Starting phenix.real_space_refine on Tue Sep 15 15:37:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u0m_20607/09_2026/6u0m_20607.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u0m_20607/09_2026/6u0m_20607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u0m_20607/09_2026/6u0m_20607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u0m_20607/09_2026/6u0m_20607.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6u0m_20607/09_2026/6u0m_20607.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u0m_20607/09_2026/6u0m_20607.cif" model { file = "/net/cci-nas-00/data/ceres_data/6u0m_20607/09_2026/6u0m_20607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u0m_20607/09_2026/6u0m_20607.cif" } resolution = 3.9 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= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 43 5.49 5 S 177 5.16 5 C 25863 2.51 5 N 7150 2.21 5 O 7913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41146 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1690 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 204} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1507 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1820 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 2 Chain: "E" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4472 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 537} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "2" Number of atoms: 4957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4957 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 23, 'TRANS': 610} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 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': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "3" Number of atoms: 4653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4653 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 569} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "4" Number of atoms: 5404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5404 Classifications: {'peptide': 681} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 22, 'TRANS': 658} Chain breaks: 6 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: 4663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4663 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 24, 'TRANS': 572} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "6" Number of atoms: 4691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4691 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 21, 'TRANS': 592} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "7" Number of atoms: 5212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5212 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 632} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 472 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 224 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.35, per 1000 atoms: 0.20 Number of scatterers: 41146 At special positions: 0 Unit cell: (186.876, 182.58, 139.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 177 16.00 P 43 15.00 O 7913 8.00 N 7150 7.00 C 25863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 2.0 seconds 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9726 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 44 sheets defined 38.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 3 through 24 removed outlier: 3.787A pdb=" N ASN A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 58 removed outlier: 3.867A pdb=" N ASN A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 54 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 95 removed outlier: 3.501A pdb=" N CYS A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 127 through 145 removed outlier: 4.019A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.659A pdb=" N GLN A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.709A pdb=" N ILE B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.740A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.726A pdb=" N TYR B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 105' Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.770A pdb=" N ARG B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 161 removed outlier: 3.924A pdb=" N ASP B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU B 148 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 157 " --> pdb=" O GLN B 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 158 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 198 removed outlier: 3.705A pdb=" N ARG B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 3.526A pdb=" N THR B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.202A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 86 through 91 removed outlier: 4.047A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 4.169A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 removed outlier: 3.666A pdb=" N ALA C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 124' Processing helix chain 'C' and resid 124 through 138 removed outlier: 4.382A pdb=" N LEU C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS C 137 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 173 through 192 removed outlier: 4.703A pdb=" N LYS C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 184 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 188 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 69 removed outlier: 3.715A pdb=" N ASP D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU D 63 " --> pdb=" O ASP D 59 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 80 through 107 removed outlier: 3.691A pdb=" N MET D 84 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 102 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE D 105 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 152 removed outlier: 3.894A pdb=" N LEU D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 133 " --> pdb=" O MET D 129 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG D 147 " --> pdb=" O TYR D 143 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 164 removed outlier: 4.340A pdb=" N ASP D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 195 removed outlier: 4.110A pdb=" N ILE D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 194 " --> pdb=" O TRP D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 4.092A pdb=" N TYR D 201 " --> pdb=" O ILE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 removed outlier: 3.754A pdb=" N LEU D 286 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 287 " --> pdb=" O ASP D 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 283 through 287' Processing helix chain 'E' and resid 7 through 19 removed outlier: 3.664A pdb=" N ALA E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR E 12 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 51 removed outlier: 3.671A pdb=" N ALA E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET E 44 " --> pdb=" O CYS E 40 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 48 " --> pdb=" O MET E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.535A pdb=" N TYR E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.853A pdb=" N ILE E 134 " --> pdb=" O ASN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 157 removed outlier: 4.006A pdb=" N LYS E 156 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU E 157 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 221 removed outlier: 3.628A pdb=" N SER E 221 " --> pdb=" O ASN E 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 222 through 240 removed outlier: 3.518A pdb=" N VAL E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 removed outlier: 4.076A pdb=" N GLN E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE E 255 " --> pdb=" O ILE E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 4.206A pdb=" N ILE E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU E 275 " --> pdb=" O TRP E 271 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY E 276 " --> pdb=" O LEU E 272 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR E 277 " --> pdb=" O ASN E 273 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 302 removed outlier: 3.634A pdb=" N GLN E 296 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS E 300 " --> pdb=" O GLN E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 335 No H-bonds generated for 'chain 'E' and resid 333 through 335' Processing helix chain 'E' and resid 336 through 341 removed outlier: 3.935A pdb=" N TYR E 340 " --> pdb=" O ASP E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 347 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 380 through 392 removed outlier: 3.516A pdb=" N ILE E 384 " --> pdb=" O MET E 380 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG E 386 " --> pdb=" O HIS E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 400 removed outlier: 4.271A pdb=" N TYR E 399 " --> pdb=" O ASN E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 434 removed outlier: 3.550A pdb=" N LEU E 428 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 433 " --> pdb=" O THR E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 482 removed outlier: 4.553A pdb=" N ASN E 468 " --> pdb=" O GLN E 464 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG E 472 " --> pdb=" O ASN E 468 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL E 474 " --> pdb=" O ARG E 470 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER E 475 " --> pdb=" O LYS E 471 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP E 481 " --> pdb=" O PHE E 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 485 No H-bonds generated for 'chain 'E' and resid 483 through 485' Processing helix chain 'E' and resid 491 through 517 removed outlier: 3.576A pdb=" N GLY E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN E 500 " --> pdb=" O ILE E 496 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP E 501 " --> pdb=" O GLN E 497 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 502 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG E 504 " --> pdb=" O GLN E 500 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR E 509 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 510 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA E 512 " --> pdb=" O ASN E 508 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 541 removed outlier: 4.074A pdb=" N LEU E 538 " --> pdb=" O ASP E 535 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR E 539 " --> pdb=" O LEU E 536 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG E 540 " --> pdb=" O ASP E 537 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ASN E 541 " --> pdb=" O LEU E 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 535 through 541' Processing helix chain 'E' and resid 542 through 556 removed outlier: 3.509A pdb=" N LEU E 546 " --> pdb=" O PRO E 542 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG E 547 " --> pdb=" O LEU E 543 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU E 554 " --> pdb=" O ASN E 550 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS E 556 " --> pdb=" O LEU E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 578 removed outlier: 4.155A pdb=" N ASP E 577 " --> pdb=" O GLU E 574 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 578 " --> pdb=" O ASN E 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 574 through 578' Processing helix chain 'E' and resid 604 through 616 removed outlier: 3.872A pdb=" N ALA E 608 " --> pdb=" O ASN E 604 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN E 611 " --> pdb=" O MET E 607 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR E 616 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 643 removed outlier: 4.015A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix removed outlier: 3.926A pdb=" N GLU E 642 " --> pdb=" O SER E 638 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 643 " --> pdb=" O PRO E 639 " (cutoff:3.500A) Processing helix chain '2' and resid 202 through 217 removed outlier: 4.061A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA 2 208 " --> pdb=" O SER 2 204 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG 2 209 " --> pdb=" O ARG 2 205 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE 2 214 " --> pdb=" O GLU 2 210 " (cutoff:3.500A) Processing helix chain '2' and resid 226 through 237 removed outlier: 3.630A pdb=" N ILE 2 231 " --> pdb=" O TYR 2 227 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG 2 232 " --> pdb=" O GLY 2 228 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR 2 233 " --> pdb=" O ALA 2 229 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU 2 234 " --> pdb=" O ARG 2 230 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 252 Processing helix chain '2' and resid 256 through 260 Processing helix chain '2' and resid 265 through 281 removed outlier: 3.557A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA 2 275 " --> pdb=" O PHE 2 271 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET 2 276 " --> pdb=" O ASP 2 272 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU 2 277 " --> pdb=" O LEU 2 273 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU 2 281 " --> pdb=" O GLU 2 277 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 289 Processing helix chain '2' and resid 310 through 314 Processing helix chain '2' and resid 411 through 415 removed outlier: 3.937A pdb=" N VAL 2 415 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) Processing helix chain '2' and resid 493 through 498 removed outlier: 4.147A pdb=" N ILE 2 498 " --> pdb=" O ILE 2 494 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 removed outlier: 4.604A pdb=" N LYS 2 512 " --> pdb=" O HIS 2 508 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU 2 519 " --> pdb=" O VAL 2 515 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE 2 520 " --> pdb=" O ALA 2 516 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 560 removed outlier: 3.672A pdb=" N ILE 2 552 " --> pdb=" O ALA 2 548 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS 2 554 " --> pdb=" O SER 2 550 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 2 557 " --> pdb=" O LEU 2 553 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS 2 558 " --> pdb=" O LYS 2 554 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 removed outlier: 4.007A pdb=" N LEU 2 598 " --> pdb=" O GLY 2 594 " (cutoff:3.500A) Processing helix chain '2' and resid 609 through 617 removed outlier: 4.156A pdb=" N ASP 2 614 " --> pdb=" O ASP 2 610 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLN 2 615 " --> pdb=" O LYS 2 611 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG 2 617 " --> pdb=" O ASN 2 613 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 Processing helix chain '2' and resid 670 through 675 removed outlier: 3.836A pdb=" N LEU 2 674 " --> pdb=" O THR 2 670 " (cutoff:3.500A) Processing helix chain '2' and resid 689 through 703 removed outlier: 3.583A pdb=" N LEU 2 695 " --> pdb=" O ALA 2 691 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE 2 698 " --> pdb=" O ARG 2 694 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL 2 700 " --> pdb=" O ALA 2 696 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP 2 701 " --> pdb=" O THR 2 697 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER 2 702 " --> pdb=" O PHE 2 698 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS 2 703 " --> pdb=" O VAL 2 699 " (cutoff:3.500A) Processing helix chain '2' and resid 738 through 751 removed outlier: 3.568A pdb=" N LYS 2 750 " --> pdb=" O GLN 2 746 " (cutoff:3.500A) Processing helix chain '2' and resid 763 through 765 No H-bonds generated for 'chain '2' and resid 763 through 765' Processing helix chain '2' and resid 766 through 771 Processing helix chain '2' and resid 783 through 785 No H-bonds generated for 'chain '2' and resid 783 through 785' Processing helix chain '2' and resid 786 through 797 Processing helix chain '2' and resid 806 through 823 removed outlier: 4.249A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU 2 811 " --> pdb=" O VAL 2 807 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE 2 820 " --> pdb=" O ILE 2 816 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA 2 821 " --> pdb=" O ALA 2 817 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET 2 823 " --> pdb=" O SER 2 819 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 839 removed outlier: 3.934A pdb=" N ASP 2 835 " --> pdb=" O SER 2 831 " (cutoff:3.500A) Processing helix chain '2' and resid 841 through 847 Processing helix chain '2' and resid 856 through 861 removed outlier: 4.268A pdb=" N PHE 2 861 " --> pdb=" O LEU 2 857 " (cutoff:3.500A) Processing helix chain '3' and resid 21 through 31 Processing helix chain '3' and resid 38 through 48 removed outlier: 3.873A pdb=" N ARG 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN 3 46 " --> pdb=" O VAL 3 42 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR 3 48 " --> pdb=" O SER 3 44 " (cutoff:3.500A) Processing helix chain '3' and resid 48 through 53 Processing helix chain '3' and resid 99 through 105 removed outlier: 3.810A pdb=" N LEU 3 103 " --> pdb=" O SER 3 99 " (cutoff:3.500A) Processing helix chain '3' and resid 108 through 113 removed outlier: 3.674A pdb=" N GLY 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 114 through 116 No H-bonds generated for 'chain '3' and resid 114 through 116' Processing helix chain '3' and resid 121 through 135 removed outlier: 3.798A pdb=" N ALA 3 125 " --> pdb=" O PHE 3 121 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP 3 131 " --> pdb=" O LYS 3 127 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA 3 133 " --> pdb=" O LEU 3 129 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP 3 134 " --> pdb=" O THR 3 130 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER 3 135 " --> pdb=" O ASP 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 205 through 207 No H-bonds generated for 'chain '3' and resid 205 through 207' Processing helix chain '3' and resid 245 through 248 Processing helix chain '3' and resid 279 through 283 removed outlier: 3.781A pdb=" N VAL 3 283 " --> pdb=" O ASP 3 280 " (cutoff:3.500A) Processing helix chain '3' and resid 343 through 353 removed outlier: 3.537A pdb=" N ILE 3 347 " --> pdb=" O THR 3 343 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN 3 351 " --> pdb=" O ILE 3 347 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 366 removed outlier: 3.611A pdb=" N SER 3 364 " --> pdb=" O PHE 3 360 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN 3 365 " --> pdb=" O ASP 3 361 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 removed outlier: 4.073A pdb=" N LEU 3 382 " --> pdb=" O LYS 3 378 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET 3 386 " --> pdb=" O LEU 3 382 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY 3 387 " --> pdb=" O LEU 3 383 " (cutoff:3.500A) Processing helix chain '3' and resid 447 through 451 removed outlier: 4.284A pdb=" N GLU 3 451 " --> pdb=" O THR 3 448 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 492 removed outlier: 4.312A pdb=" N ARG 3 483 " --> pdb=" O THR 3 479 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL 3 484 " --> pdb=" O ASP 3 480 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS 3 487 " --> pdb=" O ARG 3 483 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET 3 490 " --> pdb=" O ILE 3 486 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 543 removed outlier: 3.776A pdb=" N LEU 3 540 " --> pdb=" O PRO 3 536 " (cutoff:3.500A) Processing helix chain '3' and resid 556 through 565 removed outlier: 3.766A pdb=" N GLU 3 563 " --> pdb=" O ARG 3 559 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS 3 564 " --> pdb=" O SER 3 560 " (cutoff:3.500A) Processing helix chain '3' and resid 652 through 661 Processing helix chain '3' and resid 674 through 688 removed outlier: 3.782A pdb=" N ILE 3 679 " --> pdb=" O ALA 3 675 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL 3 680 " --> pdb=" O ILE 3 676 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS 3 681 " --> pdb=" O ASN 3 677 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP 3 685 " --> pdb=" O LYS 3 681 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU 3 686 " --> pdb=" O ASN 3 682 " (cutoff:3.500A) Processing helix chain '3' and resid 700 through 717 removed outlier: 3.537A pdb=" N THR 3 704 " --> pdb=" O ARG 3 700 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA 3 709 " --> pdb=" O LEU 3 705 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG 3 716 " --> pdb=" O HIS 3 712 " (cutoff:3.500A) Processing helix chain '3' and resid 724 through 738 removed outlier: 3.876A pdb=" N VAL 3 728 " --> pdb=" O VAL 3 724 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA 3 729 " --> pdb=" O ASP 3 725 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA 3 730 " --> pdb=" O ALA 3 726 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU 3 733 " --> pdb=" O ALA 3 729 " (cutoff:3.500A) Processing helix chain '4' and resid 188 through 200 removed outlier: 3.782A pdb=" N THR 4 192 " --> pdb=" O GLN 4 188 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 235 removed outlier: 3.657A pdb=" N LYS 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN 4 231 " --> pdb=" O ILE 4 227 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG 4 234 " --> pdb=" O LEU 4 230 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 262 removed outlier: 3.768A pdb=" N LEU 4 262 " --> pdb=" O TYR 4 258 " (cutoff:3.500A) Processing helix chain '4' and resid 266 through 285 removed outlier: 4.332A pdb=" N GLN 4 274 " --> pdb=" O SER 4 270 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS 4 277 " --> pdb=" O ASP 4 273 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU 4 283 " --> pdb=" O CYS 4 279 " (cutoff:3.500A) Processing helix chain '4' and resid 290 through 294 removed outlier: 3.797A pdb=" N LEU 4 293 " --> pdb=" O ASP 4 290 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP 4 294 " --> pdb=" O TYR 4 291 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 290 through 294' Processing helix chain '4' and resid 503 through 515 Processing helix chain '4' and resid 517 through 526 removed outlier: 3.716A pdb=" N ILE 4 526 " --> pdb=" O LEU 4 522 " (cutoff:3.500A) Processing helix chain '4' and resid 535 through 545 removed outlier: 4.473A pdb=" N GLY 4 539 " --> pdb=" O ASP 4 535 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE 4 540 " --> pdb=" O VAL 4 536 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU 4 541 " --> pdb=" O LYS 4 537 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 removed outlier: 3.820A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 644 through 651 Processing helix chain '4' and resid 695 through 700 removed outlier: 3.646A pdb=" N LEU 4 699 " --> pdb=" O PRO 4 695 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER 4 700 " --> pdb=" O PRO 4 696 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 695 through 700' Processing helix chain '4' and resid 716 through 726 removed outlier: 3.508A pdb=" N LEU 4 724 " --> pdb=" O LEU 4 720 " (cutoff:3.500A) Processing helix chain '4' and resid 745 through 758 removed outlier: 3.796A pdb=" N ALA 4 754 " --> pdb=" O TYR 4 750 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLU 4 756 " --> pdb=" O SER 4 752 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS 4 757 " --> pdb=" O TYR 4 753 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE 4 758 " --> pdb=" O ALA 4 754 " (cutoff:3.500A) Processing helix chain '4' and resid 763 through 778 removed outlier: 4.292A pdb=" N LYS 4 767 " --> pdb=" O THR 4 763 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR 4 774 " --> pdb=" O LEU 4 770 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 812 removed outlier: 3.579A pdb=" N SER 4 800 " --> pdb=" O ARG 4 796 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET 4 801 " --> pdb=" O GLN 4 797 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE 4 802 " --> pdb=" O LEU 4 798 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG 4 803 " --> pdb=" O GLU 4 799 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA 4 807 " --> pdb=" O ARG 4 803 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) Processing helix chain '4' and resid 821 through 833 removed outlier: 4.152A pdb=" N ARG 4 827 " --> pdb=" O GLN 4 823 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) Processing helix chain '4' and resid 855 through 876 removed outlier: 3.793A pdb=" N GLU 4 863 " --> pdb=" O ARG 4 859 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP 4 864 " --> pdb=" O LYS 4 860 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU 4 868 " --> pdb=" O ASP 4 864 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 4 869 " --> pdb=" O LEU 4 865 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN 4 876 " --> pdb=" O VAL 4 872 " (cutoff:3.500A) Processing helix chain '4' and resid 882 through 893 removed outlier: 3.782A pdb=" N LYS 4 888 " --> pdb=" O ASN 4 884 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE 4 890 " --> pdb=" O LEU 4 886 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN 4 891 " --> pdb=" O ILE 4 887 " (cutoff:3.500A) Processing helix chain '4' and resid 904 through 912 removed outlier: 4.240A pdb=" N SER 4 908 " --> pdb=" O GLN 4 904 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG 4 909 " --> pdb=" O GLU 4 905 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU 4 910 " --> pdb=" O ALA 4 906 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN 4 912 " --> pdb=" O SER 4 908 " (cutoff:3.500A) Processing helix chain '5' and resid 25 through 33 removed outlier: 3.501A pdb=" N PHE 5 31 " --> pdb=" O ILE 5 27 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN 5 33 " --> pdb=" O LYS 5 29 " (cutoff:3.500A) Processing helix chain '5' and resid 46 through 51 Processing helix chain '5' and resid 52 through 54 No H-bonds generated for 'chain '5' and resid 52 through 54' Processing helix chain '5' and resid 64 through 69 removed outlier: 3.639A pdb=" N ILE 5 69 " --> pdb=" O MET 5 65 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 81 removed outlier: 3.636A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU 5 79 " --> pdb=" O ILE 5 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP 5 81 " --> pdb=" O LYS 5 77 " (cutoff:3.500A) Processing helix chain '5' and resid 85 through 101 Processing helix chain '5' and resid 279 through 283 Processing helix chain '5' and resid 351 through 362 removed outlier: 3.829A pdb=" N GLU 5 356 " --> pdb=" O GLU 5 352 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE 5 357 " --> pdb=" O GLU 5 353 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 374 removed outlier: 4.103A pdb=" N THR 5 371 " --> pdb=" O TYR 5 367 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN 5 372 " --> pdb=" O GLU 5 368 " (cutoff:3.500A) Processing helix chain '5' and resid 381 through 394 removed outlier: 3.906A pdb=" N ALA 5 387 " --> pdb=" O ASP 5 383 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS 5 390 " --> pdb=" O LYS 5 386 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET 5 393 " --> pdb=" O VAL 5 389 " (cutoff:3.500A) Processing helix chain '5' and resid 425 through 433 removed outlier: 3.573A pdb=" N VAL 5 429 " --> pdb=" O LEU 5 425 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU 5 430 " --> pdb=" O LEU 5 426 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS 5 431 " --> pdb=" O LYS 5 427 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL 5 432 " --> pdb=" O PHE 5 428 " (cutoff:3.500A) Processing helix chain '5' and resid 446 through 451 removed outlier: 4.138A pdb=" N THR 5 450 " --> pdb=" O ALA 5 446 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA 5 451 " --> pdb=" O ALA 5 447 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 446 through 451' Processing helix chain '5' and resid 488 through 494 removed outlier: 3.558A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS 5 494 " --> pdb=" O ARG 5 490 " (cutoff:3.500A) Processing helix chain '5' and resid 529 through 534 removed outlier: 3.913A pdb=" N LYS 5 534 " --> pdb=" O ASP 5 531 " (cutoff:3.500A) Processing helix chain '5' and resid 563 through 577 removed outlier: 4.087A pdb=" N SER 5 567 " --> pdb=" O GLU 5 563 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE 5 573 " --> pdb=" O ALA 5 569 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN 5 574 " --> pdb=" O ASN 5 570 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE 5 575 " --> pdb=" O HIS 5 571 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR 5 577 " --> pdb=" O ILE 5 573 " (cutoff:3.500A) Processing helix chain '5' and resid 580 through 585 Processing helix chain '5' and resid 595 through 608 removed outlier: 4.141A pdb=" N MET 5 599 " --> pdb=" O SER 5 595 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS 5 600 " --> pdb=" O ILE 5 596 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR 5 604 " --> pdb=" O LYS 5 600 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR 5 605 " --> pdb=" O ARG 5 601 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU 5 608 " --> pdb=" O THR 5 604 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 617 No H-bonds generated for 'chain '5' and resid 615 through 617' Processing helix chain '5' and resid 618 through 635 removed outlier: 3.953A pdb=" N LEU 5 622 " --> pdb=" O ALA 5 618 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER 5 623 " --> pdb=" O ALA 5 619 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL 5 627 " --> pdb=" O SER 5 623 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR 5 628 " --> pdb=" O SER 5 624 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE 5 629 " --> pdb=" O ASN 5 625 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS 5 631 " --> pdb=" O VAL 5 627 " (cutoff:3.500A) Processing helix chain '5' and resid 636 through 640 removed outlier: 3.689A pdb=" N SER 5 640 " --> pdb=" O GLU 5 637 " (cutoff:3.500A) Processing helix chain '5' and resid 652 through 668 removed outlier: 3.837A pdb=" N ILE 5 657 " --> pdb=" O LEU 5 653 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG 5 658 " --> pdb=" O GLU 5 654 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU 5 661 " --> pdb=" O ILE 5 657 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU 5 663 " --> pdb=" O ILE 5 659 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA 5 664 " --> pdb=" O THR 5 660 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 685 removed outlier: 4.030A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) Processing helix chain '5' and resid 686 through 692 removed outlier: 5.637A pdb=" N MET 5 689 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASP 5 690 " --> pdb=" O SER 5 687 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA 5 691 " --> pdb=" O THR 5 688 " (cutoff:3.500A) Processing helix chain '6' and resid 104 through 121 Processing helix chain '6' and resid 134 through 147 removed outlier: 3.921A pdb=" N ILE 6 145 " --> pdb=" O GLU 6 141 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 160 Processing helix chain '6' and resid 166 through 171 removed outlier: 3.721A pdb=" N SER 6 171 " --> pdb=" O ALA 6 167 " (cutoff:3.500A) Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix removed outlier: 3.989A pdb=" N GLN 6 182 " --> pdb=" O LEU 6 178 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS 6 183 " --> pdb=" O PRO 6 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY 6 184 " --> pdb=" O PHE 6 180 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG 6 190 " --> pdb=" O ARG 6 186 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS 6 191 " --> pdb=" O ARG 6 187 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 368 removed outlier: 3.773A pdb=" N GLU 6 367 " --> pdb=" O ASN 6 364 " (cutoff:3.500A) removed outlier: 3.792A 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 '6' and resid 433 through 437 removed outlier: 3.642A pdb=" N GLY 6 436 " --> pdb=" O LEU 6 433 " (cutoff:3.500A) Processing helix chain '6' and resid 511 through 520 removed outlier: 3.529A pdb=" N LEU 6 516 " --> pdb=" O GLU 6 512 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS 6 517 " --> pdb=" O ILE 6 513 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 531 removed outlier: 3.808A pdb=" N VAL 6 530 " --> pdb=" O TYR 6 526 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG 6 531 " --> pdb=" O ASP 6 527 " (cutoff:3.500A) Processing helix chain '6' and resid 540 through 552 removed outlier: 3.669A pdb=" N LYS 6 545 " --> pdb=" O GLU 6 541 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY 6 546 " --> pdb=" O ALA 6 542 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU 6 548 " --> pdb=" O LYS 6 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU 6 549 " --> pdb=" O LYS 6 545 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 592 removed outlier: 4.441A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL 6 589 " --> pdb=" O LEU 6 585 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY 6 590 " --> pdb=" O LYS 6 586 " (cutoff:3.500A) Processing helix chain '6' and resid 628 through 632 removed outlier: 3.621A pdb=" N ASP 6 632 " --> pdb=" O MET 6 629 " (cutoff:3.500A) Processing helix chain '6' and resid 647 through 658 removed outlier: 3.751A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS 6 653 " --> pdb=" O GLN 6 649 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU 6 657 " --> pdb=" O HIS 6 653 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN 6 658 " --> pdb=" O GLU 6 654 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 removed outlier: 4.204A pdb=" N ASN 6 698 " --> pdb=" O SER 6 694 " (cutoff:3.500A) Processing helix chain '6' and resid 703 through 709 Processing helix chain '6' and resid 722 through 736 removed outlier: 3.920A pdb=" N ASP 6 733 " --> pdb=" O SER 6 729 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU 6 734 " --> pdb=" O HIS 6 730 " (cutoff:3.500A) Processing helix chain '6' and resid 747 through 759 removed outlier: 3.538A pdb=" N LEU 6 751 " --> pdb=" O SER 6 747 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS 6 756 " --> pdb=" O ARG 6 752 " (cutoff:3.500A) Processing helix chain '6' and resid 769 through 785 removed outlier: 3.992A pdb=" N GLU 6 775 " --> pdb=" O SER 6 771 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS 6 776 " --> pdb=" O TYR 6 772 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR 6 777 " --> pdb=" O LEU 6 773 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS 6 782 " --> pdb=" O LYS 6 778 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP 6 783 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA 6 785 " --> pdb=" O ARG 6 781 " (cutoff:3.500A) Processing helix chain '6' and resid 798 through 806 removed outlier: 4.278A pdb=" N SER 6 802 " --> pdb=" O ARG 6 798 " (cutoff:3.500A) Processing helix chain '6' and resid 806 through 814 removed outlier: 3.877A pdb=" N ALA 6 811 " --> pdb=" O SER 6 807 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN 6 814 " --> pdb=" O ILE 6 810 " (cutoff:3.500A) Processing helix chain '6' and resid 824 through 839 removed outlier: 3.795A pdb=" N ASP 6 829 " --> pdb=" O ALA 6 825 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU 6 830 " --> pdb=" O GLU 6 826 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU 6 831 " --> pdb=" O ALA 6 827 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG 6 837 " --> pdb=" O GLN 6 833 " (cutoff:3.500A) Processing helix chain '7' and resid 14 through 23 removed outlier: 4.152A pdb=" N GLU 7 20 " --> pdb=" O ASN 7 16 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 removed outlier: 3.623A pdb=" N LYS 7 69 " --> pdb=" O ALA 7 65 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL 7 70 " --> pdb=" O MET 7 66 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA 7 71 " --> pdb=" O LEU 7 67 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN 7 72 " --> pdb=" O GLN 7 68 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 91 removed outlier: 4.386A pdb=" N TYR 7 88 " --> pdb=" O ASP 7 84 " (cutoff:3.500A) Processing helix chain '7' and resid 101 through 109 removed outlier: 4.394A pdb=" N ALA 7 105 " --> pdb=" O ASP 7 101 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN 7 107 " --> pdb=" O VAL 7 103 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 113 Processing helix chain '7' and resid 114 through 122 removed outlier: 3.698A pdb=" N ASP 7 122 " --> pdb=" O CYS 7 118 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 125 No H-bonds generated for 'chain '7' and resid 123 through 125' Processing helix chain '7' and resid 139 through 152 removed outlier: 3.639A pdb=" N ASN 7 144 " --> pdb=" O ASP 7 140 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN 7 150 " --> pdb=" O ARG 7 146 " (cutoff:3.500A) Processing helix chain '7' and resid 153 through 155 No H-bonds generated for 'chain '7' and resid 153 through 155' Processing helix chain '7' and resid 226 through 230 removed outlier: 3.917A pdb=" N ILE 7 230 " --> pdb=" O VAL 7 227 " (cutoff:3.500A) Processing helix chain '7' and resid 397 through 408 removed outlier: 4.169A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE 7 405 " --> pdb=" O VAL 7 401 " (cutoff:3.500A) Processing helix chain '7' and resid 412 through 418 Processing helix chain '7' and resid 429 through 438 removed outlier: 3.996A pdb=" N LEU 7 433 " --> pdb=" O LYS 7 429 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU 7 435 " --> pdb=" O ALA 7 431 " (cutoff:3.500A) Processing helix chain '7' and resid 466 through 475 removed outlier: 3.967A pdb=" N ALA 7 472 " --> pdb=" O GLN 7 468 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE 7 473 " --> pdb=" O LEU 7 469 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS 7 474 " --> pdb=" O LEU 7 470 " (cutoff:3.500A) Processing helix chain '7' and resid 529 through 537 removed outlier: 5.513A pdb=" N THR 7 535 " --> pdb=" O GLU 7 531 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA 7 536 " --> pdb=" O SER 7 532 " (cutoff:3.500A) Processing helix chain '7' and resid 537 through 542 removed outlier: 3.883A pdb=" N MET 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) Processing helix chain '7' and resid 586 through 592 removed outlier: 3.911A pdb=" N LEU 7 590 " --> pdb=" O LEU 7 586 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER 7 592 " --> pdb=" O ALA 7 588 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 618 removed outlier: 3.632A pdb=" N ASP 7 609 " --> pdb=" O SER 7 605 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 619 through 621 No H-bonds generated for 'chain '7' and resid 619 through 621' Processing helix chain '7' and resid 635 through 647 Processing helix chain '7' and resid 659 through 667 Processing helix chain '7' and resid 670 through 675 removed outlier: 3.634A pdb=" N GLU 7 674 " --> pdb=" O ASP 7 670 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET 7 675 " --> pdb=" O SER 7 671 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 670 through 675' Processing helix chain '7' and resid 685 through 703 removed outlier: 4.145A pdb=" N GLY 7 691 " --> pdb=" O ARG 7 687 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE 7 692 " --> pdb=" O THR 7 688 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN 7 697 " --> pdb=" O ILE 7 693 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 722 removed outlier: 3.893A pdb=" N GLU 7 715 " --> pdb=" O ASP 7 711 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA 7 716 " --> pdb=" O ASP 7 712 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL 7 722 " --> pdb=" O ARG 7 718 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 165 removed outlier: 3.589A pdb=" N ILE A 163 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 191 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 190 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER E 56 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE E 29 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE E 61 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL E 31 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AA3, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AA4, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.963A pdb=" N MET D 277 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 228 " --> pdb=" O MET D 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 318 through 319 removed outlier: 4.019A pdb=" N ASN E 319 " --> pdb=" O VAL E 410 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL E 410 " --> pdb=" O ASN E 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 520 through 521 Processing sheet with id=AA7, first strand: chain 'E' and resid 568 through 569 removed outlier: 3.668A pdb=" N LEU E 569 " --> pdb=" O ALA E 582 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA E 582 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 390 through 391 removed outlier: 3.647A pdb=" N VAL 2 424 " --> pdb=" O GLY 2 322 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU 2 452 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 331 through 333 removed outlier: 3.515A pdb=" N TYR 2 385 " --> pdb=" O PHE 2 331 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '2' and resid 649 through 650 removed outlier: 6.567A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '2' and resid 565 through 567 removed outlier: 7.944A pdb=" N ALA 2 566 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain '2' and resid 579 through 581 removed outlier: 3.655A pdb=" N SER 2 579 " --> pdb=" O GLU 2 592 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG 2 581 " --> pdb=" O THR 2 590 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR 2 590 " --> pdb=" O ARG 2 581 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 179 through 185 removed outlier: 3.529A pdb=" N VAL 3 180 " --> pdb=" O GLY 3 296 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY 3 296 " --> pdb=" O VAL 3 180 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL 3 295 " --> pdb=" O THR 3 325 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR 3 325 " --> pdb=" O VAL 3 295 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 212 through 213 removed outlier: 3.777A pdb=" N ARG 3 193 " --> pdb=" O HIS 3 253 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN 3 254 " --> pdb=" O LEU 3 278 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 3 278 " --> pdb=" O GLN 3 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '3' and resid 208 through 209 Processing sheet with id=AB7, first strand: chain '3' and resid 406 through 409 removed outlier: 7.547A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL 3 408 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '3' and resid 494 through 495 removed outlier: 3.649A pdb=" N VAL 3 495 " --> pdb=" O LEU 3 506 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 3 506 " --> pdb=" O VAL 3 495 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain '4' and resid 240 through 243 removed outlier: 6.633A pdb=" N LEU 4 241 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain '4' and resid 414 through 416 removed outlier: 7.064A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 4 328 " --> pdb=" O VAL 4 435 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL 4 435 " --> pdb=" O LEU 4 328 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS 4 465 " --> pdb=" O THR 4 436 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE 4 442 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N THR 4 459 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 348 through 349 Processing sheet with id=AC3, first strand: chain '4' and resid 564 through 566 removed outlier: 4.024A pdb=" N ILE 4 564 " --> pdb=" O ILE 4 671 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS 4 629 " --> pdb=" O LEU 4 672 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER 4 674 " --> pdb=" O CYS 4 629 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE 4 631 " --> pdb=" O SER 4 674 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 653 through 657 removed outlier: 3.843A pdb=" N LEU 4 665 " --> pdb=" O ILE 4 654 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE 4 656 " --> pdb=" O THR 4 663 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR 4 663 " --> pdb=" O ILE 4 656 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '4' and resid 917 through 918 removed outlier: 4.329A pdb=" N ARG 4 925 " --> pdb=" O ILE 4 917 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 257 through 260 removed outlier: 7.128A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE 5 167 " --> pdb=" O LYS 5 257 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 175 through 178 removed outlier: 6.586A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 189 through 190 removed outlier: 3.940A pdb=" N MET 5 182 " --> pdb=" O ILE 5 242 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 300 through 301 removed outlier: 3.812A pdb=" N TYR 5 301 " --> pdb=" O THR 5 325 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR 5 325 " --> pdb=" O TYR 5 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '5' and resid 436 through 438 removed outlier: 3.622A pdb=" N VAL 5 437 " --> pdb=" O VAL 5 476 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA 5 521 " --> pdb=" O VAL 5 412 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '5' and resid 452 through 456 removed outlier: 6.536A pdb=" N SER 5 452 " --> pdb=" O GLU 5 465 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN 5 454 " --> pdb=" O TYR 5 463 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR 5 463 " --> pdb=" O GLN 5 454 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU 5 461 " --> pdb=" O ASP 5 456 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '5' and resid 501 through 503 removed outlier: 4.182A pdb=" N ILE 5 502 " --> pdb=" O LEU 5 513 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU 5 513 " --> pdb=" O ILE 5 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain '6' and resid 153 through 154 removed outlier: 6.697A pdb=" N ILE 6 153 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain '6' and resid 293 through 295 removed outlier: 3.696A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '6' and resid 293 through 295 removed outlier: 3.696A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN 6 357 " --> pdb=" O LEU 6 381 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL 6 359 " --> pdb=" O VAL 6 379 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 400 through 404 removed outlier: 3.638A pdb=" N VAL 6 400 " --> pdb=" O LEU 6 455 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE 6 402 " --> pdb=" O SER 6 453 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS 6 451 " --> pdb=" O VAL 6 404 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '6' and resid 571 through 572 removed outlier: 6.990A pdb=" N ILE 6 571 " --> pdb=" O ALA 6 680 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA 6 681 " --> pdb=" O ILE 6 638 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 661 through 663 removed outlier: 3.984A pdb=" N LEU 6 672 " --> pdb=" O ILE 6 661 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE 6 663 " --> pdb=" O ALA 6 670 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '6' and resid 764 through 765 removed outlier: 7.944A pdb=" N ILE 6 764 " --> pdb=" O ILE 6 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain '7' and resid 80 through 81 removed outlier: 7.401A pdb=" N ILE 7 80 " --> pdb=" O LYS 7 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain '7' and resid 238 through 246 removed outlier: 3.578A pdb=" N ILE 7 244 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS 7 313 " --> pdb=" O ILE 7 333 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU 7 331 " --> pdb=" O ILE 7 315 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN 7 332 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA 7 378 " --> pdb=" O ASN 7 332 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N HIS 7 334 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE 7 380 " --> pdb=" O HIS 7 334 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU 7 356 " --> pdb=" O TYR 7 375 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR 7 352 " --> pdb=" O GLN 7 379 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL 7 381 " --> pdb=" O ASP 7 350 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ASP 7 350 " --> pdb=" O VAL 7 381 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL 7 349 " --> pdb=" O GLY 7 243 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY 7 353 " --> pdb=" O ILE 7 239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '7' and resid 254 through 255 Processing sheet with id=AE5, first strand: chain '7' and resid 260 through 261 Processing sheet with id=AE6, first strand: chain '7' and resid 456 through 459 removed outlier: 6.604A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '7' and resid 496 through 497 Processing sheet with id=AE8, first strand: chain '7' and resid 546 through 547 removed outlier: 3.851A pdb=" N ILE 7 546 " --> pdb=" O LEU 7 557 " (cutoff:3.500A) 977 hydrogen bonds defined for protein. 2757 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: 9.29 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12056 1.33 - 1.46: 7754 1.46 - 1.58: 21686 1.58 - 1.70: 82 1.70 - 1.82: 290 Bond restraints: 41868 Sorted by residual: bond pdb=" C4 ATP 31001 " pdb=" C5 ATP 31001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C4 ATP 2 901 " pdb=" C5 ATP 2 901 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.77e+01 bond pdb=" C4 ATP 5 801 " pdb=" C5 ATP 5 801 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.62e+01 bond pdb=" C5 ATP 5 801 " pdb=" C6 ATP 5 801 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C5 ATP 2 901 " pdb=" C6 ATP 2 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.61e+01 ... (remaining 41863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 56367 4.63 - 9.26: 346 9.26 - 13.88: 23 13.88 - 18.51: 6 18.51 - 23.14: 6 Bond angle restraints: 56748 Sorted by residual: angle pdb=" PB ATP 5 801 " pdb=" O3B ATP 5 801 " pdb=" PG ATP 5 801 " ideal model delta sigma weight residual 139.87 116.73 23.14 1.00e+00 1.00e+00 5.35e+02 angle pdb=" PA ATP 31001 " pdb=" O3A ATP 31001 " pdb=" PB ATP 31001 " ideal model delta sigma weight residual 136.83 113.91 22.92 1.00e+00 1.00e+00 5.25e+02 angle pdb=" PB ATP 31001 " pdb=" O3B ATP 31001 " pdb=" PG ATP 31001 " ideal model delta sigma weight residual 139.87 117.26 22.61 1.00e+00 1.00e+00 5.11e+02 angle pdb=" PA ATP 2 901 " pdb=" O3A ATP 2 901 " pdb=" PB ATP 2 901 " ideal model delta sigma weight residual 136.83 117.98 18.85 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP 2 901 " pdb=" O3B ATP 2 901 " pdb=" PG ATP 2 901 " ideal model delta sigma weight residual 139.87 121.35 18.52 1.00e+00 1.00e+00 3.43e+02 ... (remaining 56743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 22036 17.95 - 35.91: 2817 35.91 - 53.86: 565 53.86 - 71.82: 149 71.82 - 89.77: 36 Dihedral angle restraints: 25603 sinusoidal: 10648 harmonic: 14955 Sorted by residual: dihedral pdb=" CA MET E 366 " pdb=" C MET E 366 " pdb=" N GLY E 367 " pdb=" CA GLY E 367 " ideal model delta harmonic sigma weight residual 180.00 150.22 29.78 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA PHE 5 44 " pdb=" C PHE 5 44 " pdb=" N ILE 5 45 " pdb=" CA ILE 5 45 " ideal model delta harmonic sigma weight residual -180.00 -150.57 -29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA PRO 5 266 " pdb=" C PRO 5 266 " pdb=" N VAL 5 267 " pdb=" CA VAL 5 267 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 25600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 6240 0.119 - 0.239: 318 0.239 - 0.358: 15 0.358 - 0.478: 2 0.478 - 0.597: 1 Chirality restraints: 6576 Sorted by residual: chirality pdb=" CA PRO 5 88 " pdb=" N PRO 5 88 " pdb=" C PRO 5 88 " pdb=" CB PRO 5 88 " both_signs ideal model delta sigma weight residual False 2.72 2.12 0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" CA ASP 4 875 " pdb=" N ASP 4 875 " pdb=" C ASP 4 875 " pdb=" CB ASP 4 875 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB VAL 5 265 " pdb=" CA VAL 5 265 " pdb=" CG1 VAL 5 265 " pdb=" CG2 VAL 5 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 6573 not shown) Planarity restraints: 7158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 5 87 " 0.153 5.00e-02 4.00e+02 2.31e-01 8.56e+01 pdb=" N PRO 5 88 " -0.400 5.00e-02 4.00e+02 pdb=" CA PRO 5 88 " 0.131 5.00e-02 4.00e+02 pdb=" CD PRO 5 88 " 0.116 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 335 " 0.023 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C TYR E 335 " -0.078 2.00e-02 2.50e+03 pdb=" O TYR E 335 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP E 336 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO 3 123 " -0.064 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO 3 124 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO 3 124 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO 3 124 " -0.054 5.00e-02 4.00e+02 ... (remaining 7155 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5562 2.75 - 3.29: 40507 3.29 - 3.82: 68007 3.82 - 4.36: 74211 4.36 - 4.90: 118681 Nonbonded interactions: 306968 Sorted by model distance: nonbonded pdb=" O PHE E 327 " pdb=" OH TYR E 340 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR 6 621 " pdb=" O ILE 6 668 " model vdw 2.255 3.040 nonbonded pdb=" O VAL E 148 " pdb=" OG1 THR E 151 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR 3 523 " pdb=" O ASN 3 532 " model vdw 2.276 3.040 nonbonded pdb=" O LEU 4 828 " pdb=" OG SER 4 831 " model vdw 2.281 3.040 ... (remaining 306963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.640 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 37.870 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 41868 Z= 0.316 Angle : 1.045 23.140 56748 Z= 0.619 Chirality : 0.060 0.597 6576 Planarity : 0.007 0.231 7158 Dihedral : 16.767 89.774 15877 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.16 % Favored : 86.66 % Rotamer: Outliers : 0.47 % Allowed : 14.77 % Favored : 84.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.28 (0.09), residues: 5015 helix: -3.84 (0.08), residues: 1532 sheet: -3.60 (0.19), residues: 440 loop : -3.46 (0.10), residues: 3043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 3 435 TYR 0.028 0.002 TYR E 339 PHE 0.036 0.002 PHE 3 31 TRP 0.023 0.002 TRP C 190 HIS 0.013 0.002 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.32 (41868) covalent geometry : angle 1.04456 / 0.62 (56748) hydrogen bonds : bond 0.31611 / 20.46 ( 974) hydrogen bonds : angle 10.13779 / 6.99 ( 2757) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 961 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.4281 (pmm) cc_final: 0.3830 (pmm) REVERT: A 132 LYS cc_start: 0.9496 (tttt) cc_final: 0.9158 (tppt) REVERT: B 18 PHE cc_start: 0.8302 (t80) cc_final: 0.7935 (t80) REVERT: B 176 LEU cc_start: 0.7701 (tt) cc_final: 0.7169 (tt) REVERT: C 12 ASP cc_start: 0.5430 (m-30) cc_final: 0.4312 (p0) REVERT: C 71 PHE cc_start: 0.5911 (m-80) cc_final: 0.5703 (m-80) REVERT: C 85 MET cc_start: 0.7871 (ppp) cc_final: 0.7625 (ppp) REVERT: C 107 LEU cc_start: 0.5922 (mp) cc_final: 0.5581 (mt) REVERT: C 110 LYS cc_start: 0.8138 (mttp) cc_final: 0.6915 (tptp) REVERT: D 218 MET cc_start: 0.6459 (mpp) cc_final: 0.5864 (mpp) REVERT: D 226 LYS cc_start: 0.8001 (tmmt) cc_final: 0.7605 (tmmt) REVERT: E 157 GLU cc_start: 0.8670 (pt0) cc_final: 0.8422 (pm20) REVERT: E 434 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8856 (t) REVERT: E 490 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6874 (tp30) REVERT: E 528 CYS cc_start: 0.7410 (p) cc_final: 0.6927 (p) REVERT: E 607 MET cc_start: 0.7920 (mtm) cc_final: 0.7454 (mmt) REVERT: 2 300 PHE cc_start: 0.7143 (t80) cc_final: 0.6895 (t80) REVERT: 2 315 SER cc_start: 0.9088 (m) cc_final: 0.8518 (p) REVERT: 2 431 LYS cc_start: 0.8009 (mtpt) cc_final: 0.6829 (mtmm) REVERT: 2 437 ASN cc_start: 0.7002 (t0) cc_final: 0.6653 (p0) REVERT: 2 452 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7123 (mt-10) REVERT: 2 620 ILE cc_start: 0.9107 (pt) cc_final: 0.8686 (pt) REVERT: 2 625 GLU cc_start: 0.5969 (tt0) cc_final: 0.3401 (pt0) REVERT: 3 278 LEU cc_start: 0.7205 (pt) cc_final: 0.6802 (pt) REVERT: 3 314 LEU cc_start: 0.7953 (tt) cc_final: 0.6949 (tt) REVERT: 3 478 MET cc_start: 0.4729 (mmm) cc_final: 0.4280 (mmm) REVERT: 3 555 GLU cc_start: 0.7741 (mp0) cc_final: 0.7477 (tp30) REVERT: 4 292 ASP cc_start: 0.7815 (m-30) cc_final: 0.7342 (t70) REVERT: 4 331 LEU cc_start: 0.9078 (tp) cc_final: 0.8842 (tp) REVERT: 4 629 CYS cc_start: 0.7682 (m) cc_final: 0.7464 (m) REVERT: 4 631 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7901 (tp) REVERT: 4 761 ILE cc_start: 0.8284 (tp) cc_final: 0.7887 (mp) REVERT: 4 806 GLU cc_start: 0.7438 (tp30) cc_final: 0.7079 (pt0) REVERT: 4 829 ILE cc_start: 0.7990 (pt) cc_final: 0.7671 (pt) REVERT: 5 41 ASP cc_start: 0.8048 (m-30) cc_final: 0.7846 (m-30) REVERT: 5 509 ILE cc_start: 0.7328 (pt) cc_final: 0.7070 (pt) REVERT: 5 550 PHE cc_start: 0.7700 (m-80) cc_final: 0.7437 (m-80) REVERT: 5 606 CYS cc_start: 0.8436 (p) cc_final: 0.8043 (t) REVERT: 6 143 MET cc_start: 0.6500 (tpp) cc_final: 0.5327 (tmm) REVERT: 6 147 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7705 (t0) REVERT: 6 174 TYR cc_start: 0.6584 (p90) cc_final: 0.5933 (p90) REVERT: 6 267 PHE cc_start: 0.7701 (m-80) cc_final: 0.7475 (m-80) REVERT: 6 358 LYS cc_start: 0.9173 (tttm) cc_final: 0.8841 (ttmm) REVERT: 6 571 ILE cc_start: 0.8473 (mm) cc_final: 0.8230 (pt) REVERT: 6 641 PHE cc_start: 0.8345 (m-10) cc_final: 0.8014 (m-80) REVERT: 6 711 LEU cc_start: 0.7571 (mt) cc_final: 0.7232 (mt) REVERT: 6 713 PHE cc_start: 0.5289 (m-80) cc_final: 0.4421 (t80) REVERT: 6 756 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8039 (tmtt) REVERT: 6 830 LEU cc_start: 0.8898 (tt) cc_final: 0.8408 (pp) REVERT: 7 1 MET cc_start: 0.2489 (mtp) cc_final: 0.1145 (tpt) REVERT: 7 143 LEU cc_start: 0.6591 (mt) cc_final: 0.5874 (pp) REVERT: 7 276 ARG cc_start: 0.7617 (mpp80) cc_final: 0.7129 (tmt170) REVERT: 7 277 THR cc_start: 0.7261 (m) cc_final: 0.6886 (t) REVERT: 7 402 MET cc_start: 0.8911 (mmt) cc_final: 0.8610 (ppp) REVERT: 7 521 CYS cc_start: 0.8442 (t) cc_final: 0.8166 (p) outliers start: 22 outliers final: 4 residues processed: 981 average time/residue: 0.2529 time to fit residues: 395.4789 Evaluate side-chains 490 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 483 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain 2 residue 231 ILE Chi-restraints excluded: chain 2 residue 580 VAL Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 6 residue 147 ASP Chi-restraints excluded: chain 7 residue 535 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 0.0980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 193 GLN B 6 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 167 HIS C 21 GLN C 41 ASN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN E 22 HIS E 57 GLN E 70 HIS E 141 GLN ** 2 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 333 GLN 2 340 ASN ** 2 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 528 ASN 2 531 HIS 2 551 GLN ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 239 ASN 3 253 HIS 3 259 GLN ** 3 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 417 GLN 3 507 ASN 3 531 GLN 3 554 ASN 3 661 GLN 3 677 ASN 3 731 ASN 4 184 ASN 4 247 ASN 4 259 HIS 4 260 GLN 4 274 GLN 4 413 HIS ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 646 HIS 4 683 ASN 4 912 GLN 5 33 ASN ** 5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 67 HIS ** 5 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 253 GLN 5 254 GLN ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 574 ASN 5 581 ASN 6 139 GLN 6 357 GLN 6 362 GLN 6 550 GLN 6 669 HIS 6 750 GLN 6 814 ASN 7 30 GLN 7 68 GLN 7 87 GLN 7 237 GLN 7 274 ASN 7 326 HIS 7 585 ASN 7 622 HIS 7 683 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.093957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.078955 restraints weight = 262885.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.080590 restraints weight = 179287.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.081716 restraints weight = 133890.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.082627 restraints weight = 106795.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.083243 restraints weight = 89633.197| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 41868 Z= 0.217 Angle : 0.855 14.441 56748 Z= 0.445 Chirality : 0.048 0.224 6576 Planarity : 0.006 0.116 7158 Dihedral : 10.554 85.740 5937 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.03 % Favored : 88.93 % Rotamer: Outliers : 3.69 % Allowed : 20.47 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.61 (0.10), residues: 5015 helix: -2.75 (0.10), residues: 1694 sheet: -3.02 (0.20), residues: 477 loop : -3.39 (0.10), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 189 TYR 0.038 0.002 TYR 6 777 PHE 0.029 0.002 PHE 5 31 TRP 0.023 0.002 TRP C 190 HIS 0.013 0.002 HIS 5 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (41868) covalent geometry : angle 0.85459 / 0.44 (56748) hydrogen bonds : bond 0.06699 / 4.34 ( 974) hydrogen bonds : angle 6.85141 / 4.76 ( 2757) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 522 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5915 (pp20) REVERT: A 62 MET cc_start: 0.4771 (pmm) cc_final: 0.4199 (pmm) REVERT: A 79 MET cc_start: 0.2239 (mmt) cc_final: 0.1664 (mmt) REVERT: A 149 ILE cc_start: 0.3198 (OUTLIER) cc_final: 0.2975 (mp) REVERT: B 18 PHE cc_start: 0.8318 (t80) cc_final: 0.8072 (t80) REVERT: B 105 GLU cc_start: 0.7429 (pp20) cc_final: 0.6704 (tp30) REVERT: C 12 ASP cc_start: 0.5690 (m-30) cc_final: 0.5390 (p0) REVERT: C 15 GLU cc_start: 0.4628 (OUTLIER) cc_final: 0.4239 (pm20) REVERT: C 71 PHE cc_start: 0.5878 (m-80) cc_final: 0.5648 (m-80) REVERT: C 79 MET cc_start: 0.7865 (ppp) cc_final: 0.7176 (pmm) REVERT: C 105 PHE cc_start: 0.5913 (t80) cc_final: 0.5710 (t80) REVERT: C 107 LEU cc_start: 0.6392 (mp) cc_final: 0.6088 (mt) REVERT: C 110 LYS cc_start: 0.8294 (mttp) cc_final: 0.7821 (mtmt) REVERT: C 117 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6770 (pm20) REVERT: C 182 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8183 (tm-30) REVERT: D 186 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.7071 (p-80) REVERT: D 258 VAL cc_start: 0.7268 (OUTLIER) cc_final: 0.6986 (p) REVERT: E 157 GLU cc_start: 0.8604 (pt0) cc_final: 0.8354 (pm20) REVERT: E 546 LEU cc_start: 0.8780 (pp) cc_final: 0.8530 (pp) REVERT: E 607 MET cc_start: 0.7837 (mtm) cc_final: 0.7259 (mmp) REVERT: 2 269 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9431 (mmmt) REVERT: 2 272 ASP cc_start: 0.7337 (m-30) cc_final: 0.6997 (m-30) REVERT: 2 315 SER cc_start: 0.9281 (m) cc_final: 0.8794 (p) REVERT: 2 437 ASN cc_start: 0.6966 (t0) cc_final: 0.6612 (p0) REVERT: 2 536 ASP cc_start: 0.8238 (p0) cc_final: 0.7442 (t0) REVERT: 2 567 THR cc_start: 0.7902 (m) cc_final: 0.7696 (p) REVERT: 2 612 MET cc_start: 0.6754 (ttp) cc_final: 0.6153 (ttp) REVERT: 2 616 ASP cc_start: 0.8778 (p0) cc_final: 0.8355 (p0) REVERT: 3 251 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8397 (mp) REVERT: 3 306 MET cc_start: 0.7314 (tmm) cc_final: 0.7081 (tmm) REVERT: 3 384 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7070 (tmm) REVERT: 3 385 LEU cc_start: 0.8459 (pp) cc_final: 0.8129 (pp) REVERT: 3 405 ILE cc_start: 0.8516 (pt) cc_final: 0.8116 (pt) REVERT: 3 731 ASN cc_start: 0.8228 (m-40) cc_final: 0.7968 (p0) REVERT: 4 292 ASP cc_start: 0.7631 (m-30) cc_final: 0.7251 (t0) REVERT: 4 456 LEU cc_start: 0.9090 (tp) cc_final: 0.8593 (tt) REVERT: 4 799 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: 5 495 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: 5 689 MET cc_start: 0.7338 (tmm) cc_final: 0.7129 (tpp) REVERT: 6 119 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8356 (mt) REVERT: 6 143 MET cc_start: 0.7130 (tpp) cc_final: 0.6048 (tmm) REVERT: 6 147 ASP cc_start: 0.8334 (m-30) cc_final: 0.7851 (t0) REVERT: 6 267 PHE cc_start: 0.8063 (m-80) cc_final: 0.7788 (m-80) REVERT: 6 713 PHE cc_start: 0.5708 (m-80) cc_final: 0.5168 (m-10) REVERT: 6 756 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8173 (tmtt) REVERT: 7 1 MET cc_start: 0.2799 (mtp) cc_final: 0.1722 (tpp) REVERT: 7 106 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8256 (pt) REVERT: 7 116 LEU cc_start: 0.6297 (mm) cc_final: 0.6072 (mm) REVERT: 7 143 LEU cc_start: 0.6715 (mt) cc_final: 0.6429 (pp) REVERT: 7 276 ARG cc_start: 0.7985 (mpp80) cc_final: 0.7014 (tpt90) REVERT: 7 277 THR cc_start: 0.8148 (m) cc_final: 0.7789 (t) REVERT: 7 402 MET cc_start: 0.8771 (mmt) cc_final: 0.8458 (ppp) REVERT: 7 448 MET cc_start: 0.7489 (ptp) cc_final: 0.6957 (pmm) REVERT: 7 498 MET cc_start: 0.7838 (ttt) cc_final: 0.7375 (mpp) REVERT: 7 521 CYS cc_start: 0.8524 (t) cc_final: 0.8265 (p) REVERT: 7 638 MET cc_start: 0.7637 (mtm) cc_final: 0.7186 (mtt) REVERT: 7 707 MET cc_start: 0.0414 (ppp) cc_final: 0.0211 (ppp) outliers start: 165 outliers final: 81 residues processed: 652 average time/residue: 0.2237 time to fit residues: 244.6150 Evaluate side-chains 519 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 427 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain 2 residue 231 ILE Chi-restraints excluded: chain 2 residue 246 TYR Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 418 SER Chi-restraints excluded: chain 2 residue 495 ASP Chi-restraints excluded: chain 2 residue 555 TYR Chi-restraints excluded: chain 2 residue 580 VAL Chi-restraints excluded: chain 2 residue 704 VAL Chi-restraints excluded: chain 2 residue 843 ASP Chi-restraints excluded: chain 3 residue 18 ASP Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 181 SER Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 249 THR Chi-restraints excluded: chain 3 residue 251 ILE Chi-restraints excluded: chain 3 residue 256 ILE Chi-restraints excluded: chain 3 residue 383 LEU Chi-restraints excluded: chain 3 residue 384 MET Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 503 HIS Chi-restraints excluded: chain 3 residue 539 LEU Chi-restraints excluded: chain 3 residue 668 ILE Chi-restraints excluded: chain 3 residue 690 ASP Chi-restraints excluded: chain 3 residue 706 ILE Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 396 VAL Chi-restraints excluded: chain 4 residue 578 LEU Chi-restraints excluded: chain 4 residue 602 THR Chi-restraints excluded: chain 4 residue 622 VAL Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 744 VAL Chi-restraints excluded: chain 4 residue 799 GLU Chi-restraints excluded: chain 5 residue 33 ASN Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 242 ILE Chi-restraints excluded: chain 5 residue 251 ILE Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 450 THR Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 479 ILE Chi-restraints excluded: chain 5 residue 495 GLU Chi-restraints excluded: chain 5 residue 572 VAL Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 304 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 569 ILE Chi-restraints excluded: chain 6 residue 584 PHE Chi-restraints excluded: chain 6 residue 636 CYS Chi-restraints excluded: chain 6 residue 716 LEU Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 63 TYR Chi-restraints excluded: chain 7 residue 106 ILE Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 302 THR Chi-restraints excluded: chain 7 residue 322 VAL Chi-restraints excluded: chain 7 residue 326 HIS Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 537 ILE Chi-restraints excluded: chain 7 residue 661 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 399 optimal weight: 0.9980 chunk 321 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 407 optimal weight: 0.5980 chunk 417 optimal weight: 20.0000 chunk 351 optimal weight: 10.0000 chunk 427 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 107 optimal weight: 0.0270 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 50 ASN A 118 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** 2 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 GLN ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 670 GLN ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 362 GLN 7 76 ASN 7 326 HIS 7 683 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.093059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.077329 restraints weight = 258758.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.079145 restraints weight = 172112.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.080441 restraints weight = 126222.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.081356 restraints weight = 99128.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.082018 restraints weight = 82720.395| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41868 Z= 0.147 Angle : 0.757 15.687 56748 Z= 0.386 Chirality : 0.046 0.209 6576 Planarity : 0.005 0.090 7158 Dihedral : 10.147 88.576 5931 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.97 % Favored : 90.01 % Rotamer: Outliers : 4.05 % Allowed : 22.51 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.10), residues: 5015 helix: -2.23 (0.11), residues: 1704 sheet: -2.75 (0.20), residues: 500 loop : -3.29 (0.10), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 6 837 TYR 0.025 0.001 TYR 3 38 PHE 0.053 0.002 PHE 5 554 TRP 0.021 0.002 TRP C 190 HIS 0.008 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (41868) covalent geometry : angle 0.75680 / 0.39 (56748) hydrogen bonds : bond 0.05479 / 3.56 ( 974) hydrogen bonds : angle 6.12955 / 4.27 ( 2757) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 457 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6129 (pp20) REVERT: A 62 MET cc_start: 0.5363 (pmm) cc_final: 0.4810 (pmm) REVERT: A 79 MET cc_start: 0.2110 (mmp) cc_final: 0.1660 (mmt) REVERT: A 149 ILE cc_start: 0.3261 (OUTLIER) cc_final: 0.3035 (mm) REVERT: B 18 PHE cc_start: 0.8429 (t80) cc_final: 0.8140 (t80) REVERT: B 93 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8718 (mm) REVERT: B 105 GLU cc_start: 0.7588 (pp20) cc_final: 0.6780 (tp30) REVERT: C 12 ASP cc_start: 0.6108 (m-30) cc_final: 0.4654 (p0) REVERT: C 103 HIS cc_start: 0.6749 (t70) cc_final: 0.5966 (t70) REVERT: C 107 LEU cc_start: 0.6314 (mp) cc_final: 0.6040 (mp) REVERT: C 174 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8757 (mmtm) REVERT: C 182 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8184 (tm-30) REVERT: D 130 GLU cc_start: 0.7776 (pp20) cc_final: 0.7533 (pt0) REVERT: D 186 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.7201 (p-80) REVERT: D 258 VAL cc_start: 0.7344 (OUTLIER) cc_final: 0.7104 (p) REVERT: E 157 GLU cc_start: 0.8751 (pt0) cc_final: 0.8433 (pm20) REVERT: E 607 MET cc_start: 0.7901 (mtm) cc_final: 0.7457 (mmp) REVERT: 2 272 ASP cc_start: 0.7762 (m-30) cc_final: 0.7508 (m-30) REVERT: 2 315 SER cc_start: 0.9297 (m) cc_final: 0.8830 (p) REVERT: 2 437 ASN cc_start: 0.7202 (t0) cc_final: 0.6679 (p0) REVERT: 2 452 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7907 (mt-10) REVERT: 2 589 TRP cc_start: 0.8323 (m-10) cc_final: 0.7988 (m100) REVERT: 2 612 MET cc_start: 0.7040 (ttp) cc_final: 0.6168 (ttt) REVERT: 2 616 ASP cc_start: 0.8652 (p0) cc_final: 0.8188 (p0) REVERT: 3 251 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8536 (mp) REVERT: 3 384 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7180 (tmm) REVERT: 3 385 LEU cc_start: 0.8496 (pp) cc_final: 0.8188 (pp) REVERT: 3 405 ILE cc_start: 0.8125 (pt) cc_final: 0.7860 (pt) REVERT: 3 407 MET cc_start: 0.8572 (mpp) cc_final: 0.8275 (mpp) REVERT: 3 474 GLU cc_start: 0.8177 (pm20) cc_final: 0.7717 (pm20) REVERT: 3 490 MET cc_start: 0.9160 (mmm) cc_final: 0.7516 (tpt) REVERT: 3 668 ILE cc_start: 0.6010 (OUTLIER) cc_final: 0.5431 (tp) REVERT: 3 686 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7889 (pp) REVERT: 3 731 ASN cc_start: 0.8505 (m-40) cc_final: 0.8221 (p0) REVERT: 4 292 ASP cc_start: 0.7711 (m-30) cc_final: 0.7342 (t0) REVERT: 4 456 LEU cc_start: 0.9163 (tp) cc_final: 0.8788 (tp) REVERT: 4 637 MET cc_start: 0.7352 (mmt) cc_final: 0.7047 (mmt) REVERT: 5 207 LEU cc_start: 0.8405 (mt) cc_final: 0.8103 (mt) REVERT: 6 119 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8531 (mt) REVERT: 6 143 MET cc_start: 0.7142 (tpp) cc_final: 0.6040 (tmm) REVERT: 6 147 ASP cc_start: 0.8366 (m-30) cc_final: 0.7867 (t0) REVERT: 6 267 PHE cc_start: 0.8146 (m-80) cc_final: 0.7698 (m-80) REVERT: 6 362 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8393 (tp40) REVERT: 6 701 MET cc_start: 0.6753 (mmm) cc_final: 0.6269 (mmt) REVERT: 6 756 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8129 (tmtt) REVERT: 7 1 MET cc_start: 0.2957 (mtp) cc_final: 0.1786 (tpt) REVERT: 7 143 LEU cc_start: 0.6826 (mt) cc_final: 0.6544 (pp) REVERT: 7 153 MET cc_start: 0.0969 (mmt) cc_final: 0.0681 (mmp) REVERT: 7 276 ARG cc_start: 0.7992 (mpp80) cc_final: 0.7039 (tpt90) REVERT: 7 448 MET cc_start: 0.7527 (ptp) cc_final: 0.7017 (pmm) REVERT: 7 497 VAL cc_start: 0.7049 (OUTLIER) cc_final: 0.6803 (t) REVERT: 7 498 MET cc_start: 0.8020 (ttt) cc_final: 0.7434 (mpp) REVERT: 7 521 CYS cc_start: 0.8683 (t) cc_final: 0.8283 (p) REVERT: 7 561 THR cc_start: 0.8686 (m) cc_final: 0.8441 (p) REVERT: 7 638 MET cc_start: 0.7803 (mtm) cc_final: 0.7473 (mtt) outliers start: 181 outliers final: 98 residues processed: 591 average time/residue: 0.2123 time to fit residues: 214.9843 Evaluate side-chains 519 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 409 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain 2 residue 231 ILE Chi-restraints excluded: chain 2 residue 246 TYR Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 418 SER Chi-restraints excluded: chain 2 residue 495 ASP Chi-restraints excluded: chain 2 residue 541 LEU Chi-restraints excluded: chain 2 residue 580 VAL Chi-restraints excluded: chain 2 residue 606 ILE Chi-restraints excluded: chain 2 residue 640 LEU Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 704 VAL Chi-restraints excluded: chain 3 residue 18 ASP Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 251 ILE Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 383 LEU Chi-restraints excluded: chain 3 residue 384 MET Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 430 ILE Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 503 HIS Chi-restraints excluded: chain 3 residue 539 LEU Chi-restraints excluded: chain 3 residue 653 ILE Chi-restraints excluded: chain 3 residue 668 ILE Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 686 LEU Chi-restraints excluded: chain 3 residue 704 THR Chi-restraints excluded: chain 3 residue 706 ILE Chi-restraints excluded: chain 4 residue 326 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 602 THR Chi-restraints excluded: chain 4 residue 622 VAL Chi-restraints excluded: chain 4 residue 629 CYS Chi-restraints excluded: chain 4 residue 648 VAL Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 71 TYR Chi-restraints excluded: chain 5 residue 146 ILE Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 242 ILE Chi-restraints excluded: chain 5 residue 287 ILE Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 450 THR Chi-restraints excluded: chain 5 residue 479 ILE Chi-restraints excluded: chain 5 residue 604 THR Chi-restraints excluded: chain 5 residue 650 ILE Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 6 residue 362 GLN Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 453 SER Chi-restraints excluded: chain 6 residue 569 ILE Chi-restraints excluded: chain 6 residue 584 PHE Chi-restraints excluded: chain 6 residue 613 VAL Chi-restraints excluded: chain 6 residue 636 CYS Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 6 residue 638 ILE Chi-restraints excluded: chain 6 residue 716 LEU Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 63 TYR Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 229 GLN Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 322 VAL Chi-restraints excluded: chain 7 residue 326 HIS Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 497 VAL Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 529 MET Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 661 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 246 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 290 optimal weight: 0.1980 chunk 240 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 357 optimal weight: 0.0670 chunk 420 optimal weight: 0.0870 chunk 47 optimal weight: 7.9990 chunk 276 optimal weight: 0.9980 chunk 505 optimal weight: 20.0000 overall best weight: 1.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 703 HIS ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 253 HIS 4 354 HIS ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 67 HIS ** 5 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 68 GLN 7 585 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.092448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.076759 restraints weight = 258427.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.078539 restraints weight = 172300.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.079813 restraints weight = 126724.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.080719 restraints weight = 100064.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.081376 restraints weight = 83608.166| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41868 Z= 0.132 Angle : 0.723 14.345 56748 Z= 0.364 Chirality : 0.045 0.218 6576 Planarity : 0.005 0.095 7158 Dihedral : 9.905 88.147 5931 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 4.21 % Allowed : 23.13 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.89 (0.10), residues: 5015 helix: -1.88 (0.11), residues: 1726 sheet: -2.47 (0.22), residues: 473 loop : -3.19 (0.10), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG 7 534 TYR 0.026 0.001 TYR 3 38 PHE 0.031 0.001 PHE 5 554 TRP 0.022 0.001 TRP C 190 HIS 0.017 0.001 HIS 5 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (41868) covalent geometry : angle 0.72302 / 0.36 (56748) hydrogen bonds : bond 0.04516 / 2.92 ( 974) hydrogen bonds : angle 5.77913 / 4.03 ( 2757) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 441 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6234 (pp20) REVERT: A 62 MET cc_start: 0.5140 (pmm) cc_final: 0.4573 (pmm) REVERT: A 79 MET cc_start: 0.2275 (mmp) cc_final: 0.1819 (mmt) REVERT: A 110 MET cc_start: -0.1951 (tpt) cc_final: -0.2244 (tpt) REVERT: A 149 ILE cc_start: 0.3271 (OUTLIER) cc_final: 0.3052 (mm) REVERT: B 18 PHE cc_start: 0.8412 (t80) cc_final: 0.8158 (t80) REVERT: B 105 GLU cc_start: 0.7603 (pp20) cc_final: 0.6737 (tp30) REVERT: B 160 LEU cc_start: 0.7751 (pt) cc_final: 0.7339 (mm) REVERT: C 12 ASP cc_start: 0.6333 (m-30) cc_final: 0.5792 (p0) REVERT: C 79 MET cc_start: 0.8123 (ppp) cc_final: 0.7136 (pmm) REVERT: C 85 MET cc_start: 0.6878 (ppp) cc_final: 0.6640 (ppp) REVERT: C 103 HIS cc_start: 0.6877 (t70) cc_final: 0.6128 (t70) REVERT: C 107 LEU cc_start: 0.6516 (mp) cc_final: 0.5914 (mp) REVERT: C 110 LYS cc_start: 0.8320 (mttp) cc_final: 0.7678 (mttt) REVERT: C 113 MET cc_start: 0.5686 (mmm) cc_final: 0.5438 (ptt) REVERT: C 117 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6765 (pm20) REVERT: C 182 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 130 GLU cc_start: 0.7960 (pp20) cc_final: 0.7667 (pt0) REVERT: D 186 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7315 (p-80) REVERT: D 258 VAL cc_start: 0.7249 (OUTLIER) cc_final: 0.7021 (p) REVERT: E 157 GLU cc_start: 0.8717 (pt0) cc_final: 0.8399 (pm20) REVERT: E 607 MET cc_start: 0.8064 (mtm) cc_final: 0.7576 (mmt) REVERT: 2 272 ASP cc_start: 0.7635 (m-30) cc_final: 0.7399 (m-30) REVERT: 2 315 SER cc_start: 0.9303 (m) cc_final: 0.8815 (p) REVERT: 2 437 ASN cc_start: 0.7215 (t0) cc_final: 0.6682 (p0) REVERT: 2 452 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7873 (mt-10) REVERT: 2 612 MET cc_start: 0.7156 (ttp) cc_final: 0.6099 (ttt) REVERT: 2 616 ASP cc_start: 0.8694 (p0) cc_final: 0.7979 (p0) REVERT: 2 834 LEU cc_start: 0.8002 (tp) cc_final: 0.7793 (pp) REVERT: 3 251 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8575 (mp) REVERT: 3 407 MET cc_start: 0.8538 (mpp) cc_final: 0.8066 (mpp) REVERT: 3 474 GLU cc_start: 0.8229 (pm20) cc_final: 0.7837 (pm20) REVERT: 4 292 ASP cc_start: 0.7728 (m-30) cc_final: 0.7367 (t0) REVERT: 4 314 MET cc_start: 0.7694 (mtm) cc_final: 0.7313 (ptt) REVERT: 4 456 LEU cc_start: 0.9230 (tp) cc_final: 0.8852 (tp) REVERT: 4 637 MET cc_start: 0.7595 (mmt) cc_final: 0.7347 (mmt) REVERT: 5 485 MET cc_start: 0.2993 (ptm) cc_final: 0.2721 (ptm) REVERT: 5 606 CYS cc_start: 0.8785 (t) cc_final: 0.7977 (p) REVERT: 6 119 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8567 (mt) REVERT: 6 143 MET cc_start: 0.7250 (tpp) cc_final: 0.6207 (tmm) REVERT: 6 147 ASP cc_start: 0.8342 (m-30) cc_final: 0.7872 (t0) REVERT: 6 267 PHE cc_start: 0.8058 (m-80) cc_final: 0.7654 (m-80) REVERT: 6 355 ASP cc_start: 0.7792 (p0) cc_final: 0.6395 (m-30) REVERT: 6 433 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.5085 (pp) REVERT: 6 516 LEU cc_start: 0.9117 (mm) cc_final: 0.8553 (mp) REVERT: 6 734 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8293 (pp) REVERT: 6 756 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8135 (tmtt) REVERT: 7 1 MET cc_start: 0.2953 (mtp) cc_final: 0.2097 (tpp) REVERT: 7 143 LEU cc_start: 0.6826 (mt) cc_final: 0.6548 (pp) REVERT: 7 276 ARG cc_start: 0.8059 (mpp80) cc_final: 0.7003 (tpt90) REVERT: 7 448 MET cc_start: 0.7406 (ptp) cc_final: 0.6905 (pmm) REVERT: 7 497 VAL cc_start: 0.7051 (OUTLIER) cc_final: 0.6838 (t) REVERT: 7 498 MET cc_start: 0.8007 (ttt) cc_final: 0.7420 (mpp) REVERT: 7 521 CYS cc_start: 0.8623 (t) cc_final: 0.8230 (p) REVERT: 7 533 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6470 (m-30) REVERT: 7 561 THR cc_start: 0.8688 (m) cc_final: 0.8470 (p) REVERT: 7 638 MET cc_start: 0.8006 (mtm) cc_final: 0.7723 (mtt) outliers start: 188 outliers final: 123 residues processed: 584 average time/residue: 0.2053 time to fit residues: 207.0882 Evaluate side-chains 542 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 409 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 521 HIS Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain 2 residue 231 ILE Chi-restraints excluded: chain 2 residue 246 TYR Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 2 residue 418 SER Chi-restraints excluded: chain 2 residue 495 ASP Chi-restraints excluded: chain 2 residue 541 LEU Chi-restraints excluded: chain 2 residue 580 VAL Chi-restraints excluded: chain 2 residue 606 ILE Chi-restraints excluded: chain 2 residue 640 LEU Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 669 LEU Chi-restraints excluded: chain 2 residue 704 VAL Chi-restraints excluded: chain 2 residue 840 VAL Chi-restraints excluded: chain 3 residue 18 ASP Chi-restraints excluded: chain 3 residue 116 VAL Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 181 SER Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 251 ILE Chi-restraints excluded: chain 3 residue 256 ILE Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 295 VAL Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 383 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 430 ILE Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 503 HIS Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 671 LEU Chi-restraints excluded: chain 3 residue 704 THR Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 326 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 602 THR Chi-restraints excluded: chain 4 residue 622 VAL Chi-restraints excluded: chain 4 residue 629 CYS Chi-restraints excluded: chain 4 residue 648 VAL Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 744 VAL Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 817 VAL Chi-restraints excluded: chain 4 residue 819 LEU Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 4 residue 912 GLN Chi-restraints excluded: chain 5 residue 67 HIS Chi-restraints excluded: chain 5 residue 71 TYR Chi-restraints excluded: chain 5 residue 146 ILE Chi-restraints excluded: chain 5 residue 242 ILE Chi-restraints excluded: chain 5 residue 251 ILE Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 450 THR Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 479 ILE Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 433 LEU Chi-restraints excluded: chain 6 residue 453 SER Chi-restraints excluded: chain 6 residue 569 ILE Chi-restraints excluded: chain 6 residue 612 VAL Chi-restraints excluded: chain 6 residue 636 CYS Chi-restraints excluded: chain 6 residue 638 ILE Chi-restraints excluded: chain 6 residue 716 LEU Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 63 TYR Chi-restraints excluded: chain 7 residue 197 THR Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 229 GLN Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 322 VAL Chi-restraints excluded: chain 7 residue 326 HIS Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 497 VAL Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 523 ILE Chi-restraints excluded: chain 7 residue 529 MET Chi-restraints excluded: chain 7 residue 533 ASP Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 661 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 108 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 493 optimal weight: 20.0000 chunk 349 optimal weight: 5.9990 chunk 498 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 378 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 118 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 503 GLN E 624 ASN ** 2 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 508 HIS ** 2 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 627 GLN ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 849 GLN 3 94 HIS ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 351 ASN ** 3 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 670 GLN ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS ** 7 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.086504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.070666 restraints weight = 260137.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.072351 restraints weight = 172494.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.073541 restraints weight = 127337.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.074383 restraints weight = 101076.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.074986 restraints weight = 85174.535| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 41868 Z= 0.206 Angle : 0.792 13.701 56748 Z= 0.404 Chirality : 0.047 0.335 6576 Planarity : 0.005 0.062 7158 Dihedral : 9.756 89.638 5931 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.80 % Favored : 88.18 % Rotamer: Outliers : 5.15 % Allowed : 23.53 % Favored : 71.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.11), residues: 5015 helix: -1.63 (0.11), residues: 1732 sheet: -2.65 (0.21), residues: 533 loop : -3.08 (0.11), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG 5 272 TYR 0.036 0.002 TYR D 201 PHE 0.029 0.002 PHE 5 31 TRP 0.033 0.002 TRP C 190 HIS 0.075 0.002 HIS 5 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (41868) covalent geometry : angle 0.79220 / 0.40 (56748) hydrogen bonds : bond 0.04484 / 2.91 ( 974) hydrogen bonds : angle 5.72639 / 3.99 ( 2757) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 416 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6941 (pp20) REVERT: A 62 MET cc_start: 0.5746 (pmm) cc_final: 0.5234 (pmm) REVERT: A 79 MET cc_start: 0.3319 (mmp) cc_final: 0.2617 (mmt) REVERT: A 110 MET cc_start: -0.1913 (tpt) cc_final: -0.2282 (tpt) REVERT: A 149 ILE cc_start: 0.4146 (OUTLIER) cc_final: 0.3889 (mm) REVERT: B 15 GLU cc_start: 0.7867 (pm20) cc_final: 0.7628 (pp20) REVERT: B 93 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8921 (mm) REVERT: B 160 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7752 (mm) REVERT: B 194 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8404 (tm-30) REVERT: C 12 ASP cc_start: 0.7043 (m-30) cc_final: 0.6309 (p0) REVERT: C 103 HIS cc_start: 0.7539 (t70) cc_final: 0.7043 (t70) REVERT: C 107 LEU cc_start: 0.7218 (mp) cc_final: 0.6802 (mt) REVERT: C 110 LYS cc_start: 0.8607 (mttp) cc_final: 0.8362 (mtmt) REVERT: C 117 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7345 (pm20) REVERT: C 182 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8229 (tm-30) REVERT: D 70 GLU cc_start: 0.7824 (tt0) cc_final: 0.7101 (mt-10) REVERT: D 130 GLU cc_start: 0.8042 (pp20) cc_final: 0.7829 (pt0) REVERT: D 186 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7373 (p-80) REVERT: D 258 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7271 (p) REVERT: E 92 LEU cc_start: 0.9413 (tp) cc_final: 0.9053 (pt) REVERT: E 157 GLU cc_start: 0.8692 (pt0) cc_final: 0.8341 (pm20) REVERT: E 576 THR cc_start: 0.6950 (OUTLIER) cc_final: 0.6737 (m) REVERT: E 607 MET cc_start: 0.8028 (mtm) cc_final: 0.7583 (mmp) REVERT: 2 272 ASP cc_start: 0.8116 (m-30) cc_final: 0.7745 (m-30) REVERT: 2 315 SER cc_start: 0.9371 (m) cc_final: 0.8925 (p) REVERT: 2 437 ASN cc_start: 0.7553 (t0) cc_final: 0.6810 (p0) REVERT: 2 452 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8037 (mt-10) REVERT: 2 612 MET cc_start: 0.7171 (ttp) cc_final: 0.6640 (ttm) REVERT: 2 616 ASP cc_start: 0.8675 (p0) cc_final: 0.8159 (p0) REVERT: 2 766 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.7234 (p90) REVERT: 3 111 TRP cc_start: 0.8690 (t60) cc_final: 0.8228 (t60) REVERT: 3 264 MET cc_start: 0.3379 (mmt) cc_final: 0.3154 (mmt) REVERT: 3 474 GLU cc_start: 0.8523 (pm20) cc_final: 0.8060 (pm20) REVERT: 3 490 MET cc_start: 0.9301 (mmm) cc_final: 0.7863 (tpt) REVERT: 3 670 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.5700 (mp10) REVERT: 4 292 ASP cc_start: 0.7825 (m-30) cc_final: 0.7437 (t0) REVERT: 4 456 LEU cc_start: 0.9290 (tp) cc_final: 0.8813 (tp) REVERT: 4 637 MET cc_start: 0.7767 (mmt) cc_final: 0.7549 (mmt) REVERT: 4 806 GLU cc_start: 0.8302 (tp30) cc_final: 0.7823 (tt0) REVERT: 5 65 MET cc_start: 0.8934 (ptm) cc_final: 0.8110 (ppp) REVERT: 6 143 MET cc_start: 0.7535 (tpp) cc_final: 0.6496 (tmm) REVERT: 6 267 PHE cc_start: 0.8348 (m-80) cc_final: 0.7966 (m-80) REVERT: 6 355 ASP cc_start: 0.7959 (p0) cc_final: 0.6664 (m-30) REVERT: 6 433 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.5325 (pp) REVERT: 6 571 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8561 (mm) REVERT: 6 623 ILE cc_start: 0.8654 (tp) cc_final: 0.8385 (pt) REVERT: 6 637 CYS cc_start: 0.9522 (OUTLIER) cc_final: 0.8660 (t) REVERT: 6 641 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: 6 756 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8217 (tmtt) REVERT: 7 1 MET cc_start: 0.3135 (mtp) cc_final: 0.2047 (tpt) REVERT: 7 143 LEU cc_start: 0.7028 (mt) cc_final: 0.6736 (pp) REVERT: 7 276 ARG cc_start: 0.8212 (mpp80) cc_final: 0.7186 (tpt90) REVERT: 7 448 MET cc_start: 0.7378 (ptp) cc_final: 0.6930 (pmm) REVERT: 7 498 MET cc_start: 0.8138 (ttt) cc_final: 0.7862 (ttp) REVERT: 7 520 ILE cc_start: 0.8750 (mp) cc_final: 0.8545 (pt) REVERT: 7 521 CYS cc_start: 0.8768 (t) cc_final: 0.8251 (p) REVERT: 7 601 LEU cc_start: 0.0665 (mt) cc_final: 0.0443 (pt) REVERT: 7 678 LYS cc_start: 0.5791 (OUTLIER) cc_final: 0.5049 (pptt) outliers start: 230 outliers final: 129 residues processed: 602 average time/residue: 0.2032 time to fit residues: 212.8020 Evaluate side-chains 524 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 381 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 521 HIS Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 231 ILE Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 495 ASP Chi-restraints excluded: chain 2 residue 541 LEU Chi-restraints excluded: chain 2 residue 580 VAL Chi-restraints excluded: chain 2 residue 588 GLU Chi-restraints excluded: chain 2 residue 606 ILE Chi-restraints excluded: chain 2 residue 640 LEU Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 669 LEU Chi-restraints excluded: chain 2 residue 674 LEU Chi-restraints excluded: chain 2 residue 679 ILE Chi-restraints excluded: chain 2 residue 704 VAL Chi-restraints excluded: chain 2 residue 766 TYR Chi-restraints excluded: chain 2 residue 840 VAL Chi-restraints excluded: chain 3 residue 18 ASP Chi-restraints excluded: chain 3 residue 116 VAL Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 180 VAL Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 256 ILE Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 367 LEU Chi-restraints excluded: chain 3 residue 383 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 503 HIS Chi-restraints excluded: chain 3 residue 539 LEU Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 704 THR Chi-restraints excluded: chain 3 residue 706 ILE Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 326 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 602 THR Chi-restraints excluded: chain 4 residue 622 VAL Chi-restraints excluded: chain 4 residue 648 VAL Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 61 LEU Chi-restraints excluded: chain 5 residue 71 TYR Chi-restraints excluded: chain 5 residue 146 ILE Chi-restraints excluded: chain 5 residue 251 ILE Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 450 THR Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 479 ILE Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 650 ILE Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 433 LEU Chi-restraints excluded: chain 6 residue 453 SER Chi-restraints excluded: chain 6 residue 516 LEU Chi-restraints excluded: chain 6 residue 571 ILE Chi-restraints excluded: chain 6 residue 613 VAL Chi-restraints excluded: chain 6 residue 636 CYS Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 6 residue 638 ILE Chi-restraints excluded: chain 6 residue 639 ASP Chi-restraints excluded: chain 6 residue 641 PHE Chi-restraints excluded: chain 6 residue 716 LEU Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 63 TYR Chi-restraints excluded: chain 7 residue 197 THR Chi-restraints excluded: chain 7 residue 229 GLN Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 322 VAL Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 523 ILE Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 661 VAL Chi-restraints excluded: chain 7 residue 678 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 507 optimal weight: 50.0000 chunk 356 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 431 optimal weight: 7.9990 chunk 481 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 503 GLN E 624 ASN ** 2 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 779 HIS 3 259 GLN 3 330 HIS 3 374 HIS ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 670 GLN ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 145 GLN 5 539 ASN 6 434 ASN 7 274 ASN 7 334 HIS 7 622 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.088793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.073418 restraints weight = 283196.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.074867 restraints weight = 183559.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.075818 restraints weight = 134658.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.076529 restraints weight = 108971.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.077026 restraints weight = 93930.200| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.6515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 41868 Z= 0.252 Angle : 0.815 14.711 56748 Z= 0.425 Chirality : 0.048 0.308 6576 Planarity : 0.006 0.103 7158 Dihedral : 9.851 87.682 5931 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 5.32 % Allowed : 24.77 % Favored : 69.91 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.11), residues: 5015 helix: -1.48 (0.11), residues: 1752 sheet: -2.66 (0.21), residues: 522 loop : -3.10 (0.11), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 3 339 TYR 0.035 0.002 TYR 6 174 PHE 0.057 0.003 PHE D 251 TRP 0.027 0.002 TRP C 190 HIS 0.048 0.002 HIS 3 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 (41868) covalent geometry : angle 0.81522 / 0.43 (56748) hydrogen bonds : bond 0.04326 / 2.75 ( 974) hydrogen bonds : angle 5.72340 / 3.99 ( 2757) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 374 time to evaluate : 1.449 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: A 12 GLU cc_start: 0.7901 (pp20) cc_final: 0.7580 (pp20) REVERT: A 34 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7597 (mp0) REVERT: A 43 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7140 (pp20) REVERT: A 62 MET cc_start: 0.5408 (pmm) cc_final: 0.4803 (pmm) REVERT: A 81 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7886 (tpp80) REVERT: A 110 MET cc_start: -0.1725 (tpt) cc_final: -0.2061 (tpt) REVERT: A 149 ILE cc_start: 0.5059 (OUTLIER) cc_final: 0.4730 (mm) REVERT: C 79 MET cc_start: 0.7966 (ppp) cc_final: 0.6846 (pmm) REVERT: C 110 LYS cc_start: 0.8486 (mttp) cc_final: 0.8053 (mmtt) REVERT: C 117 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6680 (pm20) REVERT: C 177 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8213 (p90) REVERT: C 182 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7913 (tm-30) REVERT: D 70 GLU cc_start: 0.7630 (tt0) cc_final: 0.7053 (tt0) REVERT: D 186 HIS cc_start: 0.8309 (OUTLIER) cc_final: 0.7944 (p-80) REVERT: D 280 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: E 92 LEU cc_start: 0.9358 (tp) cc_final: 0.9085 (pp) REVERT: E 607 MET cc_start: 0.7993 (mtm) cc_final: 0.7604 (mmt) REVERT: 2 259 PHE cc_start: 0.3028 (OUTLIER) cc_final: 0.2071 (m-80) REVERT: 2 315 SER cc_start: 0.9453 (m) cc_final: 0.9079 (p) REVERT: 2 437 ASN cc_start: 0.6960 (t0) cc_final: 0.6493 (p0) REVERT: 2 501 MET cc_start: 0.7229 (tmm) cc_final: 0.6851 (tmm) REVERT: 2 612 MET cc_start: 0.6532 (ttp) cc_final: 0.6171 (ttp) REVERT: 2 616 ASP cc_start: 0.8598 (p0) cc_final: 0.8160 (p0) REVERT: 2 766 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.8100 (p90) REVERT: 3 48 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8282 (p90) REVERT: 3 385 LEU cc_start: 0.8266 (pp) cc_final: 0.7960 (tt) REVERT: 3 708 LEU cc_start: 0.8668 (mp) cc_final: 0.8144 (tt) REVERT: 4 292 ASP cc_start: 0.7478 (m-30) cc_final: 0.7236 (t0) REVERT: 4 456 LEU cc_start: 0.9325 (tp) cc_final: 0.8921 (tt) REVERT: 5 65 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7837 (ppp) REVERT: 5 485 MET cc_start: 0.3708 (ptm) cc_final: 0.3477 (ttp) REVERT: 6 143 MET cc_start: 0.7484 (tpp) cc_final: 0.6393 (tmm) REVERT: 6 355 ASP cc_start: 0.7878 (p0) cc_final: 0.7240 (m-30) REVERT: 6 433 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5553 (pp) REVERT: 6 637 CYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8563 (t) REVERT: 6 641 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: 7 1 MET cc_start: 0.2702 (mtp) cc_final: 0.1650 (tpt) REVERT: 7 143 LEU cc_start: 0.7103 (mt) cc_final: 0.6830 (pp) REVERT: 7 276 ARG cc_start: 0.8240 (mpp80) cc_final: 0.7121 (tpt90) REVERT: 7 448 MET cc_start: 0.7237 (ptp) cc_final: 0.6806 (pmm) REVERT: 7 498 MET cc_start: 0.8022 (ttt) cc_final: 0.7397 (mpp) REVERT: 7 521 CYS cc_start: 0.8577 (t) cc_final: 0.8135 (p) REVERT: 7 675 MET cc_start: 0.6876 (mmt) cc_final: 0.6640 (mmp) REVERT: 7 678 LYS cc_start: 0.5285 (OUTLIER) cc_final: 0.4455 (pptt) outliers start: 238 outliers final: 152 residues processed: 574 average time/residue: 0.1990 time to fit residues: 200.3571 Evaluate side-chains 507 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 341 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 516 LYS Chi-restraints excluded: chain E residue 521 HIS Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 231 ILE Chi-restraints excluded: chain 2 residue 249 LEU Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 259 PHE Chi-restraints excluded: chain 2 residue 282 HIS Chi-restraints excluded: chain 2 residue 289 ILE Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 414 LEU Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 495 ASP Chi-restraints excluded: chain 2 residue 497 ILE Chi-restraints excluded: chain 2 residue 508 HIS Chi-restraints excluded: chain 2 residue 541 LEU Chi-restraints excluded: chain 2 residue 552 ILE Chi-restraints excluded: chain 2 residue 580 VAL Chi-restraints excluded: chain 2 residue 588 GLU Chi-restraints excluded: chain 2 residue 606 ILE Chi-restraints excluded: chain 2 residue 640 LEU Chi-restraints excluded: chain 2 residue 704 VAL Chi-restraints excluded: chain 2 residue 766 TYR Chi-restraints excluded: chain 2 residue 787 SER Chi-restraints excluded: chain 2 residue 827 GLU Chi-restraints excluded: chain 2 residue 840 VAL Chi-restraints excluded: chain 3 residue 18 ASP Chi-restraints excluded: chain 3 residue 48 TYR Chi-restraints excluded: chain 3 residue 139 VAL Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 180 VAL Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 222 THR Chi-restraints excluded: chain 3 residue 251 ILE Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 367 LEU Chi-restraints excluded: chain 3 residue 383 LEU Chi-restraints excluded: chain 3 residue 405 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 452 THR Chi-restraints excluded: chain 3 residue 503 HIS Chi-restraints excluded: chain 3 residue 539 LEU Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 668 ILE Chi-restraints excluded: chain 3 residue 704 THR Chi-restraints excluded: chain 3 residue 706 ILE Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 326 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 389 CYS Chi-restraints excluded: chain 4 residue 602 THR Chi-restraints excluded: chain 4 residue 622 VAL Chi-restraints excluded: chain 4 residue 629 CYS Chi-restraints excluded: chain 4 residue 648 VAL Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 744 VAL Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 817 VAL Chi-restraints excluded: chain 4 residue 819 LEU Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 61 LEU Chi-restraints excluded: chain 5 residue 65 MET Chi-restraints excluded: chain 5 residue 71 TYR Chi-restraints excluded: chain 5 residue 146 ILE Chi-restraints excluded: chain 5 residue 251 ILE Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 450 THR Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 650 ILE Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 284 ILE Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 6 residue 304 LEU Chi-restraints excluded: chain 6 residue 378 ASP Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 433 LEU Chi-restraints excluded: chain 6 residue 516 LEU Chi-restraints excluded: chain 6 residue 612 VAL Chi-restraints excluded: chain 6 residue 613 VAL Chi-restraints excluded: chain 6 residue 636 CYS Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 6 residue 638 ILE Chi-restraints excluded: chain 6 residue 639 ASP Chi-restraints excluded: chain 6 residue 641 PHE Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 669 HIS Chi-restraints excluded: chain 6 residue 716 LEU Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 6 residue 783 ASP Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 63 TYR Chi-restraints excluded: chain 7 residue 197 THR Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 229 GLN Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 322 VAL Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 523 ILE Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 661 VAL Chi-restraints excluded: chain 7 residue 678 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 424 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 344 optimal weight: 4.9990 chunk 420 optimal weight: 2.9990 chunk 461 optimal weight: 10.0000 chunk 379 optimal weight: 4.9990 chunk 384 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 508 optimal weight: 50.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN 2 245 ASN ** 2 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 517 ASN ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 67 HIS 5 494 HIS 7 543 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.089254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.074012 restraints weight = 281128.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.075504 restraints weight = 179689.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.076529 restraints weight = 131629.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.077172 restraints weight = 105662.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.077711 restraints weight = 91246.149| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.6827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41868 Z= 0.146 Angle : 0.753 13.428 56748 Z= 0.373 Chirality : 0.046 0.192 6576 Planarity : 0.005 0.096 7158 Dihedral : 9.687 89.057 5931 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.77 % Favored : 89.21 % Rotamer: Outliers : 4.30 % Allowed : 26.51 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.11), residues: 5015 helix: -1.38 (0.11), residues: 1773 sheet: -2.57 (0.21), residues: 516 loop : -2.96 (0.11), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 100 TYR 0.023 0.001 TYR 6 174 PHE 0.033 0.002 PHE 3 31 TRP 0.048 0.002 TRP C 49 HIS 0.008 0.001 HIS C 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (41868) covalent geometry : angle 0.75338 / 0.37 (56748) hydrogen bonds : bond 0.03849 / 2.45 ( 974) hydrogen bonds : angle 5.46779 / 3.82 ( 2757) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 369 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8109 (pp20) cc_final: 0.7903 (pp20) REVERT: A 43 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7113 (pp20) REVERT: A 62 MET cc_start: 0.5715 (pmm) cc_final: 0.5166 (pmm) REVERT: A 110 MET cc_start: -0.1841 (tpt) cc_final: -0.2091 (tpt) REVERT: A 149 ILE cc_start: 0.5077 (OUTLIER) cc_final: 0.4791 (mm) REVERT: C 79 MET cc_start: 0.7955 (ppp) cc_final: 0.6936 (pmm) REVERT: C 110 LYS cc_start: 0.8760 (mttp) cc_final: 0.7864 (tptt) REVERT: C 174 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8393 (mttp) REVERT: C 182 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7264 (tm-30) REVERT: D 183 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7167 (t-90) REVERT: D 186 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7891 (p-80) REVERT: D 280 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: E 92 LEU cc_start: 0.9410 (tp) cc_final: 0.9162 (pp) REVERT: E 607 MET cc_start: 0.8057 (mtm) cc_final: 0.7629 (mmt) REVERT: 2 315 SER cc_start: 0.9439 (m) cc_final: 0.9056 (p) REVERT: 2 437 ASN cc_start: 0.7122 (t0) cc_final: 0.6559 (p0) REVERT: 2 501 MET cc_start: 0.7433 (tmm) cc_final: 0.7157 (tmm) REVERT: 2 612 MET cc_start: 0.6845 (ttp) cc_final: 0.6321 (ttp) REVERT: 2 616 ASP cc_start: 0.8726 (p0) cc_final: 0.8151 (p0) REVERT: 2 766 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8115 (p90) REVERT: 3 48 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8424 (p90) REVERT: 3 111 TRP cc_start: 0.8783 (t60) cc_final: 0.8187 (t60) REVERT: 3 385 LEU cc_start: 0.8487 (pp) cc_final: 0.8153 (tt) REVERT: 3 407 MET cc_start: 0.8606 (mpp) cc_final: 0.8342 (mpp) REVERT: 3 708 LEU cc_start: 0.8689 (mp) cc_final: 0.8139 (tt) REVERT: 4 292 ASP cc_start: 0.7604 (m-30) cc_final: 0.7362 (t0) REVERT: 5 65 MET cc_start: 0.8725 (ptm) cc_final: 0.8274 (ppp) REVERT: 5 689 MET cc_start: 0.7710 (pmm) cc_final: 0.6753 (tpt) REVERT: 6 143 MET cc_start: 0.7446 (tpp) cc_final: 0.6446 (tmm) REVERT: 6 355 ASP cc_start: 0.7838 (p0) cc_final: 0.7216 (m-30) REVERT: 6 571 ILE cc_start: 0.8411 (mm) cc_final: 0.7950 (mm) REVERT: 6 637 CYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8779 (t) REVERT: 6 641 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: 7 1 MET cc_start: 0.2730 (mtp) cc_final: 0.1592 (tpt) REVERT: 7 143 LEU cc_start: 0.7122 (mt) cc_final: 0.6864 (pp) REVERT: 7 291 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: 7 498 MET cc_start: 0.7986 (ttt) cc_final: 0.7348 (mpp) REVERT: 7 521 CYS cc_start: 0.8678 (t) cc_final: 0.8146 (p) REVERT: 7 678 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.4649 (pptt) outliers start: 192 outliers final: 138 residues processed: 538 average time/residue: 0.1945 time to fit residues: 184.0169 Evaluate side-chains 501 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 351 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 231 ILE Chi-restraints excluded: chain 2 residue 249 LEU Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 414 LEU Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 495 ASP Chi-restraints excluded: chain 2 residue 541 LEU Chi-restraints excluded: chain 2 residue 580 VAL Chi-restraints excluded: chain 2 residue 588 GLU Chi-restraints excluded: chain 2 residue 606 ILE Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 640 LEU Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 669 LEU Chi-restraints excluded: chain 2 residue 679 ILE Chi-restraints excluded: chain 2 residue 704 VAL Chi-restraints excluded: chain 2 residue 766 TYR Chi-restraints excluded: chain 2 residue 827 GLU Chi-restraints excluded: chain 2 residue 840 VAL Chi-restraints excluded: chain 3 residue 48 TYR Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 129 LEU Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 273 SER Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 367 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 503 HIS Chi-restraints excluded: chain 3 residue 539 LEU Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 668 ILE Chi-restraints excluded: chain 3 residue 672 THR Chi-restraints excluded: chain 3 residue 704 THR Chi-restraints excluded: chain 3 residue 706 ILE Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 326 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 389 CYS Chi-restraints excluded: chain 4 residue 602 THR Chi-restraints excluded: chain 4 residue 622 VAL Chi-restraints excluded: chain 4 residue 629 CYS Chi-restraints excluded: chain 4 residue 648 VAL Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 744 VAL Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 817 VAL Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 61 LEU Chi-restraints excluded: chain 5 residue 71 TYR Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 251 ILE Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 410 ILE Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 480 ASP Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 650 ILE Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 6 residue 378 ASP Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 402 ILE Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 516 LEU Chi-restraints excluded: chain 6 residue 612 VAL Chi-restraints excluded: chain 6 residue 613 VAL Chi-restraints excluded: chain 6 residue 636 CYS Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 6 residue 638 ILE Chi-restraints excluded: chain 6 residue 639 ASP Chi-restraints excluded: chain 6 residue 641 PHE Chi-restraints excluded: chain 6 residue 716 LEU Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 6 residue 783 ASP Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 63 TYR Chi-restraints excluded: chain 7 residue 197 THR Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 291 GLN Chi-restraints excluded: chain 7 residue 302 THR Chi-restraints excluded: chain 7 residue 322 VAL Chi-restraints excluded: chain 7 residue 326 HIS Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 523 ILE Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 661 VAL Chi-restraints excluded: chain 7 residue 678 LYS Chi-restraints excluded: chain 7 residue 715 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 199 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 333 optimal weight: 7.9990 chunk 469 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 339 optimal weight: 2.9990 chunk 266 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 415 optimal weight: 30.0000 chunk 418 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN 2 340 ASN ** 2 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.079406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.063423 restraints weight = 256603.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.065062 restraints weight = 163415.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.066190 restraints weight = 118064.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.066974 restraints weight = 93580.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.067534 restraints weight = 79158.686| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.7529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 41868 Z= 0.193 Angle : 0.785 13.144 56748 Z= 0.392 Chirality : 0.047 0.338 6576 Planarity : 0.005 0.085 7158 Dihedral : 9.656 88.520 5931 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.57 % Favored : 88.41 % Rotamer: Outliers : 4.43 % Allowed : 26.80 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.11), residues: 5015 helix: -1.28 (0.12), residues: 1785 sheet: -2.52 (0.21), residues: 512 loop : -2.93 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 81 TYR 0.025 0.002 TYR 6 174 PHE 0.034 0.002 PHE 3 31 TRP 0.041 0.002 TRP C 49 HIS 0.011 0.001 HIS 6 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (41868) covalent geometry : angle 0.78494 / 0.39 (56748) hydrogen bonds : bond 0.03938 / 2.51 ( 974) hydrogen bonds : angle 5.53835 / 3.86 ( 2757) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 341 time to evaluate : 1.413 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 62 MET cc_start: 0.6233 (pmm) cc_final: 0.5691 (pmm) REVERT: A 79 MET cc_start: 0.4658 (mmt) cc_final: 0.3799 (mmt) REVERT: A 82 ASN cc_start: 0.8057 (m110) cc_final: 0.7623 (m-40) REVERT: A 149 ILE cc_start: 0.5754 (OUTLIER) cc_final: 0.5490 (mm) REVERT: B 115 LEU cc_start: 0.7233 (tp) cc_final: 0.7019 (mt) REVERT: B 126 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8996 (mm) REVERT: B 191 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7701 (tppt) REVERT: C 79 MET cc_start: 0.8034 (ppp) cc_final: 0.6852 (pmm) REVERT: C 110 LYS cc_start: 0.8982 (mttp) cc_final: 0.8359 (tptm) REVERT: C 174 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8673 (mttp) REVERT: C 177 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8301 (p90) REVERT: D 169 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6641 (mm) REVERT: D 183 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7610 (t-90) REVERT: D 186 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8215 (p-80) REVERT: D 280 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: E 92 LEU cc_start: 0.9551 (tp) cc_final: 0.9282 (pp) REVERT: 2 259 PHE cc_start: 0.2692 (OUTLIER) cc_final: 0.2067 (m-80) REVERT: 2 272 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7583 (p0) REVERT: 2 315 SER cc_start: 0.9396 (m) cc_final: 0.9029 (p) REVERT: 2 437 ASN cc_start: 0.7338 (t0) cc_final: 0.6400 (p0) REVERT: 2 501 MET cc_start: 0.7933 (tmm) cc_final: 0.7694 (tmm) REVERT: 2 612 MET cc_start: 0.7728 (ttp) cc_final: 0.7127 (ttp) REVERT: 2 616 ASP cc_start: 0.8864 (p0) cc_final: 0.8175 (p0) REVERT: 2 766 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8428 (p90) REVERT: 3 158 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6634 (tptt) REVERT: 3 407 MET cc_start: 0.8546 (mpp) cc_final: 0.8201 (mpp) REVERT: 3 708 LEU cc_start: 0.8946 (mp) cc_final: 0.8373 (tt) REVERT: 4 292 ASP cc_start: 0.7773 (m-30) cc_final: 0.7432 (t0) REVERT: 4 314 MET cc_start: 0.8266 (mtm) cc_final: 0.8008 (mpp) REVERT: 4 382 MET cc_start: 0.7330 (tpt) cc_final: 0.7009 (tpt) REVERT: 4 819 LEU cc_start: 0.8485 (pt) cc_final: 0.8114 (tp) REVERT: 5 65 MET cc_start: 0.9138 (ptm) cc_final: 0.8722 (ppp) REVERT: 5 469 MET cc_start: 0.8712 (mtp) cc_final: 0.8436 (mmm) REVERT: 6 140 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8552 (tt) REVERT: 6 143 MET cc_start: 0.7592 (tpp) cc_final: 0.6632 (tmm) REVERT: 6 355 ASP cc_start: 0.8129 (p0) cc_final: 0.7285 (m-30) REVERT: 6 548 LEU cc_start: 0.9513 (mp) cc_final: 0.9286 (mm) REVERT: 6 571 ILE cc_start: 0.8520 (mm) cc_final: 0.8067 (mm) REVERT: 6 638 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9115 (pt) REVERT: 6 641 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: 7 1 MET cc_start: 0.2779 (mtp) cc_final: 0.1879 (tpt) REVERT: 7 143 LEU cc_start: 0.7129 (mt) cc_final: 0.6848 (pp) REVERT: 7 291 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: 7 498 MET cc_start: 0.8147 (ttt) cc_final: 0.7471 (mpp) REVERT: 7 521 CYS cc_start: 0.8941 (t) cc_final: 0.8241 (p) REVERT: 7 533 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6688 (m-30) REVERT: 7 628 LEU cc_start: 0.5038 (mt) cc_final: 0.4694 (tp) REVERT: 7 638 MET cc_start: 0.8198 (mtt) cc_final: 0.7105 (mmt) REVERT: 7 678 LYS cc_start: 0.5293 (OUTLIER) cc_final: 0.4529 (pptt) outliers start: 198 outliers final: 143 residues processed: 513 average time/residue: 0.1967 time to fit residues: 177.5562 Evaluate side-chains 482 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 321 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 521 HIS Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 231 ILE Chi-restraints excluded: chain 2 residue 249 LEU Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 259 PHE Chi-restraints excluded: chain 2 residue 272 ASP Chi-restraints excluded: chain 2 residue 282 HIS Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 495 ASP Chi-restraints excluded: chain 2 residue 508 HIS Chi-restraints excluded: chain 2 residue 541 LEU Chi-restraints excluded: chain 2 residue 580 VAL Chi-restraints excluded: chain 2 residue 588 GLU Chi-restraints excluded: chain 2 residue 606 ILE Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 640 LEU Chi-restraints excluded: chain 2 residue 704 VAL Chi-restraints excluded: chain 2 residue 766 TYR Chi-restraints excluded: chain 2 residue 827 GLU Chi-restraints excluded: chain 2 residue 840 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 129 LEU Chi-restraints excluded: chain 3 residue 158 LYS Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 503 HIS Chi-restraints excluded: chain 3 residue 539 LEU Chi-restraints excluded: chain 3 residue 672 THR Chi-restraints excluded: chain 3 residue 704 THR Chi-restraints excluded: chain 3 residue 706 ILE Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 326 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 389 CYS Chi-restraints excluded: chain 4 residue 602 THR Chi-restraints excluded: chain 4 residue 616 LEU Chi-restraints excluded: chain 4 residue 622 VAL Chi-restraints excluded: chain 4 residue 629 CYS Chi-restraints excluded: chain 4 residue 648 VAL Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 744 VAL Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 817 VAL Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 61 LEU Chi-restraints excluded: chain 5 residue 71 TYR Chi-restraints excluded: chain 5 residue 146 ILE Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 251 ILE Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 410 ILE Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 480 ASP Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 650 ILE Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 284 ILE Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 6 residue 304 LEU Chi-restraints excluded: chain 6 residue 378 ASP Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 402 ILE Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 516 LEU Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 6 residue 612 VAL Chi-restraints excluded: chain 6 residue 613 VAL Chi-restraints excluded: chain 6 residue 636 CYS Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 6 residue 638 ILE Chi-restraints excluded: chain 6 residue 639 ASP Chi-restraints excluded: chain 6 residue 641 PHE Chi-restraints excluded: chain 6 residue 716 LEU Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 6 residue 783 ASP Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 63 TYR Chi-restraints excluded: chain 7 residue 197 THR Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 291 GLN Chi-restraints excluded: chain 7 residue 302 THR Chi-restraints excluded: chain 7 residue 322 VAL Chi-restraints excluded: chain 7 residue 326 HIS Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 523 ILE Chi-restraints excluded: chain 7 residue 533 ASP Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 661 VAL Chi-restraints excluded: chain 7 residue 678 LYS Chi-restraints excluded: chain 7 residue 715 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 378 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 203 optimal weight: 0.0470 chunk 225 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 505 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN 2 465 ASN ** 2 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 351 ASN ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** 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 = 0.3843 r_free = 0.3843 target = 0.080462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.064263 restraints weight = 252769.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.065988 restraints weight = 159589.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.067183 restraints weight = 114983.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.068007 restraints weight = 90609.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.068611 restraints weight = 76299.964| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41868 Z= 0.128 Angle : 0.762 13.176 56748 Z= 0.370 Chirality : 0.046 0.388 6576 Planarity : 0.004 0.083 7158 Dihedral : 9.546 89.244 5931 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.99 % Favored : 89.99 % Rotamer: Outliers : 3.60 % Allowed : 27.99 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.11), residues: 5015 helix: -1.16 (0.12), residues: 1771 sheet: -2.38 (0.21), residues: 528 loop : -2.83 (0.11), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 81 TYR 0.024 0.001 TYR 3 48 PHE 0.029 0.001 PHE 3 31 TRP 0.025 0.002 TRP C 190 HIS 0.009 0.001 HIS C 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (41868) covalent geometry : angle 0.76216 / 0.37 (56748) hydrogen bonds : bond 0.03569 / 2.25 ( 974) hydrogen bonds : angle 5.31458 / 3.69 ( 2757) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 351 time to evaluate : 1.153 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 62 MET cc_start: 0.6216 (pmm) cc_final: 0.5817 (pmm) REVERT: A 82 ASN cc_start: 0.8088 (m110) cc_final: 0.7611 (m-40) REVERT: A 85 CYS cc_start: 0.9080 (m) cc_final: 0.7970 (t) REVERT: A 149 ILE cc_start: 0.5672 (OUTLIER) cc_final: 0.5408 (mm) REVERT: B 191 LYS cc_start: 0.8060 (mtmm) cc_final: 0.7674 (tppt) REVERT: C 79 MET cc_start: 0.8011 (ppp) cc_final: 0.6996 (pmm) REVERT: C 110 LYS cc_start: 0.8990 (mttp) cc_final: 0.8413 (tptm) REVERT: C 174 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8618 (mttp) REVERT: C 177 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8308 (p90) REVERT: D 183 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7599 (t-90) REVERT: D 280 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: E 92 LEU cc_start: 0.9497 (tp) cc_final: 0.9263 (pp) REVERT: E 558 GLU cc_start: 0.2194 (OUTLIER) cc_final: 0.1666 (pp20) REVERT: E 607 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7726 (pmm) REVERT: 2 259 PHE cc_start: 0.2585 (OUTLIER) cc_final: 0.1957 (m-80) REVERT: 2 272 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7548 (p0) REVERT: 2 315 SER cc_start: 0.9336 (m) cc_final: 0.8964 (p) REVERT: 2 437 ASN cc_start: 0.7302 (t0) cc_final: 0.6454 (p0) REVERT: 2 501 MET cc_start: 0.7874 (tmm) cc_final: 0.7631 (tmm) REVERT: 2 612 MET cc_start: 0.7701 (ttp) cc_final: 0.7134 (ttp) REVERT: 2 616 ASP cc_start: 0.8844 (p0) cc_final: 0.8151 (p0) REVERT: 2 766 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8404 (p90) REVERT: 3 158 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6672 (tptt) REVERT: 3 252 ASP cc_start: 0.7815 (m-30) cc_final: 0.7178 (m-30) REVERT: 3 264 MET cc_start: 0.4579 (mmt) cc_final: 0.4371 (mmt) REVERT: 3 407 MET cc_start: 0.8476 (mpp) cc_final: 0.8163 (mpp) REVERT: 3 708 LEU cc_start: 0.8911 (mp) cc_final: 0.8330 (tt) REVERT: 4 292 ASP cc_start: 0.7755 (m-30) cc_final: 0.7429 (t0) REVERT: 4 314 MET cc_start: 0.8236 (mtm) cc_final: 0.7956 (mpp) REVERT: 4 534 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: 4 777 MET cc_start: 0.8898 (tpt) cc_final: 0.8544 (ptp) REVERT: 4 819 LEU cc_start: 0.8464 (pt) cc_final: 0.8118 (tp) REVERT: 5 65 MET cc_start: 0.9027 (ptm) cc_final: 0.8409 (ppp) REVERT: 5 469 MET cc_start: 0.8684 (mtp) cc_final: 0.8355 (mmm) REVERT: 6 140 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8538 (tt) REVERT: 6 143 MET cc_start: 0.7470 (tpp) cc_final: 0.6491 (tmm) REVERT: 6 355 ASP cc_start: 0.8051 (p0) cc_final: 0.7201 (m-30) REVERT: 6 638 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9136 (pt) REVERT: 6 641 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: 6 701 MET cc_start: 0.7623 (mmm) cc_final: 0.7093 (mmt) REVERT: 6 736 MET cc_start: 0.8710 (mmm) cc_final: 0.8382 (mpp) REVERT: 7 1 MET cc_start: 0.2769 (mtp) cc_final: 0.2038 (tpt) REVERT: 7 143 LEU cc_start: 0.7076 (mt) cc_final: 0.6793 (pp) REVERT: 7 276 ARG cc_start: 0.8299 (mpp80) cc_final: 0.7192 (tpt90) REVERT: 7 291 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: 7 300 MET cc_start: 0.9060 (mmp) cc_final: 0.8801 (mmp) REVERT: 7 498 MET cc_start: 0.8059 (ttt) cc_final: 0.7384 (mpp) REVERT: 7 521 CYS cc_start: 0.8950 (t) cc_final: 0.8311 (p) REVERT: 7 533 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6638 (m-30) REVERT: 7 628 LEU cc_start: 0.5045 (mt) cc_final: 0.4651 (tp) REVERT: 7 678 LYS cc_start: 0.5292 (OUTLIER) cc_final: 0.4519 (pptt) REVERT: 7 707 MET cc_start: 0.0845 (ppp) cc_final: 0.0626 (ppp) outliers start: 161 outliers final: 125 residues processed: 488 average time/residue: 0.1957 time to fit residues: 169.6432 Evaluate side-chains 471 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 328 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 558 GLU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain 2 residue 231 ILE Chi-restraints excluded: chain 2 residue 249 LEU Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 259 PHE Chi-restraints excluded: chain 2 residue 272 ASP Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 495 ASP Chi-restraints excluded: chain 2 residue 541 LEU Chi-restraints excluded: chain 2 residue 580 VAL Chi-restraints excluded: chain 2 residue 588 GLU Chi-restraints excluded: chain 2 residue 606 ILE Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 640 LEU Chi-restraints excluded: chain 2 residue 704 VAL Chi-restraints excluded: chain 2 residue 766 TYR Chi-restraints excluded: chain 2 residue 827 GLU Chi-restraints excluded: chain 2 residue 840 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 129 LEU Chi-restraints excluded: chain 3 residue 139 VAL Chi-restraints excluded: chain 3 residue 158 LYS Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 222 THR Chi-restraints excluded: chain 3 residue 273 SER Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 503 HIS Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 672 THR Chi-restraints excluded: chain 3 residue 704 THR Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 326 ILE Chi-restraints excluded: chain 4 residue 458 LYS Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 602 THR Chi-restraints excluded: chain 4 residue 622 VAL Chi-restraints excluded: chain 4 residue 629 CYS Chi-restraints excluded: chain 4 residue 648 VAL Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 744 VAL Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 817 VAL Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 61 LEU Chi-restraints excluded: chain 5 residue 71 TYR Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 251 ILE Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 410 ILE Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 480 ASP Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 6 residue 378 ASP Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 402 ILE Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 443 LEU Chi-restraints excluded: chain 6 residue 612 VAL Chi-restraints excluded: chain 6 residue 613 VAL Chi-restraints excluded: chain 6 residue 636 CYS Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 6 residue 638 ILE Chi-restraints excluded: chain 6 residue 639 ASP Chi-restraints excluded: chain 6 residue 641 PHE Chi-restraints excluded: chain 6 residue 716 LEU Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 63 TYR Chi-restraints excluded: chain 7 residue 197 THR Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 291 GLN Chi-restraints excluded: chain 7 residue 302 THR Chi-restraints excluded: chain 7 residue 322 VAL Chi-restraints excluded: chain 7 residue 326 HIS Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 523 ILE Chi-restraints excluded: chain 7 residue 527 ASP Chi-restraints excluded: chain 7 residue 533 ASP Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 661 VAL Chi-restraints excluded: chain 7 residue 678 LYS Chi-restraints excluded: chain 7 residue 715 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 313 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 178 optimal weight: 0.0370 chunk 363 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 chunk 198 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 412 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 overall best weight: 1.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 289 ASN ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 517 ASN ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 458 HIS 6 550 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.080286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.064125 restraints weight = 250267.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.065850 restraints weight = 158391.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.067034 restraints weight = 114289.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.067862 restraints weight = 90109.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.068395 restraints weight = 75853.990| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.7821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 41868 Z= 0.126 Angle : 0.763 13.212 56748 Z= 0.368 Chirality : 0.046 0.308 6576 Planarity : 0.004 0.078 7158 Dihedral : 9.475 87.561 5931 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 3.20 % Allowed : 28.26 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.11), residues: 5015 helix: -1.11 (0.12), residues: 1779 sheet: -2.33 (0.21), residues: 534 loop : -2.79 (0.11), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 386 TYR 0.026 0.001 TYR 3 48 PHE 0.029 0.001 PHE 3 31 TRP 0.022 0.002 TRP C 190 HIS 0.013 0.001 HIS 6 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (41868) covalent geometry : angle 0.76250 / 0.37 (56748) hydrogen bonds : bond 0.03421 / 2.17 ( 974) hydrogen bonds : angle 5.22642 / 3.63 ( 2757) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 341 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8271 (pm20) REVERT: A 62 MET cc_start: 0.6219 (pmm) cc_final: 0.5819 (pmm) REVERT: A 82 ASN cc_start: 0.8351 (m110) cc_final: 0.7866 (m-40) REVERT: A 85 CYS cc_start: 0.9098 (m) cc_final: 0.8026 (t) REVERT: A 149 ILE cc_start: 0.5696 (OUTLIER) cc_final: 0.5431 (mm) REVERT: B 134 PHE cc_start: 0.7651 (t80) cc_final: 0.7423 (t80) REVERT: B 191 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7708 (tppt) REVERT: C 12 ASP cc_start: 0.8051 (m-30) cc_final: 0.7223 (p0) REVERT: C 79 MET cc_start: 0.7898 (ppp) cc_final: 0.6813 (pmm) REVERT: C 110 LYS cc_start: 0.9042 (mttp) cc_final: 0.8828 (mtpt) REVERT: C 113 MET cc_start: 0.6447 (mmm) cc_final: 0.6096 (ptp) REVERT: C 174 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8662 (pttm) REVERT: C 177 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8312 (p90) REVERT: D 183 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7734 (t-90) REVERT: D 280 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: E 92 LEU cc_start: 0.9501 (tp) cc_final: 0.9269 (pp) REVERT: E 558 GLU cc_start: 0.2149 (OUTLIER) cc_final: 0.1632 (pp20) REVERT: E 607 MET cc_start: 0.8009 (mpp) cc_final: 0.7757 (pmm) REVERT: 2 259 PHE cc_start: 0.2560 (OUTLIER) cc_final: 0.1938 (m-80) REVERT: 2 272 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7546 (p0) REVERT: 2 315 SER cc_start: 0.9327 (m) cc_final: 0.8934 (t) REVERT: 2 437 ASN cc_start: 0.7228 (t0) cc_final: 0.6375 (p0) REVERT: 2 612 MET cc_start: 0.7713 (ttp) cc_final: 0.7159 (ttp) REVERT: 2 616 ASP cc_start: 0.8842 (p0) cc_final: 0.8154 (p0) REVERT: 2 766 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8366 (p90) REVERT: 3 158 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6709 (tptt) REVERT: 3 252 ASP cc_start: 0.7842 (m-30) cc_final: 0.7216 (m-30) REVERT: 3 264 MET cc_start: 0.4640 (mmt) cc_final: 0.4410 (mmt) REVERT: 3 407 MET cc_start: 0.8454 (mpp) cc_final: 0.8110 (mpp) REVERT: 3 708 LEU cc_start: 0.8928 (mp) cc_final: 0.8338 (tt) REVERT: 4 292 ASP cc_start: 0.7751 (m-30) cc_final: 0.7429 (t0) REVERT: 4 314 MET cc_start: 0.8273 (mtm) cc_final: 0.7971 (mpp) REVERT: 4 534 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: 4 637 MET cc_start: 0.7561 (mmp) cc_final: 0.7289 (mmt) REVERT: 4 777 MET cc_start: 0.8901 (tpt) cc_final: 0.8456 (ptp) REVERT: 4 819 LEU cc_start: 0.8454 (pt) cc_final: 0.8110 (tp) REVERT: 5 65 MET cc_start: 0.9052 (ptm) cc_final: 0.8440 (ppp) REVERT: 5 469 MET cc_start: 0.8679 (mtp) cc_final: 0.8352 (mmm) REVERT: 6 140 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8541 (tt) REVERT: 6 143 MET cc_start: 0.7406 (tpp) cc_final: 0.6507 (tmm) REVERT: 6 355 ASP cc_start: 0.8055 (p0) cc_final: 0.7195 (m-30) REVERT: 6 641 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: 6 701 MET cc_start: 0.7673 (mmm) cc_final: 0.7136 (mmt) REVERT: 7 1 MET cc_start: 0.2465 (mtp) cc_final: 0.2016 (tpp) REVERT: 7 143 LEU cc_start: 0.7065 (mt) cc_final: 0.6785 (pp) REVERT: 7 276 ARG cc_start: 0.8377 (mpp80) cc_final: 0.7077 (tpt90) REVERT: 7 291 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.7022 (pm20) REVERT: 7 300 MET cc_start: 0.9019 (mmp) cc_final: 0.8763 (mmp) REVERT: 7 498 MET cc_start: 0.8045 (ttt) cc_final: 0.7365 (mpp) REVERT: 7 521 CYS cc_start: 0.8915 (t) cc_final: 0.8261 (p) REVERT: 7 533 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6669 (m-30) REVERT: 7 628 LEU cc_start: 0.5314 (mt) cc_final: 0.4969 (tp) REVERT: 7 678 LYS cc_start: 0.5301 (OUTLIER) cc_final: 0.4530 (pptt) REVERT: 7 707 MET cc_start: 0.0856 (ppp) cc_final: 0.0650 (ppp) outliers start: 143 outliers final: 118 residues processed: 469 average time/residue: 0.1970 time to fit residues: 163.2404 Evaluate side-chains 465 residues out of total 4561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 331 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 558 GLU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain 2 residue 231 ILE Chi-restraints excluded: chain 2 residue 249 LEU Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 259 PHE Chi-restraints excluded: chain 2 residue 272 ASP Chi-restraints excluded: chain 2 residue 282 HIS Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 495 ASP Chi-restraints excluded: chain 2 residue 508 HIS Chi-restraints excluded: chain 2 residue 541 LEU Chi-restraints excluded: chain 2 residue 580 VAL Chi-restraints excluded: chain 2 residue 588 GLU Chi-restraints excluded: chain 2 residue 606 ILE Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 640 LEU Chi-restraints excluded: chain 2 residue 704 VAL Chi-restraints excluded: chain 2 residue 766 TYR Chi-restraints excluded: chain 2 residue 840 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 129 LEU Chi-restraints excluded: chain 3 residue 139 VAL Chi-restraints excluded: chain 3 residue 158 LYS Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 251 ILE Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 503 HIS Chi-restraints excluded: chain 3 residue 672 THR Chi-restraints excluded: chain 3 residue 704 THR Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 326 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 389 CYS Chi-restraints excluded: chain 4 residue 458 LYS Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 602 THR Chi-restraints excluded: chain 4 residue 622 VAL Chi-restraints excluded: chain 4 residue 629 CYS Chi-restraints excluded: chain 4 residue 648 VAL Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 744 VAL Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 817 VAL Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 61 LEU Chi-restraints excluded: chain 5 residue 71 TYR Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 251 ILE Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 410 ILE Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 480 ASP Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 443 LEU Chi-restraints excluded: chain 6 residue 612 VAL Chi-restraints excluded: chain 6 residue 613 VAL Chi-restraints excluded: chain 6 residue 636 CYS Chi-restraints excluded: chain 6 residue 639 ASP Chi-restraints excluded: chain 6 residue 641 PHE Chi-restraints excluded: chain 6 residue 716 LEU Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 63 TYR Chi-restraints excluded: chain 7 residue 197 THR Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 291 GLN Chi-restraints excluded: chain 7 residue 322 VAL Chi-restraints excluded: chain 7 residue 326 HIS Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 523 ILE Chi-restraints excluded: chain 7 residue 533 ASP Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 661 VAL Chi-restraints excluded: chain 7 residue 678 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 222 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 387 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 447 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 72 optimal weight: 50.0000 chunk 113 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 342 ASN E 503 GLN ** 2 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 779 HIS ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.076780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.060702 restraints weight = 258379.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.062361 restraints weight = 161542.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.063491 restraints weight = 116189.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.064285 restraints weight = 91908.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.064815 restraints weight = 77587.529| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.8562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 41868 Z= 0.197 Angle : 0.811 12.813 56748 Z= 0.402 Chirality : 0.047 0.251 6576 Planarity : 0.005 0.073 7158 Dihedral : 9.543 88.718 5931 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.84 % Favored : 88.12 % Rotamer: Outliers : 3.42 % Allowed : 28.19 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.11), residues: 5015 helix: -1.10 (0.12), residues: 1783 sheet: -2.36 (0.21), residues: 522 loop : -2.84 (0.11), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 386 TYR 0.025 0.002 TYR 3 48 PHE 0.032 0.002 PHE 3 31 TRP 0.029 0.002 TRP C 190 HIS 0.009 0.001 HIS C 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (41868) covalent geometry : angle 0.81055 / 0.40 (56748) hydrogen bonds : bond 0.03892 / 2.53 ( 974) hydrogen bonds : angle 5.54024 / 3.84 ( 2757) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8245.84 seconds wall clock time: 143 minutes 8.30 seconds (8588.30 seconds total)