5.13009 ( 2278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 358 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7645 (m-10) REVERT: B 162 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6630 (t80) REVERT: C 5 ASP cc_start: 0.8408 (t0) cc_final: 0.7491 (t70) REVERT: C 8 ASP cc_start: 0.8443 (m-30) cc_final: 0.7800 (m-30) REVERT: C 18 CYS cc_start: 0.8977 (m) cc_final: 0.8653 (m) REVERT: C 23 ASP cc_start: 0.8258 (m-30) cc_final: 0.8021 (m-30) REVERT: C 117 GLU cc_start: 0.8485 (tt0) cc_final: 0.8105 (tt0) REVERT: D 202 MET cc_start: 0.7169 (ttp) cc_final: 0.6295 (ttp) REVERT: D 207 GLN cc_start: 0.7504 (mt0) cc_final: 0.7055 (mm-40) REVERT: D 289 ASP cc_start: 0.8247 (t70) cc_final: 0.7905 (t70) REVERT: c 127 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7727 (mtp180) REVERT: c 129 TRP cc_start: 0.5317 (OUTLIER) cc_final: 0.4446 (m-90) REVERT: c 465 LYS cc_start: 0.8421 (mttt) cc_final: 0.7930 (tptt) REVERT: 2 272 ASP cc_start: 0.7454 (m-30) cc_final: 0.7193 (m-30) REVERT: 2 276 MET cc_start: 0.8329 (tpt) cc_final: 0.7951 (tpt) REVERT: 2 293 ILE cc_start: 0.8480 (mp) cc_final: 0.8261 (mm) REVERT: 2 340 ASN cc_start: 0.9101 (t0) cc_final: 0.8703 (t0) REVERT: 3 221 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8170 (mm) REVERT: 3 260 GLU cc_start: 0.8048 (pm20) cc_final: 0.7692 (pm20) REVERT: 3 306 MET cc_start: 0.8860 (mmm) cc_final: 0.8070 (mmm) REVERT: 4 188 GLN cc_start: 0.8185 (mt0) cc_final: 0.7801 (pp30) REVERT: 4 233 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7935 (tpt) REVERT: 4 342 MET cc_start: 0.8498 (mmm) cc_final: 0.8248 (mmt) REVERT: 4 421 ASP cc_start: 0.8670 (p0) cc_final: 0.8454 (p0) REVERT: 4 442 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8600 (tp) REVERT: 5 43 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7687 (pp30) REVERT: 7 1 MET cc_start: 0.1315 (ptt) cc_final: 0.1028 (pmm) REVERT: 7 64 MET cc_start: 0.9065 (mmm) cc_final: 0.8708 (mmm) REVERT: 7 360 TYR cc_start: 0.5183 (t80) cc_final: 0.4298 (t80) REVERT: E 573 GLN cc_start: 0.8595 (mp10) cc_final: 0.8141 (mp10) REVERT: E 704 LEU cc_start: 0.9305 (tp) cc_final: 0.9070 (tt) REVERT: E 883 LEU cc_start: 0.9212 (tp) cc_final: 0.8823 (pp) REVERT: F 496 MET cc_start: 0.8350 (mtm) cc_final: 0.7971 (mpp) REVERT: G 679 PHE cc_start: 0.8986 (t80) cc_final: 0.8723 (t80) REVERT: G 729 TRP cc_start: 0.7781 (t-100) cc_final: 0.7496 (t-100) REVERT: G 821 MET cc_start: 0.7111 (tpp) cc_final: 0.6606 (tpp) outliers start: 95 outliers final: 67 residues processed: 427 average time/residue: 0.1853 time to fit residues: 137.3476 Evaluate side-chains 414 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 340 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 129 TRP Chi-restraints excluded: chain c residue 142 CYS Chi-restraints excluded: chain c residue 165 LEU Chi-restraints excluded: chain c residue 262 ILE Chi-restraints excluded: chain c residue 310 VAL Chi-restraints excluded: chain c residue 392 PHE Chi-restraints excluded: chain c residue 413 LEU Chi-restraints excluded: chain c residue 496 ILE Chi-restraints excluded: chain c residue 536 LEU Chi-restraints excluded: chain c residue 556 CYS Chi-restraints excluded: chain c residue 580 LEU Chi-restraints excluded: chain c residue 629 ILE Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 328 THR Chi-restraints excluded: chain 2 residue 444 PHE Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 161 PHE Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 200 VAL Chi-restraints excluded: chain 3 residue 221 LEU Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 258 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 4 residue 233 MET Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 43 GLN Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 265 VAL Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 333 ILE Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 173 GLN Chi-restraints excluded: chain 6 residue 273 VAL Chi-restraints excluded: chain 6 residue 395 CYS Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 215 TYR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain G residue 634 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 325 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 340 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 334 HIS G 510 GLN G 553 GLN ** G 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.108073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.078374 restraints weight = 185102.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.079849 restraints weight = 87286.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.081096 restraints weight = 58396.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081743 restraints weight = 48064.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.082254 restraints weight = 42682.350| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35051 Z= 0.133 Angle : 0.620 13.272 47431 Z= 0.313 Chirality : 0.043 0.180 5345 Planarity : 0.004 0.055 6082 Dihedral : 5.007 36.150 4667 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 3.06 % Allowed : 19.51 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.78 (0.13), residues: 4200 helix: -1.33 (0.14), residues: 1267 sheet: -1.37 (0.20), residues: 693 loop : -2.34 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 587 TYR 0.029 0.001 TYR 6 305 PHE 0.029 0.001 PHE G 679 TRP 0.016 0.001 TRP B 119 HIS 0.005 0.001 HIS c 231 Details of bonding type rmsd covalent geometry : bond 0.00309 (35050) covalent geometry : angle 0.61956 (47429) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.54370 ( 2) hydrogen bonds : bond 0.03416 ( 800) hydrogen bonds : angle 5.06243 ( 2278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 358 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: B 162 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6707 (t80) REVERT: C 5 ASP cc_start: 0.8413 (t0) cc_final: 0.7632 (t70) REVERT: C 8 ASP cc_start: 0.8421 (m-30) cc_final: 0.7821 (m-30) REVERT: C 18 CYS cc_start: 0.8956 (m) cc_final: 0.8654 (m) REVERT: C 23 ASP cc_start: 0.8284 (m-30) cc_final: 0.8036 (m-30) REVERT: C 117 GLU cc_start: 0.8454 (tt0) cc_final: 0.8081 (tt0) REVERT: D 289 ASP cc_start: 0.8239 (t70) cc_final: 0.7952 (t70) REVERT: c 127 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7591 (mtp180) REVERT: c 129 TRP cc_start: 0.5275 (OUTLIER) cc_final: 0.4446 (m-90) REVERT: c 234 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: c 465 LYS cc_start: 0.8431 (mttt) cc_final: 0.8024 (tptt) REVERT: 2 272 ASP cc_start: 0.7443 (m-30) cc_final: 0.7165 (m-30) REVERT: 2 276 MET cc_start: 0.8324 (tpt) cc_final: 0.7953 (tpt) REVERT: 2 292 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6432 (mm-30) REVERT: 2 293 ILE cc_start: 0.8461 (mp) cc_final: 0.8248 (mm) REVERT: 2 340 ASN cc_start: 0.9058 (t0) cc_final: 0.8632 (t0) REVERT: 3 221 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8137 (mm) REVERT: 3 260 GLU cc_start: 0.8068 (pm20) cc_final: 0.7708 (pm20) REVERT: 3 279 ASP cc_start: 0.8496 (p0) cc_final: 0.7982 (p0) REVERT: 3 306 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8089 (mmm) REVERT: 4 188 GLN cc_start: 0.8172 (mt0) cc_final: 0.7807 (pp30) REVERT: 4 233 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7951 (tpt) REVERT: 4 342 MET cc_start: 0.8465 (mmm) cc_final: 0.8236 (mmt) REVERT: 4 421 ASP cc_start: 0.8661 (p0) cc_final: 0.8457 (p0) REVERT: 4 442 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8607 (tp) REVERT: 5 43 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7821 (pp30) REVERT: 6 174 TYR cc_start: 0.8854 (t80) cc_final: 0.8622 (t80) REVERT: 7 1 MET cc_start: 0.1293 (ptt) cc_final: 0.1005 (pmm) REVERT: 7 64 MET cc_start: 0.9072 (mmm) cc_final: 0.8687 (mmm) REVERT: 7 360 TYR cc_start: 0.5191 (t80) cc_final: 0.4427 (t80) REVERT: E 573 GLN cc_start: 0.8592 (mp10) cc_final: 0.8158 (mp10) REVERT: E 704 LEU cc_start: 0.9271 (tp) cc_final: 0.9057 (tt) REVERT: E 754 CYS cc_start: 0.8280 (t) cc_final: 0.7965 (p) REVERT: F 496 MET cc_start: 0.8291 (mtm) cc_final: 0.7995 (mpp) REVERT: G 679 PHE cc_start: 0.8991 (t80) cc_final: 0.8721 (t80) REVERT: G 729 TRP cc_start: 0.7810 (t-100) cc_final: 0.7520 (t-100) REVERT: G 821 MET cc_start: 0.7189 (tpp) cc_final: 0.6684 (tpp) REVERT: G 880 GLU cc_start: 0.3307 (tm-30) cc_final: 0.2538 (mt-10) outliers start: 117 outliers final: 87 residues processed: 442 average time/residue: 0.1938 time to fit residues: 148.2057 Evaluate side-chains 441 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 345 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 129 TRP Chi-restraints excluded: chain c residue 142 CYS Chi-restraints excluded: chain c residue 165 LEU Chi-restraints excluded: chain c residue 234 GLU Chi-restraints excluded: chain c residue 310 VAL Chi-restraints excluded: chain c residue 392 PHE Chi-restraints excluded: chain c residue 413 LEU Chi-restraints excluded: chain c residue 419 ILE Chi-restraints excluded: chain c residue 496 ILE Chi-restraints excluded: chain c residue 536 LEU Chi-restraints excluded: chain c residue 546 LEU Chi-restraints excluded: chain c residue 556 CYS Chi-restraints excluded: chain c residue 580 LEU Chi-restraints excluded: chain c residue 629 ILE Chi-restraints excluded: chain 2 residue 211 LEU Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 328 THR Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 444 PHE Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 161 PHE Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 182 VAL Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 200 VAL Chi-restraints excluded: chain 3 residue 221 LEU Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 258 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 306 MET Chi-restraints excluded: chain 4 residue 233 MET Chi-restraints excluded: chain 4 residue 298 THR Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 43 GLN Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 265 VAL Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 333 ILE Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 273 VAL Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 7 residue 196 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 215 TYR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 659 MET Chi-restraints excluded: chain E residue 697 ILE Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain F residue 513 ILE Chi-restraints excluded: chain F residue 704 LEU Chi-restraints excluded: chain G residue 537 CYS Chi-restraints excluded: chain G residue 634 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 392 optimal weight: 8.9990 chunk 306 optimal weight: 2.9990 chunk 235 optimal weight: 0.7980 chunk 260 optimal weight: 7.9990 chunk 381 optimal weight: 0.0770 chunk 268 optimal weight: 0.0370 chunk 178 optimal weight: 20.0000 chunk 171 optimal weight: 0.5980 chunk 315 optimal weight: 0.0170 chunk 185 optimal weight: 8.9990 chunk 387 optimal weight: 7.9990 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 179 ASN D 82 GLN D 217 ASN ** c 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 173 GLN G 510 GLN ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 887 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.110107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.077736 restraints weight = 180192.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082086 restraints weight = 83528.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083383 restraints weight = 41968.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083441 restraints weight = 35568.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.083651 restraints weight = 34266.696| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 35051 Z= 0.101 Angle : 0.602 12.627 47431 Z= 0.303 Chirality : 0.042 0.224 5345 Planarity : 0.004 0.053 6082 Dihedral : 4.717 31.911 4667 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.44 % Allowed : 20.35 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.56 (0.13), residues: 4200 helix: -1.13 (0.14), residues: 1265 sheet: -1.18 (0.20), residues: 690 loop : -2.25 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 587 TYR 0.032 0.001 TYR 6 305 PHE 0.028 0.001 PHE G 679 TRP 0.016 0.001 TRP B 119 HIS 0.005 0.001 HIS c 231 Details of bonding type rmsd covalent geometry : bond 0.00233 (35050) covalent geometry : angle 0.60230 (47429) SS BOND : bond 0.00007 ( 1) SS BOND : angle 0.70279 ( 2) hydrogen bonds : bond 0.02985 ( 800) hydrogen bonds : angle 4.79258 ( 2278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 383 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7549 (tpp) cc_final: 0.7311 (tpp) REVERT: A 183 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7982 (tt) REVERT: B 134 PHE cc_start: 0.8650 (m-80) cc_final: 0.8408 (m-80) REVERT: C 5 ASP cc_start: 0.8568 (t0) cc_final: 0.7691 (t70) REVERT: C 8 ASP cc_start: 0.8443 (m-30) cc_final: 0.7939 (m-30) REVERT: D 289 ASP cc_start: 0.8373 (t70) cc_final: 0.8138 (t70) REVERT: c 127 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7618 (mtp180) REVERT: c 129 TRP cc_start: 0.5368 (OUTLIER) cc_final: 0.4482 (m-90) REVERT: c 234 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: 2 276 MET cc_start: 0.8263 (tpt) cc_final: 0.7882 (tpt) REVERT: 2 293 ILE cc_start: 0.8495 (mp) cc_final: 0.7849 (mm) REVERT: 2 340 ASN cc_start: 0.9007 (t0) cc_final: 0.8374 (t0) REVERT: 3 221 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8129 (mm) REVERT: 3 260 GLU cc_start: 0.8041 (pm20) cc_final: 0.7672 (pm20) REVERT: 3 306 MET cc_start: 0.8846 (mmm) cc_final: 0.8133 (mmm) REVERT: 4 188 GLN cc_start: 0.8169 (mt0) cc_final: 0.7774 (pp30) REVERT: 4 233 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7935 (tpt) REVERT: 4 342 MET cc_start: 0.8611 (mmm) cc_final: 0.8355 (mmt) REVERT: 4 354 HIS cc_start: 0.6962 (t70) cc_final: 0.6646 (t70) REVERT: 4 442 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8587 (tp) REVERT: 5 43 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7782 (pp30) REVERT: 6 387 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7602 (tm-30) REVERT: 7 1 MET cc_start: 0.1399 (ptt) cc_final: 0.1108 (pmm) REVERT: 7 64 MET cc_start: 0.9138 (mmm) cc_final: 0.8795 (mmm) REVERT: 7 360 TYR cc_start: 0.5123 (t80) cc_final: 0.4362 (t80) REVERT: E 704 LEU cc_start: 0.9252 (tp) cc_final: 0.8994 (tt) REVERT: E 754 CYS cc_start: 0.8113 (t) cc_final: 0.7889 (p) REVERT: E 883 LEU cc_start: 0.9209 (tp) cc_final: 0.8792 (pp) REVERT: F 496 MET cc_start: 0.8439 (mtm) cc_final: 0.7994 (mpp) REVERT: F 603 PHE cc_start: 0.8132 (m-10) cc_final: 0.7188 (m-10) REVERT: F 848 TYR cc_start: 0.7335 (m-10) cc_final: 0.7106 (m-10) REVERT: G 496 MET cc_start: 0.7614 (ttm) cc_final: 0.7373 (mtt) REVERT: G 535 ASP cc_start: 0.8431 (p0) cc_final: 0.7680 (t0) REVERT: G 679 PHE cc_start: 0.8966 (t80) cc_final: 0.8719 (t80) REVERT: G 729 TRP cc_start: 0.7722 (t-100) cc_final: 0.7454 (t-100) REVERT: G 821 MET cc_start: 0.7028 (tpp) cc_final: 0.6511 (tpp) REVERT: G 880 GLU cc_start: 0.3613 (tm-30) cc_final: 0.2671 (mt-10) outliers start: 93 outliers final: 62 residues processed: 448 average time/residue: 0.1909 time to fit residues: 147.2890 Evaluate side-chains 419 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 350 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 129 TRP Chi-restraints excluded: chain c residue 142 CYS Chi-restraints excluded: chain c residue 165 LEU Chi-restraints excluded: chain c residue 234 GLU Chi-restraints excluded: chain c residue 310 VAL Chi-restraints excluded: chain c residue 392 PHE Chi-restraints excluded: chain c residue 413 LEU Chi-restraints excluded: chain c residue 536 LEU Chi-restraints excluded: chain c residue 546 LEU Chi-restraints excluded: chain c residue 629 ILE Chi-restraints excluded: chain 2 residue 211 LEU Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 444 PHE Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 161 PHE Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 182 VAL Chi-restraints excluded: chain 3 residue 221 LEU Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 258 VAL Chi-restraints excluded: chain 3 residue 263 GLU Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 4 residue 233 MET Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 43 GLN Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 265 VAL Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 173 GLN Chi-restraints excluded: chain 6 residue 273 VAL Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 418 SER Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 7 residue 196 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 215 TYR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 686 SER Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain G residue 537 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 229 optimal weight: 0.0870 chunk 399 optimal weight: 0.0870 chunk 297 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 335 optimal weight: 10.0000 chunk 383 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 277 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 128 ASN B 179 ASN C 41 ASN C 86 ASN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 510 GLN ** G 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 790 ASN ** G 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.108454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075943 restraints weight = 149681.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079968 restraints weight = 77023.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.080838 restraints weight = 42848.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081631 restraints weight = 34223.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081778 restraints weight = 32100.286| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35051 Z= 0.138 Angle : 0.630 13.888 47431 Z= 0.317 Chirality : 0.044 0.180 5345 Planarity : 0.004 0.054 6082 Dihedral : 4.757 34.485 4667 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.36 % Allowed : 20.87 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.46 (0.13), residues: 4200 helix: -0.97 (0.15), residues: 1266 sheet: -1.22 (0.20), residues: 704 loop : -2.20 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 4 315 TYR 0.032 0.001 TYR 6 305 PHE 0.028 0.001 PHE G 679 TRP 0.026 0.001 TRP B 119 HIS 0.005 0.001 HIS c 231 Details of bonding type rmsd covalent geometry : bond 0.00321 (35050) covalent geometry : angle 0.63024 (47429) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.47196 ( 2) hydrogen bonds : bond 0.03263 ( 800) hydrogen bonds : angle 4.84108 ( 2278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 354 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7979 (tt) REVERT: B 32 THR cc_start: 0.7964 (p) cc_final: 0.7739 (p) REVERT: C 5 ASP cc_start: 0.8570 (t0) cc_final: 0.7775 (t70) REVERT: C 8 ASP cc_start: 0.8463 (m-30) cc_final: 0.7915 (m-30) REVERT: D 289 ASP cc_start: 0.8519 (t70) cc_final: 0.8254 (t70) REVERT: c 127 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7663 (mtp180) REVERT: c 234 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: c 465 LYS cc_start: 0.8374 (mttt) cc_final: 0.8006 (tptt) REVERT: c 607 MET cc_start: 0.8032 (mtm) cc_final: 0.7745 (mtt) REVERT: 2 340 ASN cc_start: 0.9023 (t0) cc_final: 0.8483 (t0) REVERT: 3 221 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8106 (mm) REVERT: 3 260 GLU cc_start: 0.8026 (pm20) cc_final: 0.7641 (pm20) REVERT: 3 306 MET cc_start: 0.8880 (mmm) cc_final: 0.8153 (mmm) REVERT: 4 188 GLN cc_start: 0.8200 (mt0) cc_final: 0.7810 (pp30) REVERT: 4 233 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7964 (tpt) REVERT: 4 342 MET cc_start: 0.8546 (mmm) cc_final: 0.8270 (mmt) REVERT: 4 354 HIS cc_start: 0.7062 (t70) cc_final: 0.6759 (t70) REVERT: 4 442 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8618 (tp) REVERT: 5 43 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7827 (pp30) REVERT: 7 1 MET cc_start: 0.1404 (ptt) cc_final: 0.1099 (pmm) REVERT: 7 64 MET cc_start: 0.9140 (mmm) cc_final: 0.8769 (mmm) REVERT: 7 360 TYR cc_start: 0.5163 (t80) cc_final: 0.4370 (t80) REVERT: E 704 LEU cc_start: 0.9259 (tp) cc_final: 0.9024 (tt) REVERT: F 496 MET cc_start: 0.8410 (mtm) cc_final: 0.8003 (mpp) REVERT: F 603 PHE cc_start: 0.8139 (m-10) cc_final: 0.7172 (m-10) REVERT: F 726 MET cc_start: 0.8481 (tpt) cc_final: 0.8013 (tpt) REVERT: G 535 ASP cc_start: 0.8444 (p0) cc_final: 0.7713 (t0) REVERT: G 632 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8511 (tm-30) REVERT: G 679 PHE cc_start: 0.8938 (t80) cc_final: 0.8694 (t80) REVERT: G 729 TRP cc_start: 0.7799 (t-100) cc_final: 0.7525 (t-100) REVERT: G 821 MET cc_start: 0.7012 (tpp) cc_final: 0.6701 (tpp) REVERT: G 880 GLU cc_start: 0.3588 (tm-30) cc_final: 0.2535 (mt-10) outliers start: 91 outliers final: 67 residues processed: 416 average time/residue: 0.1884 time to fit residues: 135.8857 Evaluate side-chains 415 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 342 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 142 CYS Chi-restraints excluded: chain c residue 165 LEU Chi-restraints excluded: chain c residue 234 GLU Chi-restraints excluded: chain c residue 310 VAL Chi-restraints excluded: chain c residue 392 PHE Chi-restraints excluded: chain c residue 413 LEU Chi-restraints excluded: chain c residue 419 ILE Chi-restraints excluded: chain c residue 536 LEU Chi-restraints excluded: chain c residue 629 ILE Chi-restraints excluded: chain 2 residue 211 LEU Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 444 PHE Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 161 PHE Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 182 VAL Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 221 LEU Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 258 VAL Chi-restraints excluded: chain 3 residue 263 GLU Chi-restraints excluded: chain 4 residue 233 MET Chi-restraints excluded: chain 4 residue 298 THR Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 43 GLN Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 265 VAL Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 333 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 6 residue 273 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 418 SER Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 7 residue 196 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 215 TYR Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 659 MET Chi-restraints excluded: chain E residue 686 SER Chi-restraints excluded: chain E residue 697 ILE Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain F residue 513 ILE Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 537 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 53 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 268 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 361 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 297 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN C 41 ASN ** c 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 173 GLN ** 6 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 510 GLN ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 887 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.109825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.077390 restraints weight = 148351.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081662 restraints weight = 75272.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082572 restraints weight = 41888.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.083261 restraints weight = 32693.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083441 restraints weight = 32022.570| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 35051 Z= 0.108 Angle : 0.630 15.010 47431 Z= 0.315 Chirality : 0.043 0.208 5345 Planarity : 0.004 0.054 6082 Dihedral : 4.624 30.834 4667 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.07 % Allowed : 21.14 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.34 (0.13), residues: 4200 helix: -0.85 (0.15), residues: 1265 sheet: -1.07 (0.20), residues: 692 loop : -2.17 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 4 315 TYR 0.032 0.001 TYR 6 305 PHE 0.027 0.001 PHE G 679 TRP 0.037 0.001 TRP c 129 HIS 0.005 0.001 HIS c 231 Details of bonding type rmsd covalent geometry : bond 0.00254 (35050) covalent geometry : angle 0.62961 (47429) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.63789 ( 2) hydrogen bonds : bond 0.03085 ( 800) hydrogen bonds : angle 4.70972 ( 2278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 358 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.7892 (tt) REVERT: B 32 THR cc_start: 0.7902 (p) cc_final: 0.7692 (p) REVERT: C 5 ASP cc_start: 0.8518 (t0) cc_final: 0.7680 (t70) REVERT: C 8 ASP cc_start: 0.8452 (m-30) cc_final: 0.7923 (m-30) REVERT: D 289 ASP cc_start: 0.8498 (t70) cc_final: 0.8253 (t70) REVERT: c 127 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.7941 (mtp180) REVERT: c 234 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: c 607 MET cc_start: 0.8047 (mtm) cc_final: 0.7847 (mtt) REVERT: 2 340 ASN cc_start: 0.8945 (t0) cc_final: 0.8430 (t0) REVERT: 3 221 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8152 (mm) REVERT: 3 260 GLU cc_start: 0.8009 (pm20) cc_final: 0.7668 (pm20) REVERT: 3 306 MET cc_start: 0.8851 (mmm) cc_final: 0.8142 (mmm) REVERT: 4 188 GLN cc_start: 0.8198 (mt0) cc_final: 0.7808 (pp30) REVERT: 4 233 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7950 (tpt) REVERT: 4 342 MET cc_start: 0.8590 (mmm) cc_final: 0.8296 (mmt) REVERT: 4 354 HIS cc_start: 0.6905 (t70) cc_final: 0.6599 (t70) REVERT: 4 356 MET cc_start: 0.7766 (ppp) cc_final: 0.7426 (ppp) REVERT: 4 421 ASP cc_start: 0.8812 (p0) cc_final: 0.8425 (p0) REVERT: 4 442 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8608 (tp) REVERT: 5 43 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7811 (pp30) REVERT: 6 387 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7577 (tm-30) REVERT: 7 1 MET cc_start: 0.1340 (ptt) cc_final: 0.1078 (pmm) REVERT: 7 64 MET cc_start: 0.9122 (mmm) cc_final: 0.8776 (mmm) REVERT: 7 360 TYR cc_start: 0.5137 (t80) cc_final: 0.4392 (t80) REVERT: E 508 SER cc_start: 0.7627 (m) cc_final: 0.7296 (p) REVERT: E 704 LEU cc_start: 0.9235 (tp) cc_final: 0.9001 (tt) REVERT: E 883 LEU cc_start: 0.9174 (tp) cc_final: 0.8832 (pp) REVERT: F 496 MET cc_start: 0.8420 (mtm) cc_final: 0.8021 (mpp) REVERT: F 603 PHE cc_start: 0.8115 (m-10) cc_final: 0.7155 (m-10) REVERT: F 726 MET cc_start: 0.8395 (tpt) cc_final: 0.7928 (tpt) REVERT: G 496 MET cc_start: 0.7579 (ttm) cc_final: 0.7344 (mtt) REVERT: G 530 ASP cc_start: 0.7307 (t0) cc_final: 0.7001 (t0) REVERT: G 535 ASP cc_start: 0.8303 (p0) cc_final: 0.7700 (t0) REVERT: G 632 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8493 (tm-30) REVERT: G 679 PHE cc_start: 0.8907 (t80) cc_final: 0.8687 (t80) REVERT: G 729 TRP cc_start: 0.7776 (t-100) cc_final: 0.7496 (t-100) REVERT: G 821 MET cc_start: 0.7009 (tpp) cc_final: 0.6493 (tpp) REVERT: G 880 GLU cc_start: 0.3644 (tm-30) cc_final: 0.2636 (mt-10) outliers start: 80 outliers final: 64 residues processed: 414 average time/residue: 0.1908 time to fit residues: 136.0100 Evaluate side-chains 413 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 343 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 142 CYS Chi-restraints excluded: chain c residue 165 LEU Chi-restraints excluded: chain c residue 234 GLU Chi-restraints excluded: chain c residue 310 VAL Chi-restraints excluded: chain c residue 392 PHE Chi-restraints excluded: chain c residue 413 LEU Chi-restraints excluded: chain c residue 419 ILE Chi-restraints excluded: chain c residue 536 LEU Chi-restraints excluded: chain c residue 629 ILE Chi-restraints excluded: chain 2 residue 211 LEU Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 444 PHE Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 161 PHE Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 182 VAL Chi-restraints excluded: chain 3 residue 221 LEU Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 258 VAL Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 4 residue 233 MET Chi-restraints excluded: chain 4 residue 298 THR Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 43 GLN Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 265 VAL Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 333 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 173 GLN Chi-restraints excluded: chain 6 residue 273 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 412 LEU Chi-restraints excluded: chain 6 residue 418 SER Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 215 TYR Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 659 MET Chi-restraints excluded: chain E residue 686 SER Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain F residue 513 ILE Chi-restraints excluded: chain G residue 537 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 293 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 127 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 360 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 887 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.109669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079980 restraints weight = 156683.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081853 restraints weight = 76884.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.082695 restraints weight = 50747.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082986 restraints weight = 47300.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.083372 restraints weight = 40913.572| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.185 35051 Z= 0.149 Angle : 0.717 59.169 47431 Z= 0.383 Chirality : 0.048 1.614 5345 Planarity : 0.004 0.055 6082 Dihedral : 4.623 30.863 4667 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.91 % Allowed : 21.48 % Favored : 76.61 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.53 % 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: -2.34 (0.13), residues: 4200 helix: -0.85 (0.15), residues: 1265 sheet: -1.06 (0.20), residues: 692 loop : -2.17 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.000 ARG 4 451 TYR 0.030 0.001 TYR 6 305 PHE 0.026 0.001 PHE G 679 TRP 0.050 0.001 TRP 3 111 HIS 0.006 0.001 HIS c 231 Details of bonding type rmsd covalent geometry : bond 0.00329 (35050) covalent geometry : angle 0.71685 (47429) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.60945 ( 2) hydrogen bonds : bond 0.03120 ( 800) hydrogen bonds : angle 4.74178 ( 2278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7418.24 seconds wall clock time: 128 minutes 11.22 seconds (7691.22 seconds total)