Starting phenix.real_space_refine (version: dev) on Tue May 17 15:58:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0m_20607/05_2022/6u0m_20607_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0m_20607/05_2022/6u0m_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0m_20607/05_2022/6u0m_20607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0m_20607/05_2022/6u0m_20607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0m_20607/05_2022/6u0m_20607_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0m_20607/05_2022/6u0m_20607_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/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, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG: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: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP: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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} 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: 21.47, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 15.91 Conformation dependent library (CDL) restraints added in 5.6 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... running ksdssp... Secondary structure from input PDB file: 178 helices and 35 sheets defined 33.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 4 through 23 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 34 through 59 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) removed outlier: 5.018A pdb=" N GLN A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 97 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) removed outlier: 4.087A pdb=" N ILE A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 removed outlier: 4.019A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'B' and resid 16 through 20 removed outlier: 3.910A pdb=" N VAL B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 16 through 20' 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 101 through 104 No H-bonds generated for 'chain 'B' and resid 101 through 104' Processing helix chain 'B' and resid 119 through 125 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 143 through 162 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) removed outlier: 3.942A pdb=" N TYR B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 197 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 54 removed outlier: 4.202A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 87 through 90 No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 105 through 115 removed outlier: 4.169A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 123 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) No H-bonds generated for 'chain 'C' and resid 118 through 123' Processing helix chain 'C' and resid 125 through 137 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 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 174 through 191 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 58 through 72 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) removed outlier: 5.388A pdb=" N GLU D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 106 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 124 through 151 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 153 through 163 removed outlier: 4.527A pdb=" N LEU D 156 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG D 159 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU D 163 " --> pdb=" O GLN D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 194 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 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 284 through 286 No H-bonds generated for 'chain 'D' and resid 284 through 286' Processing helix chain 'E' and resid 8 through 18 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) Processing helix chain 'E' and resid 36 through 50 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 68 through 71 No H-bonds generated for 'chain 'E' and resid 68 through 71' Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 153 through 156 removed outlier: 4.006A pdb=" N LYS E 156 " --> pdb=" O GLY E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.518A pdb=" N VAL E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 removed outlier: 3.775A pdb=" N ILE E 255 " --> pdb=" O ILE E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 279 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) Processing helix chain 'E' and resid 289 through 301 Proline residue: E 293 - end of helix 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 336 through 340 Processing helix chain 'E' and resid 342 through 346 Processing helix chain 'E' and resid 355 through 358 No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 380 through 391 removed outlier: 5.165A pdb=" N LYS E 385 " --> pdb=" O HIS E 382 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG E 386 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 399 No H-bonds generated for 'chain 'E' and resid 396 through 399' Processing helix chain 'E' and resid 424 through 433 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 465 through 484 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) removed outlier: 5.315A pdb=" N ALA E 483 " --> pdb=" O LEU E 479 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU E 484 " --> pdb=" O SER E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 516 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) Processing helix chain 'E' and resid 536 through 539 removed outlier: 3.697A pdb=" N TYR E 539 " --> pdb=" O LEU E 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 536 through 539' Processing helix chain 'E' and resid 542 through 555 removed outlier: 4.017A pdb=" N LEU E 546 " --> pdb=" O LEU E 543 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY E 549 " --> pdb=" O LEU E 546 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE E 553 " --> pdb=" O ASN E 550 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS E 555 " --> pdb=" O LEU E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 577 No H-bonds generated for 'chain 'E' and resid 575 through 577' Processing helix chain 'E' and resid 605 through 615 removed outlier: 3.900A pdb=" N GLN E 611 " --> pdb=" O MET E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 642 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) No H-bonds generated for 'chain 'E' and resid 634 through 642' Processing helix chain '2' and resid 203 through 216 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 227 through 236 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 246 through 251 Processing helix chain '2' and resid 257 through 259 No H-bonds generated for 'chain '2' and resid 257 through 259' Processing helix chain '2' and resid 266 through 280 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) Processing helix chain '2' and resid 286 through 288 No H-bonds generated for 'chain '2' and resid 286 through 288' Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 412 through 414 No H-bonds generated for 'chain '2' and resid 412 through 414' Processing helix chain '2' and resid 494 through 497 No H-bonds generated for 'chain '2' and resid 494 through 497' Processing helix chain '2' and resid 509 through 520 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 559 removed outlier: 4.045A pdb=" N ILE 2 552 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU 2 553 " --> pdb=" O SER 2 550 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL 2 556 " --> pdb=" O LEU 2 553 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR 2 559 " --> pdb=" O VAL 2 556 " (cutoff:3.500A) Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 610 through 616 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) Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 676 removed outlier: 3.611A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) Processing helix chain '2' and resid 690 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 750 removed outlier: 3.568A pdb=" N LYS 2 750 " --> pdb=" O GLN 2 746 " (cutoff:3.500A) Processing helix chain '2' and resid 764 through 770 removed outlier: 4.779A pdb=" N HIS 2 768 " --> pdb=" O LYS 2 765 " (cutoff:3.500A) Processing helix chain '2' and resid 784 through 797 removed outlier: 4.093A pdb=" N ARG 2 788 " --> pdb=" O LYS 2 785 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR 2 790 " --> pdb=" O SER 2 787 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA 2 791 " --> pdb=" O ARG 2 788 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP 2 792 " --> pdb=" O VAL 2 789 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU 2 793 " --> pdb=" O TYR 2 790 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG 2 794 " --> pdb=" O ALA 2 791 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 824 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) removed outlier: 3.692A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 832 through 838 Processing helix chain '2' and resid 842 through 848 removed outlier: 5.575A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) Processing helix chain '2' and resid 851 through 858 removed outlier: 3.737A pdb=" N ARG 2 854 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG 2 855 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU 2 857 " --> pdb=" O ARG 2 854 " (cutoff:3.500A) Processing helix chain '2' and resid 860 through 862 No H-bonds generated for 'chain '2' and resid 860 through 862' Processing helix chain '3' and resid 22 through 30 Processing helix chain '3' and resid 39 through 47 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) Processing helix chain '3' and resid 49 through 52 No H-bonds generated for 'chain '3' and resid 49 through 52' Processing helix chain '3' and resid 100 through 104 Processing helix chain '3' and resid 109 through 115 removed outlier: 3.674A pdb=" N GLY 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE 3 114 " --> pdb=" O PHE 3 110 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 109 through 115' Processing helix chain '3' and resid 122 through 134 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) 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 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 344 through 354 removed outlier: 3.581A pdb=" N ASN 3 351 " --> pdb=" O ILE 3 347 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 365 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 375 through 386 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) Processing helix chain '3' and resid 448 through 450 No H-bonds generated for 'chain '3' and resid 448 through 450' Processing helix chain '3' and resid 480 through 491 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 537 through 542 Processing helix chain '3' and resid 557 through 564 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 653 through 663 Processing helix chain '3' and resid 675 through 687 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 716 removed outlier: 3.919A pdb=" N ILE 3 706 " --> pdb=" O GLU 3 703 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU 3 708 " --> pdb=" O LEU 3 705 " (cutoff:3.500A) Processing helix chain '3' and resid 724 through 737 removed outlier: 3.765A pdb=" N VAL 3 728 " --> pdb=" O ASP 3 725 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA 3 729 " --> pdb=" O ALA 3 726 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN 3 731 " --> pdb=" O VAL 3 728 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU 3 732 " --> pdb=" O ALA 3 729 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE 3 735 " --> pdb=" O LEU 3 732 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU 3 737 " --> pdb=" O ARG 3 734 " (cutoff:3.500A) Processing helix chain '4' and resid 189 through 199 Processing helix chain '4' and resid 225 through 236 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) removed outlier: 3.658A pdb=" N LEU 4 236 " --> pdb=" O GLU 4 232 " (cutoff:3.500A) Processing helix chain '4' and resid 255 through 261 Processing helix chain '4' and resid 267 through 284 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 291 through 293 No H-bonds generated for 'chain '4' and resid 291 through 293' Processing helix chain '4' and resid 504 through 514 Processing helix chain '4' and resid 516 through 525 removed outlier: 4.483A pdb=" N TYR 4 519 " --> pdb=" O GLU 4 516 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG 4 524 " --> pdb=" O LEU 4 521 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER 4 525 " --> pdb=" O LEU 4 522 " (cutoff:3.500A) Processing helix chain '4' and resid 536 through 544 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 574 through 584 removed outlier: 3.820A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 620 through 623 No H-bonds generated for 'chain '4' and resid 620 through 623' Processing helix chain '4' and resid 645 through 650 Processing helix chain '4' and resid 696 through 699 No H-bonds generated for 'chain '4' and resid 696 through 699' Processing helix chain '4' and resid 717 through 725 removed outlier: 3.508A pdb=" N LEU 4 724 " --> pdb=" O LEU 4 720 " (cutoff:3.500A) Processing helix chain '4' and resid 746 through 757 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) Processing helix chain '4' and resid 764 through 777 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 796 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 822 through 832 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 856 through 875 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) Processing helix chain '4' and resid 883 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 905 through 911 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) Processing helix chain '5' and resid 25 through 32 removed outlier: 3.501A pdb=" N PHE 5 31 " --> pdb=" O ILE 5 27 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 54 removed outlier: 4.768A pdb=" N ASN 5 52 " --> pdb=" O ASP 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 65 through 70 removed outlier: 3.639A pdb=" N ILE 5 69 " --> pdb=" O MET 5 65 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLY 5 70 " --> pdb=" O GLU 5 66 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 65 through 70' Processing helix chain '5' and resid 73 through 80 removed outlier: 3.704A pdb=" N LEU 5 79 " --> pdb=" O ILE 5 75 " (cutoff:3.500A) Processing helix chain '5' and resid 85 through 100 Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 352 through 361 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 366 through 373 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 382 through 393 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 428 through 432 removed outlier: 3.930A pdb=" N VAL 5 432 " --> pdb=" O PHE 5 428 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 428 through 432' Processing helix chain '5' and resid 446 through 450 removed outlier: 3.690A pdb=" N THR 5 450 " --> pdb=" O ALA 5 447 " (cutoff:3.500A) Processing helix chain '5' and resid 489 through 493 removed outlier: 3.558A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 489 through 493' Processing helix chain '5' and resid 530 through 533 Processing helix chain '5' and resid 564 through 576 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) Processing helix chain '5' and resid 581 through 584 No H-bonds generated for 'chain '5' and resid 581 through 584' Processing helix chain '5' and resid 596 through 607 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) Processing helix chain '5' and resid 617 through 634 removed outlier: 3.850A pdb=" N GLU 5 620 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU 5 622 " --> pdb=" O ALA 5 619 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER 5 623 " --> pdb=" O GLU 5 620 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE 5 626 " --> pdb=" O SER 5 623 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL 5 627 " --> pdb=" O SER 5 624 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR 5 628 " --> pdb=" O ASN 5 625 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG 5 630 " --> pdb=" O VAL 5 627 " (cutoff:3.500A) Processing helix chain '5' and resid 637 through 639 No H-bonds generated for 'chain '5' and resid 637 through 639' Processing helix chain '5' and resid 653 through 667 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 674 through 687 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) removed outlier: 3.997A pdb=" N ALA 5 686 " --> pdb=" O ARG 5 682 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER 5 687 " --> pdb=" O LEU 5 683 " (cutoff:3.500A) Processing helix chain '5' and resid 689 through 691 No H-bonds generated for 'chain '5' and resid 689 through 691' Processing helix chain '6' and resid 104 through 120 Processing helix chain '6' and resid 135 through 146 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 159 Processing helix chain '6' and resid 167 through 172 removed outlier: 3.721A pdb=" N SER 6 171 " --> pdb=" O ALA 6 167 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU 6 172 " --> pdb=" O MET 6 168 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 167 through 172' Processing helix chain '6' and resid 174 through 192 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 365 through 367 No H-bonds generated for 'chain '6' and resid 365 through 367' Processing helix chain '6' and resid 434 through 436 No H-bonds generated for 'chain '6' and resid 434 through 436' Processing helix chain '6' and resid 512 through 521 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) removed outlier: 3.748A pdb=" N LYS 6 521 " --> pdb=" O LYS 6 517 " (cutoff:3.500A) Processing helix chain '6' and resid 525 through 532 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) removed outlier: 3.614A pdb=" N SER 6 532 " --> pdb=" O LYS 6 528 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 551 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 591 removed outlier: 3.551A pdb=" N GLN 6 583 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE 6 584 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU 6 585 " --> pdb=" O SER 6 582 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL 6 588 " --> pdb=" O LEU 6 585 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL 6 589 " --> pdb=" O LYS 6 586 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY 6 590 " --> pdb=" O TYR 6 587 " (cutoff:3.500A) Processing helix chain '6' and resid 629 through 631 No H-bonds generated for 'chain '6' and resid 629 through 631' Processing helix chain '6' and resid 641 through 643 No H-bonds generated for 'chain '6' and resid 641 through 643' Processing helix chain '6' and resid 648 through 657 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) Processing helix chain '6' and resid 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 704 through 708 Processing helix chain '6' and resid 723 through 735 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 748 through 758 removed outlier: 3.588A pdb=" N LYS 6 756 " --> pdb=" O ARG 6 752 " (cutoff:3.500A) Processing helix chain '6' and resid 768 through 784 removed outlier: 3.849A pdb=" N VAL 6 774 " --> pdb=" O SER 6 771 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU 6 775 " --> pdb=" O TYR 6 772 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR 6 777 " --> pdb=" O VAL 6 774 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS 6 778 " --> pdb=" O GLU 6 775 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG 6 781 " --> pdb=" O LYS 6 778 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS 6 782 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP 6 784 " --> pdb=" O ARG 6 781 " (cutoff:3.500A) Processing helix chain '6' and resid 798 through 805 removed outlier: 4.278A pdb=" N SER 6 802 " --> pdb=" O ARG 6 798 " (cutoff:3.500A) Processing helix chain '6' and resid 807 through 813 removed outlier: 3.877A pdb=" N ALA 6 811 " --> pdb=" O SER 6 807 " (cutoff:3.500A) Processing helix chain '6' and resid 825 through 838 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 15 through 24 removed outlier: 4.152A pdb=" N GLU 7 20 " --> pdb=" O ASN 7 16 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE 7 24 " --> pdb=" O GLU 7 20 " (cutoff:3.500A) Processing helix chain '7' and resid 62 through 71 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) Processing helix chain '7' and resid 83 through 90 removed outlier: 4.386A pdb=" N TYR 7 88 " --> pdb=" O ASP 7 84 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 108 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 112 No H-bonds generated for 'chain '7' and resid 110 through 112' Processing helix chain '7' and resid 115 through 124 removed outlier: 3.698A pdb=" N ASP 7 122 " --> pdb=" O CYS 7 118 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASN 7 123 " --> pdb=" O ARG 7 119 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 140 through 154 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) removed outlier: 3.765A pdb=" N MET 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 227 through 229 No H-bonds generated for 'chain '7' and resid 227 through 229' Processing helix chain '7' and resid 398 through 407 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 413 through 417 Processing helix chain '7' and resid 426 through 437 removed outlier: 3.596A pdb=" N LYS 7 430 " --> pdb=" O LEU 7 426 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 7 431 " --> pdb=" O ASP 7 427 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU 7 432 " --> pdb=" O VAL 7 428 " (cutoff:3.500A) 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 474 removed outlier: 4.611A pdb=" N LYS 7 471 " --> pdb=" O GLN 7 468 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA 7 472 " --> pdb=" O LEU 7 469 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 541 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) removed outlier: 4.110A pdb=" N HIS 7 538 " --> pdb=" O ARG 7 534 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL 7 540 " --> pdb=" O ALA 7 536 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) Processing helix chain '7' and resid 587 through 591 Processing helix chain '7' and resid 606 through 620 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) removed outlier: 4.736A pdb=" N VAL 7 619 " --> pdb=" O HIS 7 615 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N HIS 7 620 " --> pdb=" O VAL 7 616 " (cutoff:3.500A) Processing helix chain '7' and resid 635 through 647 Processing helix chain '7' and resid 660 through 666 Processing helix chain '7' and resid 668 through 674 removed outlier: 3.634A pdb=" N GLU 7 674 " --> pdb=" O ASP 7 670 " (cutoff:3.500A) Processing helix chain '7' and resid 686 through 702 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 710 through 721 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) Processing sheet with id= A, 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) Processing sheet with id= B, first strand: chain 'B' and resid 24 through 26 Processing sheet with id= C, first strand: chain 'B' and resid 27 through 29 Processing sheet with id= D, first strand: chain 'C' and resid 15 through 18 Processing sheet with id= E, first strand: chain 'D' and resid 228 through 230 removed outlier: 3.628A pdb=" N VAL D 228 " --> pdb=" O MET D 277 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET D 277 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.571A pdb=" N VAL E 31 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 120 through 122 removed outlier: 4.068A pdb=" N VAL E 122 " --> pdb=" O GLN E 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '2' and resid 317 through 323 removed outlier: 3.647A pdb=" N VAL 2 424 " --> pdb=" O GLY 2 322 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU 2 425 " --> pdb=" O LYS 2 457 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS 2 457 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR 2 427 " --> pdb=" O SER 2 455 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) Processing sheet with id= I, 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= J, first strand: chain '2' and resid 389 through 391 removed outlier: 3.735A pdb=" N LEU 2 390 " --> pdb=" O ARG 2 406 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '2' and resid 540 through 542 Processing sheet with id= L, first strand: chain '2' and resid 565 through 567 removed outlier: 6.793A pdb=" N VAL 2 603 " --> pdb=" O ALA 2 566 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, 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= N, 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: 4.130A pdb=" N VAL 3 295 " --> pdb=" O ASN 3 324 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU 3 322 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU 3 301 " --> pdb=" O LYS 3 318 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS 3 318 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '3' and resid 201 through 203 Processing sheet with id= P, first strand: chain '3' and resid 254 through 258 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= Q, first strand: chain '3' and resid 406 through 409 removed outlier: 3.697A pdb=" N PHE 3 547 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '3' and resid 193 through 198 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) Processing sheet with id= S, first strand: chain '4' and resid 240 through 243 removed outlier: 7.120A pdb=" N LYS 4 302 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU 4 243 " --> pdb=" O LYS 4 302 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG 4 304 " --> pdb=" O LEU 4 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain '4' and resid 414 through 416 removed outlier: 4.065A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (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= U, first strand: chain '4' and resid 563 through 566 removed outlier: 6.962A pdb=" N ILE 4 671 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N LEU 4 566 " --> pdb=" O ILE 4 671 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA 4 673 " --> pdb=" O LEU 4 566 " (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) No H-bonds generated for sheet with id= U Processing sheet with id= V, 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= W, first strand: chain '5' and resid 290 through 296 removed outlier: 4.654A pdb=" N THR 5 290 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE 5 166 " --> pdb=" O THR 5 290 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE 5 167 " --> pdb=" O LYS 5 257 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU 5 258 " --> pdb=" O LEU 5 274 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 181 through 183 removed outlier: 3.940A pdb=" N MET 5 182 " --> pdb=" O ILE 5 242 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 436 through 438 removed outlier: 6.935A pdb=" N VAL 5 476 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, 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= Z Processing sheet with id= AA, 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= AB, first strand: chain '5' and resid 452 through 456 removed outlier: 3.718A pdb=" N SER 5 452 " --> pdb=" O GLY 5 466 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY 5 466 " --> pdb=" O SER 5 452 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLN 5 454 " --> pdb=" O LEU 5 464 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU 5 464 " --> pdb=" O GLN 5 454 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP 5 456 " --> pdb=" O PHE 5 462 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE 5 462 " --> pdb=" O ASP 5 456 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, 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= AD, first strand: chain '6' and resid 301 through 303 Processing sheet with id= AE, 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= AF, first strand: chain '6' and resid 637 through 639 removed outlier: 5.683A pdb=" N LEU 6 679 " --> pdb=" O ILE 6 638 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, 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= AH, first strand: chain '7' and resid 331 through 333 removed outlier: 3.753A pdb=" N LEU 7 331 " --> pdb=" O ILE 7 315 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS 7 313 " --> pdb=" O ILE 7 333 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE 7 244 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY 7 353 " --> pdb=" O ILE 7 239 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL 7 349 " --> pdb=" O GLY 7 243 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '7' and resid 456 through 459 766 hydrogen bonds defined for protein. 2007 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: 11.67 Time building geometry restraints manager: 17.19 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: 97.03 - 104.99: 794 104.99 - 112.96: 22780 112.96 - 120.92: 20601 120.92 - 128.89: 12343 128.89 - 136.85: 230 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: 22026 17.95 - 35.91: 2805 35.91 - 53.86: 551 53.86 - 71.82: 149 71.82 - 89.77: 36 Dihedral angle restraints: 25567 sinusoidal: 10612 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 25564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 6241 0.119 - 0.239: 317 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: 5617 2.75 - 3.29: 40628 3.29 - 3.82: 68249 3.82 - 4.36: 74540 4.36 - 4.90: 118766 Nonbonded interactions: 307800 Sorted by model distance: nonbonded pdb=" O PHE E 327 " pdb=" OH TYR E 340 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR 6 621 " pdb=" O ILE 6 668 " model vdw 2.255 2.440 nonbonded pdb=" O VAL E 148 " pdb=" OG1 THR E 151 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR 3 523 " pdb=" O ASN 3 532 " model vdw 2.276 2.440 nonbonded pdb=" O LEU 4 828 " pdb=" OG SER 4 831 " model vdw 2.281 2.440 ... (remaining 307795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.200 Check model and map are aligned: 0.560 Convert atoms to be neutral: 0.320 Process input model: 92.130 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.250 ------------------------------------------------------------------------------- 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 : 0.005 0.078 41868 Z= 0.356 Angle : 1.046 23.140 56748 Z= 0.612 Chirality : 0.060 0.597 6576 Planarity : 0.007 0.231 7158 Dihedral : 16.737 89.774 15841 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.16 % Favored : 86.66 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 22 poor density : 961 time to evaluate : 5.433 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: 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 outliers start: 22 outliers final: 4 residues processed: 981 average time/residue: 0.5607 time to fit residues: 872.9999 Evaluate side-chains 459 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 455 time to evaluate : 4.873 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3401 time to fit residues: 9.2366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 429 optimal weight: 5.9990 chunk 385 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 398 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 chunk 462 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 59 GLN A 90 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 6 HIS B 128 ASN B 167 HIS ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 103 HIS ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 162 ASN D 249 ASN E 7 GLN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 70 HIS ** E 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 604 ASN ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 508 HIS 2 528 ASN 2 531 HIS 2 551 GLN ** 2 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 849 GLN ** 3 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 253 HIS ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 417 GLN 3 507 ASN 3 517 ASN 3 531 GLN 3 677 ASN 4 184 ASN ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 247 ASN 4 259 HIS 4 260 GLN 4 274 GLN ** 4 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 413 HIS ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 646 HIS 4 683 ASN 4 726 ASN 4 911 GLN 4 912 GLN 5 145 GLN ** 5 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 494 HIS 5 539 ASN 5 574 ASN 5 581 ASN ** 5 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 139 GLN 6 434 ASN 6 550 GLN 6 669 HIS ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 6 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 814 ASN 7 30 GLN 7 76 ASN 7 87 GLN 7 237 GLN ** 7 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS 7 585 ASN 7 683 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.118 41868 Z= 0.430 Angle : 0.981 15.030 56748 Z= 0.511 Chirality : 0.051 0.293 6576 Planarity : 0.008 0.142 7158 Dihedral : 10.467 72.928 5891 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.74 % Favored : 87.22 % Rotamer Outliers : 5.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.10), residues: 5015 helix: -2.66 (0.10), residues: 1693 sheet: -3.18 (0.19), residues: 528 loop : -3.42 (0.10), residues: 2794 *********************** 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 716 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 464 time to evaluate : 5.000 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 outliers start: 252 outliers final: 125 residues processed: 675 average time/residue: 0.4749 time to fit residues: 543.3802 Evaluate side-chains 485 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 360 time to evaluate : 4.792 Switching outliers to nearest non-outliers outliers start: 125 outliers final: 1 residues processed: 125 average time/residue: 0.3728 time to fit residues: 94.1206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 256 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 384 optimal weight: 20.0000 chunk 314 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 463 optimal weight: 9.9990 chunk 500 optimal weight: 6.9990 chunk 412 optimal weight: 7.9990 chunk 459 optimal weight: 40.0000 chunk 157 optimal weight: 7.9990 chunk 371 optimal weight: 0.3980 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 333 GLN ** 2 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 253 HIS ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 374 HIS ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 254 GLN 5 676 HIS ** 6 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 585 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 41868 Z= 0.330 Angle : 0.811 14.002 56748 Z= 0.416 Chirality : 0.048 0.262 6576 Planarity : 0.007 0.112 7158 Dihedral : 10.255 81.953 5891 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer Outliers : 5.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.10), residues: 5015 helix: -2.12 (0.11), residues: 1728 sheet: -2.93 (0.19), residues: 557 loop : -3.29 (0.11), residues: 2730 *********************** 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 627 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 388 time to evaluate : 5.420 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 outliers start: 239 outliers final: 93 residues processed: 591 average time/residue: 0.4664 time to fit residues: 474.4294 Evaluate side-chains 411 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 318 time to evaluate : 5.373 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 0 residues processed: 93 average time/residue: 0.3613 time to fit residues: 70.4221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 457 optimal weight: 0.0970 chunk 348 optimal weight: 0.0670 chunk 240 optimal weight: 0.0470 chunk 51 optimal weight: 9.9990 chunk 220 optimal weight: 0.9990 chunk 310 optimal weight: 30.0000 chunk 464 optimal weight: 7.9990 chunk 492 optimal weight: 0.5980 chunk 242 optimal weight: 20.0000 chunk 440 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN ** 2 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 627 GLN ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 94 HIS ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 312 ASN 3 349 ASN 3 569 HIS ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 579 GLN ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 632 GLN 6 274 HIS 6 357 GLN ** 6 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.101 41868 Z= 0.178 Angle : 0.705 18.991 56748 Z= 0.345 Chirality : 0.044 0.230 6576 Planarity : 0.005 0.083 7158 Dihedral : 9.718 74.112 5891 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.11), residues: 5015 helix: -1.75 (0.11), residues: 1701 sheet: -2.60 (0.20), residues: 539 loop : -3.06 (0.11), residues: 2775 *********************** 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 493 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 386 time to evaluate : 5.624 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 outliers start: 107 outliers final: 47 residues processed: 477 average time/residue: 0.4731 time to fit residues: 387.2172 Evaluate side-chains 375 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 328 time to evaluate : 4.954 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3589 time to fit residues: 38.4566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 409 optimal weight: 0.8980 chunk 279 optimal weight: 0.5980 chunk 7 optimal weight: 0.0040 chunk 366 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 419 optimal weight: 0.0170 chunk 340 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 251 optimal weight: 4.9990 chunk 441 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 overall best weight: 0.3430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 497 GLN ** 2 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 294 HIS ** 2 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 49 ASN ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 549 ASN 4 579 GLN 4 683 ASN 5 67 HIS 6 653 HIS 6 735 HIS ** 6 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 41868 Z= 0.168 Angle : 0.681 13.758 56748 Z= 0.331 Chirality : 0.044 0.273 6576 Planarity : 0.005 0.107 7158 Dihedral : 9.415 66.376 5891 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.57 % Favored : 90.41 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.11), residues: 5015 helix: -1.53 (0.12), residues: 1678 sheet: -2.42 (0.21), residues: 529 loop : -2.89 (0.11), residues: 2808 *********************** 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 453 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 368 time to evaluate : 4.971 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 outliers start: 85 outliers final: 31 residues processed: 430 average time/residue: 0.4780 time to fit residues: 358.0479 Evaluate side-chains 358 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 327 time to evaluate : 4.916 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3958 time to fit residues: 30.0744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 165 optimal weight: 6.9990 chunk 443 optimal weight: 20.0000 chunk 97 optimal weight: 0.4980 chunk 288 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 492 optimal weight: 0.2980 chunk 408 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 40 optimal weight: 0.0070 chunk 162 optimal weight: 9.9990 chunk 258 optimal weight: 4.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 579 GLN 5 632 GLN 6 735 HIS ** 6 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.235 41868 Z= 0.186 Angle : 0.678 22.096 56748 Z= 0.333 Chirality : 0.043 0.254 6576 Planarity : 0.004 0.084 7158 Dihedral : 9.246 64.120 5891 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.87 % Favored : 90.11 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.11), residues: 5015 helix: -1.32 (0.12), residues: 1686 sheet: -2.34 (0.21), residues: 529 loop : -2.79 (0.11), residues: 2800 *********************** 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 420 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 355 time to evaluate : 4.530 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 outliers start: 65 outliers final: 28 residues processed: 407 average time/residue: 0.4771 time to fit residues: 336.7734 Evaluate side-chains 356 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 328 time to evaluate : 4.921 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3604 time to fit residues: 25.8449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 474 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 280 optimal weight: 8.9990 chunk 359 optimal weight: 2.9990 chunk 278 optimal weight: 20.0000 chunk 414 optimal weight: 0.0020 chunk 275 optimal weight: 5.9990 chunk 490 optimal weight: 40.0000 chunk 307 optimal weight: 7.9990 chunk 299 optimal weight: 10.0000 chunk 226 optimal weight: 8.9990 overall best weight: 2.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** 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** ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 579 GLN ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS ** 6 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.7677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.129 41868 Z= 0.182 Angle : 0.675 13.035 56748 Z= 0.329 Chirality : 0.043 0.238 6576 Planarity : 0.004 0.073 7158 Dihedral : 9.046 66.031 5891 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.33 % Favored : 89.65 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.11), residues: 5015 helix: -1.08 (0.12), residues: 1670 sheet: -2.36 (0.20), residues: 580 loop : -2.69 (0.11), residues: 2765 *********************** 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 397 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 335 time to evaluate : 5.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 30 residues processed: 382 average time/residue: 0.4835 time to fit residues: 320.7960 Evaluate side-chains 340 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 310 time to evaluate : 4.904 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4178 time to fit residues: 28.9918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 303 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 293 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 334 optimal weight: 30.0000 chunk 242 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 385 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 3 351 ASN ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 574 ASN ** 6 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.8605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.104 41868 Z= 0.237 Angle : 0.722 12.723 56748 Z= 0.357 Chirality : 0.044 0.256 6576 Planarity : 0.004 0.066 7158 Dihedral : 9.077 69.313 5891 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.11 % Favored : 88.85 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.11), residues: 5015 helix: -1.10 (0.12), residues: 1689 sheet: -2.35 (0.21), residues: 535 loop : -2.68 (0.11), residues: 2791 *********************** 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 365 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 316 time to evaluate : 5.023 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 22 residues processed: 352 average time/residue: 0.4723 time to fit residues: 289.6219 Evaluate side-chains 307 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 285 time to evaluate : 4.947 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3904 time to fit residues: 22.5868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 446 optimal weight: 0.8980 chunk 470 optimal weight: 6.9990 chunk 428 optimal weight: 4.9990 chunk 457 optimal weight: 0.2980 chunk 469 optimal weight: 7.9990 chunk 275 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 358 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 413 optimal weight: 5.9990 chunk 432 optimal weight: 3.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 574 ASN 6 735 HIS ** 6 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.9039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 41868 Z= 0.204 Angle : 0.718 12.817 56748 Z= 0.349 Chirality : 0.044 0.261 6576 Planarity : 0.004 0.062 7158 Dihedral : 9.012 71.291 5891 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.01 % Favored : 89.97 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.11), residues: 5015 helix: -1.05 (0.12), residues: 1696 sheet: -2.29 (0.21), residues: 531 loop : -2.63 (0.11), residues: 2788 *********************** 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 341 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 313 time to evaluate : 5.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 332 average time/residue: 0.4788 time to fit residues: 279.1180 Evaluate side-chains 296 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 282 time to evaluate : 4.970 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3801 time to fit residues: 16.7166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 455 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 483 optimal weight: 40.0000 chunk 295 optimal weight: 0.2980 chunk 229 optimal weight: 7.9990 chunk 336 optimal weight: 0.9980 chunk 507 optimal weight: 20.0000 chunk 466 optimal weight: 0.6980 chunk 403 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 311 optimal weight: 3.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 3 49 ASN 3 164 HIS ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 833 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.9308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.098 41868 Z= 0.189 Angle : 0.714 15.379 56748 Z= 0.344 Chirality : 0.043 0.264 6576 Planarity : 0.004 0.060 7158 Dihedral : 8.937 71.794 5891 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.49 % Favored : 89.49 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.11), residues: 5015 helix: -1.01 (0.12), residues: 1695 sheet: -2.17 (0.22), residues: 531 loop : -2.58 (0.11), residues: 2789 ********************** 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 315 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 299 time to evaluate : 5.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 311 average time/residue: 0.5273 time to fit residues: 288.1621 Evaluate side-chains 289 residues out of total 4561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 283 time to evaluate : 4.974 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3988 time to fit residues: 11.1287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 247 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 430 optimal weight: 0.0270 chunk 123 optimal weight: 20.0000 chunk 372 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 404 optimal weight: 0.0000 chunk 169 optimal weight: 6.9990 chunk 415 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 overall best weight: 0.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS ** 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** 2 809 HIS 3 351 ASN ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS ** 6 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.077880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.061618 restraints weight = 250883.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.063353 restraints weight = 153343.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.064536 restraints weight = 109102.841| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.9350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 41868 Z= 0.168 Angle : 0.727 14.929 56748 Z= 0.345 Chirality : 0.044 0.260 6576 Planarity : 0.004 0.099 7158 Dihedral : 8.851 70.796 5891 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.65 % Favored : 90.33 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.11), residues: 5015 helix: -0.99 (0.12), residues: 1703 sheet: -2.04 (0.22), residues: 552 loop : -2.53 (0.12), residues: 2760 =============================================================================== Job complete usr+sys time: 8313.52 seconds wall clock time: 152 minutes 27.35 seconds (9147.35 seconds total)