Starting phenix.real_space_refine on Fri Dec 27 10:54:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adn_15365/12_2024/8adn_15365.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adn_15365/12_2024/8adn_15365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8adn_15365/12_2024/8adn_15365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adn_15365/12_2024/8adn_15365.map" model { file = "/net/cci-nas-00/data/ceres_data/8adn_15365/12_2024/8adn_15365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adn_15365/12_2024/8adn_15365.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 246 5.16 5 C 30638 2.51 5 N 8052 2.21 5 O 9382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 228 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48318 Number of models: 1 Model: "" Number of chains: 30 Chain: "3" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 478 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain breaks: 2 Chain: "4" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 478 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain breaks: 2 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1858 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain: "C" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1613 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1853 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "E" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "F" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1879 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 4, 'TRANS': 229} Chain: "G" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1843 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "H" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1659 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1594 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "J" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1542 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 3, 'TRANS': 189} Chain: "K" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1509 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "L" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1690 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "M" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1662 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain: "N" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1482 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain: "O" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1858 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain: "Q" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1613 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "R" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1853 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "S" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "T" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1879 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 4, 'TRANS': 229} Chain: "U" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1843 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "V" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1659 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain: "W" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1594 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "X" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1542 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 3, 'TRANS': 189} Chain: "Y" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1509 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "Z" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1690 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "a" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1662 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain: "b" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1482 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 4, 'TRANS': 189} Time building chain proxies: 22.32, per 1000 atoms: 0.46 Number of scatterers: 48318 At special positions: 0 Unit cell: (181.308, 155.258, 128.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 246 16.00 O 9382 8.00 N 8052 7.00 C 30638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 108 " - pdb=" SG CYS G 152 " distance=2.04 Simple disulfide: pdb=" SG CYS U 108 " - pdb=" SG CYS U 152 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.49 Conformation dependent library (CDL) restraints added in 4.7 seconds 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11452 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 74 sheets defined 40.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.35 Creating SS restraints... Processing helix chain '3' and resid 81 through 86 Processing helix chain '3' and resid 102 through 106 Processing helix chain '4' and resid 81 through 86 Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.944A pdb=" N LEU A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 100 Processing helix chain 'A' and resid 104 through 122 removed outlier: 3.585A pdb=" N GLN A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.504A pdb=" N ARG A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 188 removed outlier: 4.828A pdb=" N SER A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.801A pdb=" N SER B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 91 Processing helix chain 'B' and resid 95 through 113 removed outlier: 3.658A pdb=" N ILE B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 Processing helix chain 'B' and resid 173 through 189 Processing helix chain 'B' and resid 189 through 195 removed outlier: 4.509A pdb=" N ALA B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.819A pdb=" N LYS B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.504A pdb=" N SER C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 82 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 3.899A pdb=" N PHE C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 173 removed outlier: 3.840A pdb=" N VAL C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.749A pdb=" N THR C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.505A pdb=" N VAL D 61 " --> pdb=" O PRO D 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 62 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 101 removed outlier: 4.013A pdb=" N LYS D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 4.184A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 169 through 181 removed outlier: 4.341A pdb=" N GLN D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 200 removed outlier: 3.562A pdb=" N LYS D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 4.252A pdb=" N GLN D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 29 removed outlier: 3.915A pdb=" N ASN E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 109 through 122 Processing helix chain 'E' and resid 163 through 173 removed outlier: 4.266A pdb=" N CYS E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'F' and resid 16 through 27 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 78 through 99 removed outlier: 3.872A pdb=" N TYR F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER F 93 " --> pdb=" O ASN F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 121 removed outlier: 3.899A pdb=" N GLN F 117 " --> pdb=" O ASN F 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE F 118 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR F 119 " --> pdb=" O ILE F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 173 removed outlier: 3.933A pdb=" N THR F 169 " --> pdb=" O ARG F 165 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU F 170 " --> pdb=" O ILE F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 195 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 223 through 235 removed outlier: 4.176A pdb=" N TYR F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU F 229 " --> pdb=" O ASN F 225 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE F 230 " --> pdb=" O GLN F 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 8 Processing helix chain 'G' and resid 17 through 29 Processing helix chain 'G' and resid 76 through 99 Processing helix chain 'G' and resid 103 through 121 Proline residue: G 117 - end of helix Processing helix chain 'G' and resid 163 through 175 Processing helix chain 'G' and resid 180 through 197 removed outlier: 3.775A pdb=" N SER G 195 " --> pdb=" O GLY G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 203 No H-bonds generated for 'chain 'G' and resid 201 through 203' Processing helix chain 'G' and resid 220 through 234 Processing helix chain 'H' and resid 54 through 77 Processing helix chain 'H' and resid 81 through 94 Processing helix chain 'H' and resid 95 through 97 No H-bonds generated for 'chain 'H' and resid 95 through 97' Processing helix chain 'H' and resid 136 through 148 removed outlier: 3.710A pdb=" N ILE H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 171 Processing helix chain 'H' and resid 209 through 213 removed outlier: 3.762A pdb=" N VAL H 213 " --> pdb=" O ARG H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.611A pdb=" N TYR I 8 " --> pdb=" O ILE I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 80 Processing helix chain 'I' and resid 84 through 98 Processing helix chain 'I' and resid 142 through 154 Processing helix chain 'I' and resid 159 through 176 Processing helix chain 'J' and resid 49 through 72 removed outlier: 3.586A pdb=" N ARG J 55 " --> pdb=" O GLY J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 93 removed outlier: 3.739A pdb=" N ASN J 91 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 145 removed outlier: 3.550A pdb=" N PHE J 136 " --> pdb=" O ILE J 132 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR J 138 " --> pdb=" O THR J 134 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY J 139 " --> pdb=" O TYR J 135 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL J 140 " --> pdb=" O PHE J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 169 removed outlier: 3.567A pdb=" N LEU J 165 " --> pdb=" O CYS J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 102 Processing helix chain 'K' and resid 106 through 120 Processing helix chain 'K' and resid 162 through 172 removed outlier: 3.732A pdb=" N GLU K 172 " --> pdb=" O GLY K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 198 Processing helix chain 'K' and resid 224 through 226 No H-bonds generated for 'chain 'K' and resid 224 through 226' Processing helix chain 'L' and resid 145 through 164 Processing helix chain 'L' and resid 170 through 184 Processing helix chain 'L' and resid 226 through 238 Proline residue: L 232 - end of helix Processing helix chain 'L' and resid 251 through 270 Processing helix chain 'M' and resid 56 through 73 Processing helix chain 'M' and resid 78 through 96 Processing helix chain 'M' and resid 135 through 146 removed outlier: 4.338A pdb=" N LEU M 141 " --> pdb=" O ASN M 137 " (cutoff:3.500A) Proline residue: M 142 - end of helix removed outlier: 3.760A pdb=" N THR M 146 " --> pdb=" O PRO M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 152 removed outlier: 5.487A pdb=" N LEU M 150 " --> pdb=" O CYS M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 172 Processing helix chain 'M' and resid 202 through 206 removed outlier: 4.444A pdb=" N ASN M 206 " --> pdb=" O VAL M 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 92 removed outlier: 3.781A pdb=" N GLU N 82 " --> pdb=" O GLN N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 111 Processing helix chain 'N' and resid 147 through 152 Processing helix chain 'N' and resid 153 through 161 Processing helix chain 'N' and resid 166 through 183 Processing helix chain 'N' and resid 208 through 215 Processing helix chain 'O' and resid 18 through 30 removed outlier: 3.797A pdb=" N ASP O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 100 Processing helix chain 'O' and resid 104 through 118 Processing helix chain 'O' and resid 119 through 121 No H-bonds generated for 'chain 'O' and resid 119 through 121' Processing helix chain 'O' and resid 164 through 171 removed outlier: 4.546A pdb=" N LEU O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 185 Processing helix chain 'O' and resid 186 through 189 Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'O' and resid 213 through 225 removed outlier: 3.612A pdb=" N ILE O 224 " --> pdb=" O VAL O 220 " (cutoff:3.500A) Processing helix chain 'P' and resid 12 through 24 removed outlier: 3.597A pdb=" N SER P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS P 24 " --> pdb=" O LYS P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 91 Processing helix chain 'P' and resid 95 through 113 removed outlier: 3.644A pdb=" N ILE P 99 " --> pdb=" O ASP P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 167 removed outlier: 3.866A pdb=" N PHE P 167 " --> pdb=" O LEU P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 189 Processing helix chain 'P' and resid 190 through 194 Processing helix chain 'P' and resid 213 through 229 removed outlier: 3.758A pdb=" N ARG P 223 " --> pdb=" O ASN P 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE P 224 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN P 229 " --> pdb=" O GLU P 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 28 Processing helix chain 'Q' and resid 76 through 99 removed outlier: 3.504A pdb=" N SER Q 80 " --> pdb=" O ILE Q 76 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR Q 81 " --> pdb=" O LYS Q 77 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS Q 82 " --> pdb=" O PRO Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 120 removed outlier: 3.875A pdb=" N PHE Q 118 " --> pdb=" O TYR Q 114 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR Q 119 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 171 removed outlier: 3.669A pdb=" N VAL Q 166 " --> pdb=" O LYS Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 188 Processing helix chain 'Q' and resid 211 through 220 removed outlier: 3.852A pdb=" N VAL Q 215 " --> pdb=" O GLU Q 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 11 Processing helix chain 'R' and resid 19 through 30 removed outlier: 3.745A pdb=" N ASN R 29 " --> pdb=" O MET R 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU R 30 " --> pdb=" O GLN R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 62 removed outlier: 3.616A pdb=" N VAL R 61 " --> pdb=" O PRO R 58 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS R 62 " --> pdb=" O SER R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 101 removed outlier: 4.010A pdb=" N VAL R 82 " --> pdb=" O ILE R 78 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 118 removed outlier: 4.088A pdb=" N LEU R 118 " --> pdb=" O ALA R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 122 Processing helix chain 'R' and resid 169 through 181 removed outlier: 3.744A pdb=" N GLU R 178 " --> pdb=" O GLU R 174 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLN R 179 " --> pdb=" O ASN R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 200 Processing helix chain 'R' and resid 225 through 234 Processing helix chain 'S' and resid 19 through 29 removed outlier: 3.627A pdb=" N GLU S 23 " --> pdb=" O ILE S 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN S 26 " --> pdb=" O LEU S 22 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 99 Processing helix chain 'S' and resid 106 through 108 No H-bonds generated for 'chain 'S' and resid 106 through 108' Processing helix chain 'S' and resid 109 through 122 Processing helix chain 'S' and resid 163 through 173 removed outlier: 4.192A pdb=" N CYS S 167 " --> pdb=" O ARG S 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 181 removed outlier: 4.790A pdb=" N GLU S 179 " --> pdb=" O ASP S 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 198 Processing helix chain 'S' and resid 224 through 228 removed outlier: 4.052A pdb=" N GLU S 227 " --> pdb=" O LYS S 224 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 28 removed outlier: 3.533A pdb=" N ASN T 28 " --> pdb=" O LYS T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 59 Processing helix chain 'T' and resid 78 through 97 removed outlier: 3.831A pdb=" N TYR T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 117 removed outlier: 3.782A pdb=" N GLN T 117 " --> pdb=" O ASN T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 120 No H-bonds generated for 'chain 'T' and resid 118 through 120' Processing helix chain 'T' and resid 163 through 173 removed outlier: 4.198A pdb=" N THR T 169 " --> pdb=" O ARG T 165 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU T 170 " --> pdb=" O ILE T 166 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 195 Processing helix chain 'T' and resid 214 through 216 No H-bonds generated for 'chain 'T' and resid 214 through 216' Processing helix chain 'T' and resid 223 through 235 removed outlier: 3.917A pdb=" N TYR T 227 " --> pdb=" O GLU T 223 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU T 229 " --> pdb=" O ASN T 225 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE T 230 " --> pdb=" O GLN T 226 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 7 Processing helix chain 'U' and resid 17 through 29 Processing helix chain 'U' and resid 76 through 99 Processing helix chain 'U' and resid 103 through 121 Proline residue: U 117 - end of helix Processing helix chain 'U' and resid 163 through 175 removed outlier: 3.697A pdb=" N LYS U 173 " --> pdb=" O LYS U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 180 through 197 removed outlier: 3.772A pdb=" N SER U 195 " --> pdb=" O GLY U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 201 through 203 No H-bonds generated for 'chain 'U' and resid 201 through 203' Processing helix chain 'U' and resid 220 through 234 Processing helix chain 'V' and resid 54 through 77 Processing helix chain 'V' and resid 81 through 94 Processing helix chain 'V' and resid 95 through 97 No H-bonds generated for 'chain 'V' and resid 95 through 97' Processing helix chain 'V' and resid 136 through 148 removed outlier: 3.681A pdb=" N ILE V 143 " --> pdb=" O ALA V 139 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 171 Processing helix chain 'V' and resid 209 through 213 removed outlier: 3.671A pdb=" N VAL V 213 " --> pdb=" O ARG V 210 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 9 removed outlier: 3.896A pdb=" N TYR W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 79 Processing helix chain 'W' and resid 84 through 98 Processing helix chain 'W' and resid 142 through 154 Processing helix chain 'W' and resid 159 through 177 removed outlier: 3.707A pdb=" N ARG W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 72 removed outlier: 3.545A pdb=" N ARG X 55 " --> pdb=" O GLY X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 93 removed outlier: 3.719A pdb=" N ASN X 91 " --> pdb=" O THR X 87 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG X 93 " --> pdb=" O TYR X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 145 removed outlier: 4.781A pdb=" N TYR X 138 " --> pdb=" O THR X 134 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY X 139 " --> pdb=" O TYR X 135 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL X 140 " --> pdb=" O PHE X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 169 Processing helix chain 'Y' and resid 79 through 102 Processing helix chain 'Y' and resid 106 through 120 Processing helix chain 'Y' and resid 162 through 174 removed outlier: 3.606A pdb=" N SER Y 173 " --> pdb=" O VAL Y 169 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 198 Processing helix chain 'Y' and resid 224 through 226 No H-bonds generated for 'chain 'Y' and resid 224 through 226' Processing helix chain 'Z' and resid 145 through 164 Processing helix chain 'Z' and resid 170 through 185 removed outlier: 3.769A pdb=" N LYS Z 185 " --> pdb=" O ILE Z 181 " (cutoff:3.500A) Processing helix chain 'Z' and resid 226 through 238 Proline residue: Z 232 - end of helix Processing helix chain 'Z' and resid 251 through 270 Processing helix chain 'a' and resid 56 through 73 Processing helix chain 'a' and resid 78 through 96 Processing helix chain 'a' and resid 135 through 145 removed outlier: 4.392A pdb=" N LEU a 141 " --> pdb=" O ASN a 137 " (cutoff:3.500A) Proline residue: a 142 - end of helix Processing helix chain 'a' and resid 146 through 147 No H-bonds generated for 'chain 'a' and resid 146 through 147' Processing helix chain 'a' and resid 148 through 152 Processing helix chain 'a' and resid 153 through 172 Processing helix chain 'a' and resid 201 through 205 removed outlier: 3.524A pdb=" N HIS a 205 " --> pdb=" O GLN a 202 " (cutoff:3.500A) Processing helix chain 'b' and resid 69 through 91 removed outlier: 3.973A pdb=" N GLU b 82 " --> pdb=" O GLN b 78 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN b 85 " --> pdb=" O THR b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 96 through 111 removed outlier: 3.565A pdb=" N ILE b 107 " --> pdb=" O ALA b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 152 Processing helix chain 'b' and resid 153 through 161 Processing helix chain 'b' and resid 166 through 185 removed outlier: 3.572A pdb=" N ARG b 184 " --> pdb=" O CYS b 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 208 through 215 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 157 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 67 removed outlier: 6.530A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A 140 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AA4, first strand: chain 'B' and resid 54 through 58 removed outlier: 6.602A pdb=" N VAL B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 135 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 146 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 64 removed outlier: 6.681A pdb=" N ILE C 69 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 152 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'D' and resid 163 through 166 Processing sheet with id=AA9, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.285A pdb=" N ILE D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 157 through 160 removed outlier: 3.604A pdb=" N ASP E 210 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE E 211 " --> pdb=" O ILE E 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 63 through 67 removed outlier: 6.759A pdb=" N SER E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU E 143 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 157 through 160 removed outlier: 3.538A pdb=" N ALA F 32 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 66 removed outlier: 6.350A pdb=" N ILE F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE F 143 " --> pdb=" O PHE F 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 157 through 160 Processing sheet with id=AB6, first strand: chain 'G' and resid 62 through 66 removed outlier: 6.236A pdb=" N PHE G 62 " --> pdb=" O PHE G 73 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N PHE G 73 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER G 71 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL G 143 " --> pdb=" O VAL G 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 130 through 132 removed outlier: 3.597A pdb=" N GLY H 17 " --> pdb=" O TYR H 14 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE H 178 " --> pdb=" O ASN H 193 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN H 193 " --> pdb=" O ILE H 178 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 25 through 28 removed outlier: 6.716A pdb=" N SER H 26 " --> pdb=" O ALA H 33 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 40 through 44 removed outlier: 3.524A pdb=" N ILE H 43 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE H 47 " --> pdb=" O ILE H 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 217 through 222 removed outlier: 3.568A pdb=" N LYS H 217 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP I 26 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N SER I 11 " --> pdb=" O ASP I 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 29 through 30 removed outlier: 3.537A pdb=" N SER I 37 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 43 through 47 removed outlier: 6.433A pdb=" N LEU I 50 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA I 121 " --> pdb=" O THR I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 127 through 130 Processing sheet with id=AC5, first strand: chain 'J' and resid 21 through 22 Processing sheet with id=AC6, first strand: chain 'J' and resid 35 through 38 Processing sheet with id=AC7, first strand: chain 'K' and resid 156 through 160 removed outlier: 3.574A pdb=" N GLY K 219 " --> pdb=" O LEU K 207 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE K 209 " --> pdb=" O HIS K 217 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N HIS K 217 " --> pdb=" O PHE K 209 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP K 211 " --> pdb=" O TRP K 215 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP K 215 " --> pdb=" O ASP K 211 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 65 through 69 removed outlier: 6.580A pdb=" N LEU K 72 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET K 131 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE K 142 " --> pdb=" O GLY K 154 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 220 through 223 Processing sheet with id=AD1, first strand: chain 'L' and resid 118 through 119 Processing sheet with id=AD2, first strand: chain 'L' and resid 132 through 135 removed outlier: 4.366A pdb=" N VAL L 206 " --> pdb=" O VAL L 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 32 through 35 removed outlier: 5.706A pdb=" N CYS M 33 " --> pdb=" O TYR M 29 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR M 29 " --> pdb=" O CYS M 33 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR M 48 " --> pdb=" O LEU M 44 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 32 through 35 removed outlier: 5.706A pdb=" N CYS M 33 " --> pdb=" O TYR M 29 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR M 29 " --> pdb=" O CYS M 33 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 130 through 133 removed outlier: 3.677A pdb=" N VAL M 10 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY M 18 " --> pdb=" O TYR M 15 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 130 through 133 removed outlier: 3.677A pdb=" N VAL M 10 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY M 18 " --> pdb=" O TYR M 15 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 209 through 211 Processing sheet with id=AD8, first strand: chain 'N' and resid 143 through 146 removed outlier: 3.507A pdb=" N GLY N 32 " --> pdb=" O TYR N 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET N 194 " --> pdb=" O PHE N 205 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N ILE a 210 " --> pdb=" O VAL N 202 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ARG N 204 " --> pdb=" O ILE a 210 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 41 through 43 removed outlier: 7.126A pdb=" N THR N 41 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 55 through 59 removed outlier: 6.337A pdb=" N ILE N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE N 129 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 154 through 157 removed outlier: 3.694A pdb=" N GLU O 208 " --> pdb=" O ARG O 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 63 through 65 Processing sheet with id=AE4, first strand: chain 'P' and resid 149 through 152 removed outlier: 4.531A pdb=" N ILE P 201 " --> pdb=" O LEU P 212 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG P 210 " --> pdb=" O TYR P 203 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 54 through 56 Processing sheet with id=AE6, first strand: chain 'P' and resid 146 through 147 removed outlier: 4.439A pdb=" N GLU P 146 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 156 through 159 Processing sheet with id=AE8, first strand: chain 'Q' and resid 61 through 64 removed outlier: 6.544A pdb=" N ILE Q 69 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER Q 152 " --> pdb=" O VAL Q 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 12 through 13 Processing sheet with id=AF1, first strand: chain 'R' and resid 163 through 166 removed outlier: 4.848A pdb=" N ILE R 213 " --> pdb=" O LEU R 224 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 65 through 68 removed outlier: 6.753A pdb=" N ILE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 157 through 160 removed outlier: 4.384A pdb=" N ILE S 211 " --> pdb=" O ILE S 223 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 63 through 67 removed outlier: 6.410A pdb=" N SER S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU S 143 " --> pdb=" O VAL S 155 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER S 151 " --> pdb=" O ASP S 147 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 157 through 160 Processing sheet with id=AF6, first strand: chain 'T' and resid 63 through 64 removed outlier: 3.811A pdb=" N ILE T 143 " --> pdb=" O PHE T 155 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 157 through 160 Processing sheet with id=AF8, first strand: chain 'U' and resid 62 through 66 removed outlier: 6.769A pdb=" N LEU U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL U 143 " --> pdb=" O VAL U 155 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 130 through 133 removed outlier: 3.517A pdb=" N GLY V 17 " --> pdb=" O TYR V 14 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE V 178 " --> pdb=" O ASN V 193 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN V 193 " --> pdb=" O ILE V 178 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 26 through 28 removed outlier: 6.568A pdb=" N SER V 26 " --> pdb=" O ALA V 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE V 31 " --> pdb=" O SER V 28 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 41 through 44 removed outlier: 6.231A pdb=" N ILE V 47 " --> pdb=" O ILE V 43 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 217 through 222 removed outlier: 3.519A pdb=" N LYS V 217 " --> pdb=" O GLU W 199 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER W 11 " --> pdb=" O ASP W 26 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 29 through 30 Processing sheet with id=AG5, first strand: chain 'W' and resid 43 through 47 removed outlier: 6.437A pdb=" N LEU W 50 " --> pdb=" O LEU W 46 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA W 121 " --> pdb=" O THR W 133 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 127 through 130 removed outlier: 3.712A pdb=" N PHE X 12 " --> pdb=" O GLY X 9 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 21 through 22 Processing sheet with id=AG8, first strand: chain 'X' and resid 35 through 39 removed outlier: 6.245A pdb=" N PHE X 35 " --> pdb=" O TYR X 46 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR X 46 " --> pdb=" O PHE X 35 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASN X 37 " --> pdb=" O PHE X 44 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE X 44 " --> pdb=" O ASN X 37 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN X 39 " --> pdb=" O VAL X 42 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 156 through 160 removed outlier: 3.611A pdb=" N GLY Y 219 " --> pdb=" O LEU Y 207 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE Y 209 " --> pdb=" O HIS Y 217 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS Y 217 " --> pdb=" O PHE Y 209 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP Y 211 " --> pdb=" O TRP Y 215 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP Y 215 " --> pdb=" O ASP Y 211 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 51 through 53 removed outlier: 7.094A pdb=" N ALA Y 51 " --> pdb=" O ALA Y 58 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 65 through 69 removed outlier: 6.571A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 68 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET Y 131 " --> pdb=" O THR Y 75 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS Y 139 " --> pdb=" O ASP Y 136 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE Y 142 " --> pdb=" O GLY Y 154 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 220 through 223 Processing sheet with id=AH4, first strand: chain 'Z' and resid 118 through 120 removed outlier: 5.669A pdb=" N SER Z 120 " --> pdb=" O ILE Z 124 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE Z 124 " --> pdb=" O SER Z 120 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 132 through 135 removed outlier: 4.347A pdb=" N VAL Z 206 " --> pdb=" O VAL Z 218 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 32 through 35 removed outlier: 5.650A pdb=" N CYS a 33 " --> pdb=" O TYR a 29 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR a 29 " --> pdb=" O CYS a 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR a 48 " --> pdb=" O LEU a 44 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 32 through 35 removed outlier: 5.650A pdb=" N CYS a 33 " --> pdb=" O TYR a 29 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR a 29 " --> pdb=" O CYS a 33 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 130 through 132 removed outlier: 3.626A pdb=" N GLY a 18 " --> pdb=" O TYR a 15 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'a' and resid 130 through 132 removed outlier: 3.626A pdb=" N GLY a 18 " --> pdb=" O TYR a 15 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 41 through 43 removed outlier: 6.035A pdb=" N MET b 43 " --> pdb=" O VAL b 47 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL b 47 " --> pdb=" O MET b 43 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'b' and resid 55 through 59 removed outlier: 6.312A pdb=" N ILE b 62 " --> pdb=" O ILE b 58 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE b 129 " --> pdb=" O ALA b 141 " (cutoff:3.500A) 2786 hydrogen bonds defined for protein. 7911 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: 18.91 Time building geometry restraints manager: 11.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 15787 1.35 - 1.47: 11320 1.47 - 1.59: 21659 1.59 - 1.71: 0 1.71 - 1.83: 374 Bond restraints: 49140 Sorted by residual: bond pdb=" N SER G 2 " pdb=" CA SER G 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N ALA C 6 " pdb=" CA ALA C 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N ALA F 2 " pdb=" CA ALA F 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N ALA Q 6 " pdb=" CA ALA Q 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LYS Z 90 " pdb=" CA LYS Z 90 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 49135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 64537 1.42 - 2.84: 1442 2.84 - 4.26: 251 4.26 - 5.68: 21 5.68 - 7.10: 3 Bond angle restraints: 66254 Sorted by residual: angle pdb=" N VAL K 68 " pdb=" CA VAL K 68 " pdb=" C VAL K 68 " ideal model delta sigma weight residual 112.96 109.13 3.83 1.00e+00 1.00e+00 1.47e+01 angle pdb=" N THR Y 220 " pdb=" CA THR Y 220 " pdb=" C THR Y 220 " ideal model delta sigma weight residual 110.44 106.24 4.20 1.20e+00 6.94e-01 1.22e+01 angle pdb=" CA ARG R 17 " pdb=" CB ARG R 17 " pdb=" CG ARG R 17 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" N VAL R 61 " pdb=" CA VAL R 61 " pdb=" C VAL R 61 " ideal model delta sigma weight residual 111.91 109.04 2.87 8.90e-01 1.26e+00 1.04e+01 angle pdb=" N SER W 31 " pdb=" CA SER W 31 " pdb=" C SER W 31 " ideal model delta sigma weight residual 110.88 106.82 4.06 1.28e+00 6.10e-01 1.01e+01 ... (remaining 66249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 26533 17.96 - 35.91: 2425 35.91 - 53.87: 559 53.87 - 71.82: 126 71.82 - 89.78: 63 Dihedral angle restraints: 29706 sinusoidal: 11802 harmonic: 17904 Sorted by residual: dihedral pdb=" CB CYS G 108 " pdb=" SG CYS G 108 " pdb=" SG CYS G 152 " pdb=" CB CYS G 152 " ideal model delta sinusoidal sigma weight residual 93.00 148.26 -55.26 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS U 108 " pdb=" SG CYS U 108 " pdb=" SG CYS U 152 " pdb=" CB CYS U 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.18 -54.18 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" CA THR L 273 " pdb=" C THR L 273 " pdb=" N GLY L 274 " pdb=" CA GLY L 274 " ideal model delta harmonic sigma weight residual 180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 29703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4782 0.031 - 0.062: 1693 0.062 - 0.093: 455 0.093 - 0.125: 431 0.125 - 0.156: 39 Chirality restraints: 7400 Sorted by residual: chirality pdb=" CA ILE V 9 " pdb=" N ILE V 9 " pdb=" C ILE V 9 " pdb=" CB ILE V 9 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA ILE b 119 " pdb=" N ILE b 119 " pdb=" C ILE b 119 " pdb=" CB ILE b 119 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE C 9 " pdb=" N ILE C 9 " pdb=" C ILE C 9 " pdb=" CB ILE C 9 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 7397 not shown) Planarity restraints: 8522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG b 199 " 0.218 9.50e-02 1.11e+02 9.80e-02 6.82e+00 pdb=" NE ARG b 199 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG b 199 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG b 199 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG b 199 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 199 " -0.213 9.50e-02 1.11e+02 9.58e-02 6.26e+00 pdb=" NE ARG N 199 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG N 199 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG N 199 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG N 199 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 225 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO D 226 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 226 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 226 " -0.025 5.00e-02 4.00e+02 ... (remaining 8519 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 119 2.43 - 3.05: 31768 3.05 - 3.66: 73505 3.66 - 4.28: 118120 4.28 - 4.90: 200925 Nonbonded interactions: 424437 Sorted by model distance: nonbonded pdb=" OG SER F 103 " pdb=" OD1 ASP N 91 " model vdw 1.810 3.040 nonbonded pdb=" OD1 ASP Z 96 " pdb=" OG SER Z 98 " model vdw 1.943 3.040 nonbonded pdb=" OG1 THR W 114 " pdb=" OD1 ASP W 116 " model vdw 2.041 3.040 nonbonded pdb=" OE1 GLU O 110 " pdb=" OH TYR O 149 " model vdw 2.042 3.040 nonbonded pdb=" N GLU H 186 " pdb=" OE1 GLU H 186 " model vdw 2.091 3.120 ... (remaining 424432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '3' selection = chain '4' } ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.490 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 86.910 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.003 0.039 49140 Z= 0.204 Angle : 0.542 7.096 66254 Z= 0.318 Chirality : 0.042 0.156 7400 Planarity : 0.003 0.098 8522 Dihedral : 15.313 89.781 18248 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.85 % Allowed : 13.68 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.11), residues: 6092 helix: 1.43 (0.11), residues: 2150 sheet: 0.39 (0.13), residues: 1430 loop : -0.29 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 280 HIS 0.005 0.001 HIS G 92 PHE 0.029 0.001 PHE K 221 TYR 0.019 0.001 TYR G 66 ARG 0.017 0.000 ARG b 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 722 time to evaluate : 4.431 Fit side-chains revert: symmetry clash REVERT: 3 141 ASP cc_start: 0.5517 (p0) cc_final: 0.4930 (t0) REVERT: 4 140 ASP cc_start: 0.5894 (t0) cc_final: 0.5673 (p0) REVERT: 4 143 ASN cc_start: 0.7738 (m-40) cc_final: 0.7522 (m-40) REVERT: A 80 ASP cc_start: 0.9025 (m-30) cc_final: 0.8671 (m-30) REVERT: A 142 ARG cc_start: 0.7676 (ttm170) cc_final: 0.7426 (ttp-170) REVERT: B 176 ARG cc_start: 0.7554 (ttt180) cc_final: 0.7330 (ttt-90) REVERT: C 86 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7902 (tp30) REVERT: C 153 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7217 (tm-30) REVERT: C 198 MET cc_start: 0.6505 (mpp) cc_final: 0.6260 (mpp) REVERT: D 3 ILE cc_start: 0.7991 (mt) cc_final: 0.7584 (pt) REVERT: D 203 LYS cc_start: 0.6719 (mttt) cc_final: 0.6109 (tttm) REVERT: E 147 ASP cc_start: 0.7417 (m-30) cc_final: 0.7185 (p0) REVERT: E 163 ARG cc_start: 0.7695 (ttm170) cc_final: 0.7428 (mtp85) REVERT: F 70 PHE cc_start: 0.7967 (p90) cc_final: 0.7276 (p90) REVERT: G 66 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.8981 (t80) REVERT: H 9 ILE cc_start: 0.8618 (pp) cc_final: 0.8349 (pp) REVERT: H 97 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8280 (mm110) REVERT: H 161 CYS cc_start: 0.8266 (m) cc_final: 0.8060 (t) REVERT: H 185 GLN cc_start: 0.7496 (tp40) cc_final: 0.7283 (mm110) REVERT: I 195 TYR cc_start: 0.9294 (p90) cc_final: 0.8661 (p90) REVERT: L 257 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7277 (t0) REVERT: M 138 MET cc_start: 0.8101 (mtm) cc_final: 0.7898 (mtp) REVERT: O 144 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: O 207 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7599 (mp10) REVERT: P 11 ARG cc_start: 0.7690 (mtp180) cc_final: 0.7445 (mtp85) REVERT: P 19 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8041 (mm) REVERT: P 73 MET cc_start: 0.8152 (mmp) cc_final: 0.7913 (mmm) REVERT: Q 24 GLN cc_start: 0.7430 (tt0) cc_final: 0.7015 (tt0) REVERT: Q 64 ASP cc_start: 0.7307 (t0) cc_final: 0.6443 (t0) REVERT: Q 86 GLU cc_start: 0.8220 (tp30) cc_final: 0.7983 (tp30) REVERT: Q 105 ASP cc_start: 0.7935 (t0) cc_final: 0.7711 (t70) REVERT: R 111 GLU cc_start: 0.7925 (tt0) cc_final: 0.7632 (tt0) REVERT: R 231 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8189 (tt0) REVERT: S 10 TYR cc_start: 0.8846 (p90) cc_final: 0.8484 (p90) REVERT: S 30 GLN cc_start: 0.7607 (mt0) cc_final: 0.7406 (mt0) REVERT: S 43 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6156 (p90) REVERT: T 100 MET cc_start: 0.8689 (mtt) cc_final: 0.8353 (mtm) REVERT: U 186 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8105 (mp0) REVERT: V 97 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8273 (mm110) REVERT: V 186 GLU cc_start: 0.7576 (mp0) cc_final: 0.7131 (mp0) REVERT: V 190 MET cc_start: 0.8082 (ttt) cc_final: 0.7721 (mtm) REVERT: W 80 ASN cc_start: 0.6903 (OUTLIER) cc_final: 0.6518 (m-40) REVERT: W 144 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8045 (tttm) REVERT: W 195 TYR cc_start: 0.9330 (p90) cc_final: 0.8694 (p90) REVERT: Y 175 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7987 (mtp-110) REVERT: a 1 MET cc_start: 0.8269 (ttt) cc_final: 0.7855 (ttp) REVERT: a 98 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6369 (tm-30) outliers start: 45 outliers final: 29 residues processed: 754 average time/residue: 1.2965 time to fit residues: 1214.3376 Evaluate side-chains 695 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 660 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 137 ASP Chi-restraints excluded: chain V residue 77 ASN Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain Y residue 101 ASN Chi-restraints excluded: chain a residue 181 ILE Chi-restraints excluded: chain a residue 201 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 0.6980 chunk 456 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 471 optimal weight: 1.9990 chunk 182 optimal weight: 0.5980 chunk 286 optimal weight: 4.9990 chunk 351 optimal weight: 0.3980 chunk 546 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 112 GLN B 206 ASN C 150 ASN D 64 HIS E 27 ASN F 86 ASN G 59 GLN H 92 HIS I 7 HIS I 79 ASN I 191 ASN J 39 ASN K 124 GLN K 150 GLN N 78 GLN P 112 GLN Q 39 ASN Q 116 GLN U 92 HIS U 120 GLN U 203 GLN W 79 ASN Y 124 GLN Y 196 HIS a 206 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 49140 Z= 0.262 Angle : 0.588 20.896 66254 Z= 0.319 Chirality : 0.046 0.192 7400 Planarity : 0.004 0.053 8522 Dihedral : 6.048 121.692 6751 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.87 % Allowed : 13.78 % Favored : 83.35 % 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: 0.86 (0.11), residues: 6092 helix: 1.66 (0.11), residues: 2184 sheet: 0.48 (0.13), residues: 1382 loop : -0.28 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Z 280 HIS 0.007 0.001 HIS U 92 PHE 0.020 0.002 PHE A 81 TYR 0.018 0.001 TYR L 193 ARG 0.006 0.001 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 741 time to evaluate : 4.506 Fit side-chains revert: symmetry clash REVERT: 3 130 ASP cc_start: 0.7321 (m-30) cc_final: 0.7112 (m-30) REVERT: 3 135 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8056 (ttmt) REVERT: 3 141 ASP cc_start: 0.5438 (OUTLIER) cc_final: 0.4849 (t0) REVERT: 4 135 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7958 (ttmt) REVERT: 4 143 ASN cc_start: 0.7680 (m-40) cc_final: 0.7420 (m-40) REVERT: A 64 TYR cc_start: 0.8612 (m-80) cc_final: 0.8266 (m-80) REVERT: A 80 ASP cc_start: 0.8985 (m-30) cc_final: 0.8649 (m-30) REVERT: A 149 TYR cc_start: 0.8840 (p90) cc_final: 0.8507 (p90) REVERT: B 8 GLU cc_start: 0.8224 (tp30) cc_final: 0.7930 (tp30) REVERT: B 176 ARG cc_start: 0.7552 (ttt180) cc_final: 0.7297 (ttt-90) REVERT: C 24 GLN cc_start: 0.7505 (tt0) cc_final: 0.6910 (tt0) REVERT: C 153 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7151 (tm-30) REVERT: C 198 MET cc_start: 0.6627 (mpp) cc_final: 0.6394 (mpp) REVERT: D 17 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6764 (mtm110) REVERT: D 203 LYS cc_start: 0.6747 (mttt) cc_final: 0.6142 (tttm) REVERT: E 43 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6097 (p90) REVERT: E 49 TYR cc_start: 0.8109 (t80) cc_final: 0.7803 (t80) REVERT: E 147 ASP cc_start: 0.7524 (m-30) cc_final: 0.7228 (p0) REVERT: E 226 GLU cc_start: 0.8324 (mp0) cc_final: 0.8088 (mp0) REVERT: F 70 PHE cc_start: 0.8127 (p90) cc_final: 0.7489 (p90) REVERT: F 179 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7921 (ttm) REVERT: F 211 MET cc_start: 0.8539 (ttm) cc_final: 0.8257 (ttm) REVERT: H 97 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8247 (mm110) REVERT: H 151 MET cc_start: 0.8911 (mtm) cc_final: 0.8646 (mtm) REVERT: I 116 ASP cc_start: 0.7592 (t0) cc_final: 0.7347 (t0) REVERT: I 189 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8696 (tp) REVERT: I 195 TYR cc_start: 0.9312 (p90) cc_final: 0.8789 (p90) REVERT: K 98 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8526 (tm-30) REVERT: K 175 ARG cc_start: 0.8458 (mtm110) cc_final: 0.8196 (mtp-110) REVERT: L 100 SER cc_start: 0.8633 (m) cc_final: 0.8373 (p) REVERT: L 161 GLN cc_start: 0.8151 (pp30) cc_final: 0.7930 (mp10) REVERT: L 164 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: L 293 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7621 (ttp80) REVERT: L 296 GLN cc_start: 0.7521 (pm20) cc_final: 0.7314 (pm20) REVERT: M 148 ASN cc_start: 0.7617 (p0) cc_final: 0.7239 (p0) REVERT: N 106 ASP cc_start: 0.7765 (m-30) cc_final: 0.7512 (m-30) REVERT: N 128 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.8165 (mtp85) REVERT: N 140 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: N 142 GLU cc_start: 0.8047 (tp30) cc_final: 0.7745 (pm20) REVERT: N 193 ARG cc_start: 0.8280 (mtt-85) cc_final: 0.8025 (mtp85) REVERT: O 149 TYR cc_start: 0.8992 (p90) cc_final: 0.8492 (p90) REVERT: O 207 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7538 (mp10) REVERT: P 11 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7395 (mtp85) REVERT: P 73 MET cc_start: 0.8257 (mmp) cc_final: 0.7964 (mmm) REVERT: Q 24 GLN cc_start: 0.7511 (tt0) cc_final: 0.7076 (tt0) REVERT: Q 64 ASP cc_start: 0.7515 (t0) cc_final: 0.7236 (t0) REVERT: Q 143 TYR cc_start: 0.8695 (m-80) cc_final: 0.8278 (m-80) REVERT: Q 148 ASP cc_start: 0.8225 (p0) cc_final: 0.7930 (p0) REVERT: R 111 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: S 30 GLN cc_start: 0.7662 (mt0) cc_final: 0.7452 (mt0) REVERT: S 43 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.6132 (p90) REVERT: T 100 MET cc_start: 0.8785 (mtt) cc_final: 0.8372 (mtm) REVERT: U 186 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: U 225 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7714 (tm-30) REVERT: V 97 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8267 (mm110) REVERT: W 80 ASN cc_start: 0.6698 (OUTLIER) cc_final: 0.6264 (m-40) REVERT: W 132 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: W 144 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8058 (tttm) REVERT: W 195 TYR cc_start: 0.9341 (p90) cc_final: 0.8859 (p90) REVERT: X 95 HIS cc_start: 0.7190 (m90) cc_final: 0.6831 (m90) REVERT: Z 164 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: Z 246 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6204 (tt0) REVERT: a 1 MET cc_start: 0.8191 (ttt) cc_final: 0.7818 (ttp) REVERT: a 98 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6437 (tm-30) REVERT: a 202 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.6101 (pm20) REVERT: b 86 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7246 (tpt-90) REVERT: b 106 ASP cc_start: 0.7724 (m-30) cc_final: 0.7466 (m-30) REVERT: b 140 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7618 (tp30) outliers start: 152 outliers final: 47 residues processed: 815 average time/residue: 1.2357 time to fit residues: 1261.6803 Evaluate side-chains 721 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 655 time to evaluate : 4.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 201 TRP Chi-restraints excluded: chain a residue 202 GLN Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 454 optimal weight: 5.9990 chunk 372 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 547 optimal weight: 3.9990 chunk 591 optimal weight: 3.9990 chunk 487 optimal weight: 3.9990 chunk 543 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 439 optimal weight: 0.0870 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 112 GLN B 114 ASN E 67 ASN F 139 ASN G 59 GLN G 120 GLN I 79 ASN K 124 GLN K 150 GLN M 17 ASN M 64 ASN M 87 GLN P 112 GLN Q 39 ASN Q 116 GLN R 188 ASN S 50 ASN S 59 GLN S 107 HIS U 92 HIS U 120 GLN U 203 GLN V 77 ASN V 122 HIS W 79 ASN Y 124 GLN a 87 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 49140 Z= 0.418 Angle : 0.635 21.992 66254 Z= 0.339 Chirality : 0.047 0.208 7400 Planarity : 0.004 0.054 8522 Dihedral : 5.991 113.876 6719 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.81 % Allowed : 14.46 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 6092 helix: 1.46 (0.11), residues: 2182 sheet: 0.38 (0.13), residues: 1386 loop : -0.40 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Z 280 HIS 0.009 0.002 HIS G 92 PHE 0.023 0.002 PHE J 54 TYR 0.022 0.002 TYR Z 193 ARG 0.009 0.001 ARG E 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 672 time to evaluate : 4.518 Fit side-chains revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8071 (ttmt) REVERT: 3 141 ASP cc_start: 0.5555 (OUTLIER) cc_final: 0.4892 (t0) REVERT: 4 135 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8065 (ttmt) REVERT: A 80 ASP cc_start: 0.8979 (m-30) cc_final: 0.8680 (m-30) REVERT: A 142 ARG cc_start: 0.7604 (ttm170) cc_final: 0.7388 (ttp-170) REVERT: A 149 TYR cc_start: 0.8898 (p90) cc_final: 0.8637 (p90) REVERT: B 8 GLU cc_start: 0.8023 (tp30) cc_final: 0.7753 (tp30) REVERT: B 73 MET cc_start: 0.8511 (mmm) cc_final: 0.8296 (mmp) REVERT: B 202 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8451 (tp) REVERT: C 24 GLN cc_start: 0.7547 (tt0) cc_final: 0.7332 (tt0) REVERT: C 37 ASP cc_start: 0.7681 (p0) cc_final: 0.7421 (t0) REVERT: C 40 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6683 (pm20) REVERT: C 153 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7146 (tm-30) REVERT: D 17 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6929 (mtm110) REVERT: D 176 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7422 (mtm) REVERT: D 203 LYS cc_start: 0.6805 (mttt) cc_final: 0.6138 (tttm) REVERT: E 43 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6289 (p90) REVERT: E 49 TYR cc_start: 0.8217 (t80) cc_final: 0.8005 (t80) REVERT: E 183 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7895 (ttpt) REVERT: E 222 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: E 226 GLU cc_start: 0.8316 (mp0) cc_final: 0.8114 (mp0) REVERT: F 70 PHE cc_start: 0.8229 (p90) cc_final: 0.7420 (p90) REVERT: F 211 MET cc_start: 0.8667 (ttm) cc_final: 0.8448 (ttm) REVERT: G 25 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: G 66 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.9072 (t80) REVERT: H 97 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8295 (mm110) REVERT: H 151 MET cc_start: 0.8900 (mtm) cc_final: 0.8673 (mtm) REVERT: I 116 ASP cc_start: 0.7568 (t70) cc_final: 0.7276 (t0) REVERT: I 189 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8746 (tp) REVERT: I 195 TYR cc_start: 0.9339 (p90) cc_final: 0.8739 (p90) REVERT: I 198 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7804 (mtp85) REVERT: J 124 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: J 183 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8241 (ptmm) REVERT: K 76 MET cc_start: 0.7838 (ptm) cc_final: 0.7629 (ptm) REVERT: K 98 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8472 (tm-30) REVERT: K 175 ARG cc_start: 0.8508 (mtm110) cc_final: 0.8283 (mtp-110) REVERT: L 137 ASP cc_start: 0.7655 (m-30) cc_final: 0.7428 (m-30) REVERT: L 161 GLN cc_start: 0.8236 (pp30) cc_final: 0.7941 (mp10) REVERT: L 164 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: M 148 ASN cc_start: 0.7739 (p0) cc_final: 0.7360 (p0) REVERT: N 86 ARG cc_start: 0.7747 (ttt90) cc_final: 0.7502 (tpt-90) REVERT: N 102 MET cc_start: 0.8449 (mmt) cc_final: 0.8212 (mmt) REVERT: N 106 ASP cc_start: 0.7748 (m-30) cc_final: 0.7454 (m-30) REVERT: N 140 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: N 193 ARG cc_start: 0.8382 (mtt-85) cc_final: 0.8068 (mtp85) REVERT: O 149 TYR cc_start: 0.8999 (p90) cc_final: 0.8665 (p90) REVERT: O 207 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7616 (mp10) REVERT: P 11 ARG cc_start: 0.7709 (mtp180) cc_final: 0.7377 (mtp85) REVERT: P 73 MET cc_start: 0.8457 (mmp) cc_final: 0.8227 (mmp) REVERT: P 183 LYS cc_start: 0.7706 (mtmt) cc_final: 0.7465 (mtmm) REVERT: Q 24 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7064 (tt0) REVERT: Q 64 ASP cc_start: 0.7647 (t0) cc_final: 0.7401 (t0) REVERT: Q 148 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7888 (p0) REVERT: R 111 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: S 30 GLN cc_start: 0.7857 (mt0) cc_final: 0.7611 (mt0) REVERT: S 38 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8360 (mp) REVERT: S 43 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6160 (p90) REVERT: S 163 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7826 (mtt90) REVERT: T 100 MET cc_start: 0.8754 (mtt) cc_final: 0.8308 (mtm) REVERT: T 233 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7849 (ttpt) REVERT: U 186 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: U 225 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7746 (tm-30) REVERT: V 97 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8266 (mm110) REVERT: V 154 GLU cc_start: 0.7871 (pt0) cc_final: 0.6970 (tp30) REVERT: V 200 ARG cc_start: 0.7658 (ptm160) cc_final: 0.7423 (ptm160) REVERT: W 80 ASN cc_start: 0.6753 (OUTLIER) cc_final: 0.6335 (m-40) REVERT: W 132 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: W 195 TYR cc_start: 0.9369 (p90) cc_final: 0.8874 (p90) REVERT: X 95 HIS cc_start: 0.7234 (m90) cc_final: 0.6575 (m-70) REVERT: X 183 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8422 (ptmm) REVERT: Y 98 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8332 (tm-30) REVERT: Z 137 ASP cc_start: 0.7613 (m-30) cc_final: 0.7378 (m-30) REVERT: Z 141 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.8079 (m) REVERT: Z 164 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: Z 246 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6248 (tt0) REVERT: a 98 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6424 (tm-30) REVERT: a 202 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6167 (pm20) REVERT: b 106 ASP cc_start: 0.7902 (m-30) cc_final: 0.7642 (m-30) REVERT: b 114 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8636 (mtm) REVERT: b 140 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7628 (tp30) outliers start: 202 outliers final: 81 residues processed: 799 average time/residue: 1.2704 time to fit residues: 1267.1510 Evaluate side-chains 763 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 647 time to evaluate : 4.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 198 ARG Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 172 GLU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain Q residue 198 MET Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain T residue 211 MET Chi-restraints excluded: chain T residue 229 GLU Chi-restraints excluded: chain T residue 233 LYS Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 67 PRO Chi-restraints excluded: chain U residue 149 SER Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 115 LEU Chi-restraints excluded: chain a residue 181 ILE Chi-restraints excluded: chain a residue 201 TRP Chi-restraints excluded: chain a residue 202 GLN Chi-restraints excluded: chain b residue 114 MET Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 6.9990 chunk 411 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 367 optimal weight: 9.9990 chunk 549 optimal weight: 0.9980 chunk 581 optimal weight: 2.9990 chunk 287 optimal weight: 20.0000 chunk 520 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN E 107 HIS G 52 HIS G 59 GLN H 77 ASN I 79 ASN K 124 GLN N 203 GLN O 78 GLN Q 39 ASN S 50 ASN U 92 HIS U 203 GLN V 77 ASN X 98 ASN Y 124 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 49140 Z= 0.222 Angle : 0.540 21.829 66254 Z= 0.292 Chirality : 0.044 0.179 7400 Planarity : 0.004 0.055 8522 Dihedral : 5.643 105.156 6717 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.27 % Allowed : 16.16 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.11), residues: 6092 helix: 1.71 (0.11), residues: 2198 sheet: 0.54 (0.13), residues: 1350 loop : -0.45 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 280 HIS 0.005 0.001 HIS U 92 PHE 0.023 0.001 PHE O 81 TYR 0.016 0.001 TYR C 21 ARG 0.008 0.000 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 727 time to evaluate : 4.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8081 (ttmt) REVERT: 3 140 ASP cc_start: 0.5536 (t0) cc_final: 0.5265 (p0) REVERT: 3 141 ASP cc_start: 0.5521 (OUTLIER) cc_final: 0.4905 (t0) REVERT: 4 135 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8086 (ttmt) REVERT: A 80 ASP cc_start: 0.8817 (m-30) cc_final: 0.8593 (m-30) REVERT: A 149 TYR cc_start: 0.8878 (p90) cc_final: 0.8474 (p90) REVERT: B 8 GLU cc_start: 0.7930 (tp30) cc_final: 0.7633 (tp30) REVERT: B 73 MET cc_start: 0.8398 (mmm) cc_final: 0.8016 (mmp) REVERT: B 174 MET cc_start: 0.7734 (mtp) cc_final: 0.7320 (mtp) REVERT: C 24 GLN cc_start: 0.7538 (tt0) cc_final: 0.7204 (tt0) REVERT: C 28 GLN cc_start: 0.6094 (OUTLIER) cc_final: 0.5732 (mp10) REVERT: C 37 ASP cc_start: 0.7793 (p0) cc_final: 0.7529 (t0) REVERT: C 40 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: C 153 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7170 (tm-30) REVERT: D 17 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6944 (mtm110) REVERT: D 65 TYR cc_start: 0.8444 (m-80) cc_final: 0.8238 (m-80) REVERT: D 176 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7358 (mtm) REVERT: D 203 LYS cc_start: 0.6750 (mttt) cc_final: 0.6131 (tttm) REVERT: E 43 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.6208 (p90) REVERT: E 49 TYR cc_start: 0.8063 (t80) cc_final: 0.7751 (t80) REVERT: H 97 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8221 (mm110) REVERT: H 151 MET cc_start: 0.8911 (mtm) cc_final: 0.8643 (mtm) REVERT: I 116 ASP cc_start: 0.7569 (t70) cc_final: 0.7185 (t0) REVERT: I 195 TYR cc_start: 0.9345 (p90) cc_final: 0.8826 (p90) REVERT: K 98 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8509 (tm-30) REVERT: K 175 ARG cc_start: 0.8442 (mtm110) cc_final: 0.8131 (mtp-110) REVERT: L 137 ASP cc_start: 0.7605 (m-30) cc_final: 0.7364 (m-30) REVERT: L 164 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7297 (tp30) REVERT: L 241 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8023 (tppt) REVERT: L 257 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6979 (m-30) REVERT: L 290 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7823 (mm-30) REVERT: L 293 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7770 (ttp80) REVERT: M 96 ARG cc_start: 0.8209 (mtt90) cc_final: 0.7841 (mtm-85) REVERT: M 148 ASN cc_start: 0.7722 (p0) cc_final: 0.7360 (p0) REVERT: N 86 ARG cc_start: 0.7731 (ttt90) cc_final: 0.7475 (tpt-90) REVERT: N 102 MET cc_start: 0.8332 (mmt) cc_final: 0.8129 (mmt) REVERT: N 106 ASP cc_start: 0.7763 (m-30) cc_final: 0.7413 (m-30) REVERT: N 140 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: N 142 GLU cc_start: 0.7992 (tp30) cc_final: 0.7741 (pm20) REVERT: N 193 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.8020 (mtp85) REVERT: O 149 TYR cc_start: 0.9008 (p90) cc_final: 0.8523 (p90) REVERT: O 200 ASP cc_start: 0.7874 (t0) cc_final: 0.7606 (t70) REVERT: O 207 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7654 (mp10) REVERT: P 11 ARG cc_start: 0.7701 (mtp180) cc_final: 0.7380 (mtp85) REVERT: P 73 MET cc_start: 0.8363 (mmp) cc_final: 0.8112 (mmp) REVERT: P 91 ASP cc_start: 0.8404 (t0) cc_final: 0.8120 (t0) REVERT: P 225 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6130 (tt0) REVERT: Q 20 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6405 (mm-30) REVERT: Q 24 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: Q 64 ASP cc_start: 0.7622 (t0) cc_final: 0.7351 (t0) REVERT: Q 66 ASP cc_start: 0.7472 (p0) cc_final: 0.7142 (p0) REVERT: Q 148 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7881 (p0) REVERT: R 50 LYS cc_start: 0.7725 (ttpt) cc_final: 0.7266 (tmmm) REVERT: R 111 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: R 174 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7553 (mm-30) REVERT: S 30 GLN cc_start: 0.7823 (mt0) cc_final: 0.7563 (mt0) REVERT: S 43 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.6190 (p90) REVERT: S 163 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7817 (mtt90) REVERT: T 50 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: T 100 MET cc_start: 0.8727 (mtt) cc_final: 0.8350 (mtm) REVERT: T 233 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7965 (ttpt) REVERT: U 186 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: V 97 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8228 (mm110) REVERT: V 151 MET cc_start: 0.8785 (mtm) cc_final: 0.8526 (mtm) REVERT: V 154 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: V 190 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7837 (mmt) REVERT: W 80 ASN cc_start: 0.6645 (OUTLIER) cc_final: 0.6242 (m-40) REVERT: W 189 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8849 (tp) REVERT: W 195 TYR cc_start: 0.9356 (p90) cc_final: 0.8919 (p90) REVERT: X 95 HIS cc_start: 0.7188 (m90) cc_final: 0.6575 (m-70) REVERT: X 183 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8233 (ptmm) REVERT: Y 98 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8383 (tm-30) REVERT: Z 137 ASP cc_start: 0.7589 (m-30) cc_final: 0.7364 (m-30) REVERT: Z 141 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7819 (m) REVERT: Z 164 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: Z 246 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6232 (tt0) REVERT: a 98 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6381 (tm-30) REVERT: a 202 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.5832 (pm20) REVERT: b 86 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7159 (tpt-90) REVERT: b 106 ASP cc_start: 0.7821 (m-30) cc_final: 0.7549 (m-30) REVERT: b 140 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7595 (tp30) outliers start: 173 outliers final: 51 residues processed: 834 average time/residue: 1.2560 time to fit residues: 1308.6150 Evaluate side-chains 746 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 662 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 241 LYS Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain T residue 211 MET Chi-restraints excluded: chain T residue 229 GLU Chi-restraints excluded: chain T residue 233 LYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 190 MET Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 202 GLN Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 9.9990 chunk 330 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 433 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 496 optimal weight: 2.9990 chunk 402 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 297 optimal weight: 2.9990 chunk 522 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN D 96 HIS G 59 GLN G 120 GLN G 203 GLN I 79 ASN K 124 GLN K 150 GLN M 87 GLN P 112 GLN Q 39 ASN R 196 ASN S 50 ASN S 59 GLN S 79 ASN U 92 HIS U 120 GLN V 77 ASN W 79 ASN Y 124 GLN Y 150 GLN Y 206 ASN Z 118 HIS a 87 GLN a 148 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 49140 Z= 0.432 Angle : 0.628 23.588 66254 Z= 0.334 Chirality : 0.047 0.212 7400 Planarity : 0.004 0.056 8522 Dihedral : 5.748 96.961 6706 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.93 % Allowed : 16.82 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.11), residues: 6092 helix: 1.49 (0.11), residues: 2184 sheet: 0.42 (0.13), residues: 1380 loop : -0.48 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Z 280 HIS 0.009 0.001 HIS G 92 PHE 0.035 0.002 PHE P 214 TYR 0.022 0.002 TYR Z 193 ARG 0.009 0.001 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 649 time to evaluate : 4.501 Fit side-chains revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8044 (ttmt) REVERT: 3 141 ASP cc_start: 0.5838 (OUTLIER) cc_final: 0.5094 (t0) REVERT: 4 135 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8051 (ttmt) REVERT: 4 140 ASP cc_start: 0.6549 (p0) cc_final: 0.6106 (t0) REVERT: A 118 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: A 149 TYR cc_start: 0.8853 (p90) cc_final: 0.8547 (p90) REVERT: B 8 GLU cc_start: 0.7999 (tp30) cc_final: 0.7542 (tp30) REVERT: B 73 MET cc_start: 0.8511 (mmm) cc_final: 0.8213 (mmp) REVERT: C 24 GLN cc_start: 0.7606 (tt0) cc_final: 0.6685 (tt0) REVERT: C 28 GLN cc_start: 0.6253 (OUTLIER) cc_final: 0.5909 (mp10) REVERT: C 37 ASP cc_start: 0.7601 (p0) cc_final: 0.7393 (t0) REVERT: C 40 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6649 (pm20) REVERT: C 64 ASP cc_start: 0.7508 (t0) cc_final: 0.7063 (p0) REVERT: C 153 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7168 (tm-30) REVERT: D 17 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6969 (mtm110) REVERT: D 176 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7388 (mtm) REVERT: D 203 LYS cc_start: 0.6694 (mttt) cc_final: 0.6100 (tttm) REVERT: E 43 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.6220 (p90) REVERT: E 49 TYR cc_start: 0.8302 (t80) cc_final: 0.7912 (t80) REVERT: E 183 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7891 (ttpt) REVERT: F 70 PHE cc_start: 0.8213 (p90) cc_final: 0.7449 (p90) REVERT: G 66 TYR cc_start: 0.9336 (OUTLIER) cc_final: 0.9064 (t80) REVERT: G 214 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: H 97 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8288 (mm110) REVERT: H 151 MET cc_start: 0.8891 (mtm) cc_final: 0.8691 (mtm) REVERT: I 116 ASP cc_start: 0.7574 (t70) cc_final: 0.7208 (t0) REVERT: I 195 TYR cc_start: 0.9354 (p90) cc_final: 0.8809 (p90) REVERT: J 183 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8250 (ptmm) REVERT: K 98 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8512 (tm-30) REVERT: K 175 ARG cc_start: 0.8490 (mtm110) cc_final: 0.8241 (mtp-110) REVERT: L 137 ASP cc_start: 0.7660 (m-30) cc_final: 0.7386 (m-30) REVERT: L 164 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: L 290 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7823 (mm-30) REVERT: M 96 ARG cc_start: 0.8261 (mtt90) cc_final: 0.7901 (mtm-85) REVERT: M 148 ASN cc_start: 0.7837 (p0) cc_final: 0.7483 (p0) REVERT: N 86 ARG cc_start: 0.7765 (ttt90) cc_final: 0.7448 (tpt-90) REVERT: N 102 MET cc_start: 0.8485 (mmt) cc_final: 0.8212 (mmt) REVERT: N 106 ASP cc_start: 0.7747 (m-30) cc_final: 0.7412 (m-30) REVERT: N 140 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: N 193 ARG cc_start: 0.8373 (mtt-85) cc_final: 0.8101 (mtp85) REVERT: O 33 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8470 (tm) REVERT: O 48 LEU cc_start: 0.8656 (mm) cc_final: 0.8012 (pp) REVERT: O 78 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: O 149 TYR cc_start: 0.9018 (p90) cc_final: 0.8677 (p90) REVERT: O 200 ASP cc_start: 0.7883 (t0) cc_final: 0.7357 (t0) REVERT: O 207 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7705 (mp10) REVERT: P 11 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7421 (mtp85) REVERT: P 73 MET cc_start: 0.8468 (mmp) cc_final: 0.8255 (mmp) REVERT: P 91 ASP cc_start: 0.8452 (t0) cc_final: 0.8197 (t0) REVERT: P 197 LYS cc_start: 0.8097 (mttt) cc_final: 0.7250 (ptpp) REVERT: Q 20 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6245 (mm-30) REVERT: Q 24 GLN cc_start: 0.7559 (tt0) cc_final: 0.7019 (tt0) REVERT: Q 64 ASP cc_start: 0.7644 (t0) cc_final: 0.7345 (t0) REVERT: Q 66 ASP cc_start: 0.7470 (p0) cc_final: 0.7006 (p0) REVERT: Q 148 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7892 (p0) REVERT: R 50 LYS cc_start: 0.7597 (ttpt) cc_final: 0.7208 (tmmm) REVERT: R 111 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: R 174 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7616 (mm-30) REVERT: R 208 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6448 (m-40) REVERT: S 30 GLN cc_start: 0.7968 (mt0) cc_final: 0.7715 (mt0) REVERT: S 43 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.6143 (p90) REVERT: S 89 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7330 (mptm) REVERT: S 163 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7822 (mtt90) REVERT: T 50 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7050 (mm-30) REVERT: T 100 MET cc_start: 0.8764 (mtt) cc_final: 0.8318 (mtm) REVERT: T 233 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7880 (ttpt) REVERT: U 186 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: V 97 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8259 (mm110) REVERT: V 151 MET cc_start: 0.8820 (mtm) cc_final: 0.8542 (mtm) REVERT: V 154 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7003 (tp30) REVERT: W 80 ASN cc_start: 0.6686 (OUTLIER) cc_final: 0.6222 (m-40) REVERT: W 183 MET cc_start: 0.6279 (mmm) cc_final: 0.6019 (tpp) REVERT: W 189 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8902 (tp) REVERT: W 195 TYR cc_start: 0.9376 (p90) cc_final: 0.8911 (p90) REVERT: X 95 HIS cc_start: 0.7432 (m90) cc_final: 0.6650 (m-70) REVERT: X 183 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8436 (ptmm) REVERT: Y 98 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8391 (tm-30) REVERT: Z 137 ASP cc_start: 0.7639 (m-30) cc_final: 0.7378 (m-30) REVERT: Z 164 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: Z 246 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6272 (tt0) REVERT: a 98 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6426 (tm-30) REVERT: a 138 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8286 (mtp) REVERT: a 202 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.6052 (pm20) REVERT: b 102 MET cc_start: 0.8570 (mmt) cc_final: 0.8264 (mmt) REVERT: b 106 ASP cc_start: 0.7859 (m-30) cc_final: 0.7606 (m-30) REVERT: b 140 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: b 200 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7779 (pm20) outliers start: 208 outliers final: 90 residues processed: 791 average time/residue: 1.2764 time to fit residues: 1257.1863 Evaluate side-chains 771 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 643 time to evaluate : 4.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 78 GLN Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain Q residue 198 MET Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 208 ASN Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 89 LYS Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 211 MET Chi-restraints excluded: chain T residue 229 GLU Chi-restraints excluded: chain T residue 233 LYS Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 67 PRO Chi-restraints excluded: chain U residue 149 SER Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 77 ASN Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 133 CYS Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 138 MET Chi-restraints excluded: chain a residue 181 ILE Chi-restraints excluded: chain a residue 201 TRP Chi-restraints excluded: chain a residue 202 GLN Chi-restraints excluded: chain b residue 140 GLU Chi-restraints excluded: chain b residue 200 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 0.6980 chunk 524 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 341 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 582 optimal weight: 5.9990 chunk 483 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 HIS G 59 GLN G 203 GLN I 79 ASN K 124 GLN P 112 GLN S 50 ASN T 23 GLN U 52 HIS V 77 ASN W 79 ASN Y 124 GLN a 148 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 49140 Z= 0.243 Angle : 0.551 22.964 66254 Z= 0.295 Chirality : 0.044 0.236 7400 Planarity : 0.004 0.076 8522 Dihedral : 5.488 84.390 6706 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.47 % Allowed : 17.78 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.11), residues: 6092 helix: 1.71 (0.11), residues: 2194 sheet: 0.58 (0.14), residues: 1342 loop : -0.53 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 280 HIS 0.005 0.001 HIS G 92 PHE 0.024 0.002 PHE A 81 TYR 0.019 0.001 TYR C 21 ARG 0.009 0.001 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 698 time to evaluate : 4.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8077 (ttmt) REVERT: 3 141 ASP cc_start: 0.5696 (OUTLIER) cc_final: 0.5008 (t0) REVERT: 4 135 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8075 (ttmt) REVERT: 4 140 ASP cc_start: 0.6510 (p0) cc_final: 0.6199 (t0) REVERT: A 61 LYS cc_start: 0.7886 (mttm) cc_final: 0.7565 (mtmt) REVERT: A 80 ASP cc_start: 0.8782 (m-30) cc_final: 0.8433 (m-30) REVERT: A 118 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6942 (pt0) REVERT: A 149 TYR cc_start: 0.8877 (p90) cc_final: 0.8501 (p90) REVERT: B 8 GLU cc_start: 0.7988 (tp30) cc_final: 0.7494 (tp30) REVERT: B 73 MET cc_start: 0.8395 (mmm) cc_final: 0.8024 (mmp) REVERT: C 24 GLN cc_start: 0.7613 (tt0) cc_final: 0.6772 (tt0) REVERT: C 28 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5814 (mp10) REVERT: C 37 ASP cc_start: 0.7744 (p0) cc_final: 0.7536 (t0) REVERT: C 40 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6781 (pm20) REVERT: C 153 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7162 (tm-30) REVERT: D 17 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6954 (mtm110) REVERT: D 176 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7390 (mtm) REVERT: D 203 LYS cc_start: 0.6621 (mttt) cc_final: 0.6156 (tttm) REVERT: E 43 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.6286 (p90) REVERT: E 49 TYR cc_start: 0.8094 (t80) cc_final: 0.7777 (t80) REVERT: E 183 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7894 (ttpt) REVERT: F 70 PHE cc_start: 0.8182 (p90) cc_final: 0.7514 (p90) REVERT: G 214 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: H 97 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8215 (mm110) REVERT: H 151 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8597 (mtm) REVERT: H 196 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5523 (mppt) REVERT: I 116 ASP cc_start: 0.7435 (t70) cc_final: 0.7220 (t70) REVERT: I 195 TYR cc_start: 0.9363 (p90) cc_final: 0.8835 (p90) REVERT: J 183 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8221 (ptmm) REVERT: K 98 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8497 (tm-30) REVERT: K 175 ARG cc_start: 0.8466 (mtm110) cc_final: 0.8139 (mtp-110) REVERT: L 137 ASP cc_start: 0.7693 (m-30) cc_final: 0.7424 (m-30) REVERT: L 164 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: L 257 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: L 290 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7815 (mm-30) REVERT: M 96 ARG cc_start: 0.8220 (mtt90) cc_final: 0.7848 (mtm-85) REVERT: M 148 ASN cc_start: 0.7777 (p0) cc_final: 0.7388 (p0) REVERT: N 86 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7433 (tpt-90) REVERT: N 102 MET cc_start: 0.8420 (mmt) cc_final: 0.8113 (mmt) REVERT: N 106 ASP cc_start: 0.7724 (m-30) cc_final: 0.7380 (m-30) REVERT: N 140 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: N 142 GLU cc_start: 0.7951 (tp30) cc_final: 0.7731 (pm20) REVERT: N 193 ARG cc_start: 0.8336 (mtt-85) cc_final: 0.8025 (mtp85) REVERT: O 33 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8443 (tm) REVERT: O 48 LEU cc_start: 0.8615 (mm) cc_final: 0.8039 (pp) REVERT: O 64 TYR cc_start: 0.8685 (m-80) cc_final: 0.8373 (m-80) REVERT: O 149 TYR cc_start: 0.9027 (p90) cc_final: 0.8619 (p90) REVERT: O 159 ARG cc_start: 0.6812 (pmt-80) cc_final: 0.6568 (ppt170) REVERT: O 200 ASP cc_start: 0.7880 (t0) cc_final: 0.7289 (t0) REVERT: O 207 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7700 (mp10) REVERT: P 11 ARG cc_start: 0.7748 (mtp180) cc_final: 0.7411 (mtp85) REVERT: P 73 MET cc_start: 0.8370 (mmp) cc_final: 0.8125 (mmp) REVERT: P 91 ASP cc_start: 0.8422 (t0) cc_final: 0.8164 (t0) REVERT: P 197 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7243 (ptpp) REVERT: Q 20 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6621 (mm-30) REVERT: Q 24 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: Q 64 ASP cc_start: 0.7582 (t0) cc_final: 0.7319 (t0) REVERT: Q 66 ASP cc_start: 0.7393 (p0) cc_final: 0.6982 (p0) REVERT: Q 148 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7861 (p0) REVERT: R 50 LYS cc_start: 0.7597 (ttpt) cc_final: 0.7197 (tmmm) REVERT: R 111 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: R 174 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7553 (mm-30) REVERT: S 30 GLN cc_start: 0.7942 (mt0) cc_final: 0.7718 (mt0) REVERT: S 38 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8187 (mp) REVERT: S 43 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6174 (p90) REVERT: S 163 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7858 (mtt90) REVERT: T 50 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6955 (mm-30) REVERT: T 100 MET cc_start: 0.8754 (mtt) cc_final: 0.8381 (mtm) REVERT: T 233 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.8005 (ttpt) REVERT: U 186 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: V 97 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8224 (mm110) REVERT: V 151 MET cc_start: 0.8793 (mtm) cc_final: 0.8549 (mtm) REVERT: V 154 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: V 190 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7855 (mmt) REVERT: V 196 LYS cc_start: 0.6456 (tptt) cc_final: 0.5372 (mppt) REVERT: W 80 ASN cc_start: 0.6671 (OUTLIER) cc_final: 0.6246 (m-40) REVERT: W 183 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.5816 (tpp) REVERT: W 189 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8884 (tp) REVERT: W 195 TYR cc_start: 0.9363 (p90) cc_final: 0.8834 (p90) REVERT: X 95 HIS cc_start: 0.7348 (m90) cc_final: 0.6645 (m-70) REVERT: X 183 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8214 (ptmm) REVERT: Y 98 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8384 (tm-30) REVERT: Z 137 ASP cc_start: 0.7646 (m-30) cc_final: 0.7393 (m-30) REVERT: Z 141 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7852 (m) REVERT: Z 164 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: Z 246 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6207 (tt0) REVERT: a 98 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: a 202 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.5888 (pm20) REVERT: b 86 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7237 (tpt-90) REVERT: b 102 MET cc_start: 0.8563 (mmt) cc_final: 0.8277 (mmt) REVERT: b 106 ASP cc_start: 0.7830 (m-30) cc_final: 0.7555 (m-30) REVERT: b 140 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7610 (tp30) outliers start: 184 outliers final: 74 residues processed: 815 average time/residue: 1.2888 time to fit residues: 1310.4473 Evaluate side-chains 776 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 660 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 192 ARG Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 133 CYS Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 161 GLN Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 197 LYS Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 233 LYS Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 77 ASN Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 190 MET Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 133 CYS Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 181 ILE Chi-restraints excluded: chain a residue 202 GLN Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 331 optimal weight: 6.9990 chunk 425 optimal weight: 3.9990 chunk 329 optimal weight: 10.0000 chunk 490 optimal weight: 0.8980 chunk 325 optimal weight: 2.9990 chunk 580 optimal weight: 0.9990 chunk 363 optimal weight: 0.8980 chunk 353 optimal weight: 0.9980 chunk 267 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 133 HIS A 138 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 HIS G 59 GLN G 92 HIS G 120 GLN I 79 ASN K 124 GLN M 87 GLN N 203 GLN O 117 GLN P 112 GLN U 52 HIS U 92 HIS U 120 GLN V 77 ASN V 201 ASN W 79 ASN Y 124 GLN Y 150 GLN a 87 GLN a 148 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 49140 Z= 0.191 Angle : 0.531 21.877 66254 Z= 0.284 Chirality : 0.044 0.212 7400 Planarity : 0.004 0.058 8522 Dihedral : 5.275 69.065 6706 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.00 % Allowed : 18.59 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.11), residues: 6092 helix: 1.95 (0.11), residues: 2176 sheet: 0.69 (0.13), residues: 1368 loop : -0.47 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 280 HIS 0.006 0.001 HIS U 92 PHE 0.029 0.001 PHE S 94 TYR 0.019 0.001 TYR C 21 ARG 0.010 0.000 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 729 time to evaluate : 4.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8108 (ttmt) REVERT: 3 140 ASP cc_start: 0.5870 (t0) cc_final: 0.5202 (p0) REVERT: 3 141 ASP cc_start: 0.5658 (OUTLIER) cc_final: 0.5051 (t0) REVERT: 4 135 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8049 (ttmt) REVERT: 4 140 ASP cc_start: 0.6494 (p0) cc_final: 0.6181 (t0) REVERT: A 61 LYS cc_start: 0.7847 (mttm) cc_final: 0.7569 (mtmt) REVERT: A 64 TYR cc_start: 0.8613 (m-80) cc_final: 0.8253 (m-80) REVERT: A 80 ASP cc_start: 0.8771 (m-30) cc_final: 0.8474 (m-30) REVERT: A 118 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6883 (pt0) REVERT: A 149 TYR cc_start: 0.8869 (p90) cc_final: 0.8449 (p90) REVERT: B 8 GLU cc_start: 0.8009 (tp30) cc_final: 0.7523 (tp30) REVERT: B 73 MET cc_start: 0.8371 (mmm) cc_final: 0.8019 (mmp) REVERT: C 24 GLN cc_start: 0.7616 (tt0) cc_final: 0.6760 (tt0) REVERT: C 28 GLN cc_start: 0.6070 (OUTLIER) cc_final: 0.5740 (mp10) REVERT: C 37 ASP cc_start: 0.7797 (p0) cc_final: 0.7553 (t0) REVERT: C 40 GLU cc_start: 0.7255 (pt0) cc_final: 0.6675 (pm20) REVERT: C 153 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7055 (tm-30) REVERT: D 17 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6952 (ptp-170) REVERT: D 65 TYR cc_start: 0.8538 (m-80) cc_final: 0.8282 (m-80) REVERT: D 97 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: D 176 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7349 (mtm) REVERT: D 203 LYS cc_start: 0.6600 (mttt) cc_final: 0.6148 (tttm) REVERT: E 43 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6137 (p90) REVERT: E 48 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7263 (m) REVERT: E 49 TYR cc_start: 0.7942 (t80) cc_final: 0.7687 (t80) REVERT: E 183 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7851 (ttpt) REVERT: E 210 ASP cc_start: 0.7049 (m-30) cc_final: 0.6596 (p0) REVERT: F 70 PHE cc_start: 0.8124 (p90) cc_final: 0.7498 (p90) REVERT: G 6 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7590 (mp0) REVERT: G 14 ASP cc_start: 0.8624 (t70) cc_final: 0.8257 (t0) REVERT: G 89 ASP cc_start: 0.7949 (m-30) cc_final: 0.7728 (m-30) REVERT: G 214 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: H 97 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8228 (mm110) REVERT: H 151 MET cc_start: 0.8812 (mtm) cc_final: 0.8578 (mtm) REVERT: H 192 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7420 (mmt180) REVERT: H 196 LYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5416 (mppt) REVERT: I 116 ASP cc_start: 0.7345 (t70) cc_final: 0.7100 (t70) REVERT: I 195 TYR cc_start: 0.9358 (p90) cc_final: 0.8857 (p90) REVERT: J 183 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8242 (ptmm) REVERT: K 98 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8526 (tm-30) REVERT: K 175 ARG cc_start: 0.8399 (mtm110) cc_final: 0.8088 (mtp-110) REVERT: L 137 ASP cc_start: 0.7743 (m-30) cc_final: 0.7454 (m-30) REVERT: L 161 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: L 164 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: L 241 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8168 (tppt) REVERT: L 257 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6934 (m-30) REVERT: L 268 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: L 290 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7800 (mm-30) REVERT: M 96 ARG cc_start: 0.8203 (mtt90) cc_final: 0.7837 (mtm-85) REVERT: M 148 ASN cc_start: 0.7721 (p0) cc_final: 0.7348 (p0) REVERT: N 86 ARG cc_start: 0.7740 (ttt90) cc_final: 0.7412 (tpt-90) REVERT: N 142 GLU cc_start: 0.8022 (tp30) cc_final: 0.7740 (pm20) REVERT: N 193 ARG cc_start: 0.8313 (mtt-85) cc_final: 0.7996 (mtp85) REVERT: O 33 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8416 (tm) REVERT: O 48 LEU cc_start: 0.8612 (mm) cc_final: 0.7915 (pp) REVERT: O 64 TYR cc_start: 0.8625 (m-80) cc_final: 0.8377 (m-80) REVERT: O 149 TYR cc_start: 0.8990 (p90) cc_final: 0.8488 (p90) REVERT: O 200 ASP cc_start: 0.7888 (t0) cc_final: 0.7256 (t0) REVERT: O 207 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7621 (mp10) REVERT: P 73 MET cc_start: 0.8335 (mmp) cc_final: 0.8093 (mmp) REVERT: P 91 ASP cc_start: 0.8330 (t0) cc_final: 0.8005 (t0) REVERT: P 197 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7184 (ptpp) REVERT: Q 20 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6576 (mm-30) REVERT: Q 24 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7051 (tt0) REVERT: Q 64 ASP cc_start: 0.7528 (t0) cc_final: 0.7295 (t0) REVERT: Q 66 ASP cc_start: 0.7302 (p0) cc_final: 0.6914 (p0) REVERT: Q 148 ASP cc_start: 0.8186 (p0) cc_final: 0.7869 (p0) REVERT: R 50 LYS cc_start: 0.7580 (ttpt) cc_final: 0.7135 (tmmm) REVERT: R 111 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: R 174 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7537 (mm-30) REVERT: S 10 TYR cc_start: 0.8920 (p90) cc_final: 0.8613 (p90) REVERT: S 30 GLN cc_start: 0.7926 (mt0) cc_final: 0.7641 (mt0) REVERT: S 38 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8131 (mp) REVERT: S 43 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.6204 (p90) REVERT: S 46 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8640 (m-10) REVERT: S 163 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7870 (mtt90) REVERT: T 100 MET cc_start: 0.8708 (mtt) cc_final: 0.8372 (mtm) REVERT: U 177 GLU cc_start: 0.7083 (mp0) cc_final: 0.6726 (mt-10) REVERT: U 186 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: V 97 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8202 (mm110) REVERT: V 154 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6724 (tp30) REVERT: V 190 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7738 (mmt) REVERT: W 183 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.5673 (tpp) REVERT: W 189 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8873 (tp) REVERT: W 195 TYR cc_start: 0.9350 (p90) cc_final: 0.8840 (p90) REVERT: X 95 HIS cc_start: 0.7342 (m90) cc_final: 0.6640 (m-70) REVERT: X 124 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: X 147 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8767 (mmtm) REVERT: Y 98 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8388 (tm-30) REVERT: Z 137 ASP cc_start: 0.7646 (m-30) cc_final: 0.7360 (m-30) REVERT: Z 141 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7799 (m) REVERT: Z 164 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7320 (tp30) REVERT: Z 246 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6128 (tt0) REVERT: a 98 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6372 (tm-30) REVERT: b 86 ARG cc_start: 0.7625 (ttt-90) cc_final: 0.7257 (tpt-90) REVERT: b 102 MET cc_start: 0.8529 (mmt) cc_final: 0.8322 (mmt) REVERT: b 106 ASP cc_start: 0.7816 (m-30) cc_final: 0.7544 (m-30) REVERT: b 140 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7606 (tp30) outliers start: 159 outliers final: 64 residues processed: 828 average time/residue: 1.2830 time to fit residues: 1333.4000 Evaluate side-chains 764 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 661 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 128 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 167 CYS Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 192 ARG Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain K residue 133 CYS Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 161 GLN Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 241 LYS Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 172 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 197 LYS Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 46 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 77 ASN Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 190 MET Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 133 CYS Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 368 optimal weight: 20.0000 chunk 395 optimal weight: 0.9990 chunk 286 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 456 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 138 ASN B 108 GLN B 112 GLN E 27 ASN G 52 HIS G 59 GLN G 120 GLN I 79 ASN K 124 GLN K 150 GLN N 203 GLN P 112 GLN Q 18 GLN T 71 GLN ** U 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 HIS V 77 ASN W 79 ASN Y 124 GLN Y 150 GLN a 148 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 49140 Z= 0.347 Angle : 0.603 23.745 66254 Z= 0.319 Chirality : 0.046 0.211 7400 Planarity : 0.004 0.059 8522 Dihedral : 5.395 57.196 6701 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.36 % Allowed : 18.95 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.11), residues: 6092 helix: 1.75 (0.11), residues: 2174 sheet: 0.55 (0.13), residues: 1380 loop : -0.50 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Z 280 HIS 0.008 0.001 HIS G 92 PHE 0.021 0.002 PHE Y 221 TYR 0.021 0.002 TYR Q 21 ARG 0.011 0.001 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 664 time to evaluate : 4.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8011 (ttmt) REVERT: 3 140 ASP cc_start: 0.5884 (t0) cc_final: 0.5116 (p0) REVERT: 3 141 ASP cc_start: 0.5695 (OUTLIER) cc_final: 0.5069 (t0) REVERT: 4 135 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8005 (ttmt) REVERT: 4 140 ASP cc_start: 0.6512 (p0) cc_final: 0.6254 (t0) REVERT: A 80 ASP cc_start: 0.8896 (m-30) cc_final: 0.8561 (m-30) REVERT: A 118 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6965 (pt0) REVERT: A 149 TYR cc_start: 0.8891 (p90) cc_final: 0.8493 (p90) REVERT: A 210 ARG cc_start: 0.8494 (ptm-80) cc_final: 0.8207 (ttp80) REVERT: B 8 GLU cc_start: 0.8013 (tp30) cc_final: 0.7467 (tp30) REVERT: B 73 MET cc_start: 0.8436 (mmm) cc_final: 0.8124 (mmp) REVERT: C 24 GLN cc_start: 0.7610 (tt0) cc_final: 0.6669 (tt0) REVERT: C 28 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5953 (mp10) REVERT: C 40 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6670 (pm20) REVERT: C 153 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7076 (tm-30) REVERT: D 17 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6965 (mtm110) REVERT: D 176 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7390 (mtm) REVERT: D 203 LYS cc_start: 0.6592 (mttt) cc_final: 0.6125 (tttm) REVERT: E 43 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.6247 (p90) REVERT: E 48 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7387 (m) REVERT: E 49 TYR cc_start: 0.8032 (t80) cc_final: 0.7741 (t80) REVERT: E 183 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8017 (ptmt) REVERT: E 204 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7480 (mp) REVERT: E 210 ASP cc_start: 0.7021 (m-30) cc_final: 0.6580 (p0) REVERT: F 70 PHE cc_start: 0.8166 (p90) cc_final: 0.7427 (p90) REVERT: G 6 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7533 (mp0) REVERT: G 214 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: H 97 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8243 (mm110) REVERT: H 151 MET cc_start: 0.8786 (mtm) cc_final: 0.8570 (mtm) REVERT: H 196 LYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5580 (mppt) REVERT: I 116 ASP cc_start: 0.7383 (t70) cc_final: 0.7079 (t0) REVERT: I 195 TYR cc_start: 0.9374 (p90) cc_final: 0.8853 (p90) REVERT: J 183 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8190 (ptmm) REVERT: K 98 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8457 (tm-30) REVERT: K 175 ARG cc_start: 0.8496 (mtm110) cc_final: 0.8150 (mtp-110) REVERT: L 137 ASP cc_start: 0.7710 (m-30) cc_final: 0.7432 (m-30) REVERT: L 161 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: L 164 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: L 241 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8123 (tppt) REVERT: L 249 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: L 257 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6944 (m-30) REVERT: L 268 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: L 290 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7778 (mm-30) REVERT: M 96 ARG cc_start: 0.8235 (mtt90) cc_final: 0.7862 (mtm-85) REVERT: M 148 ASN cc_start: 0.7806 (p0) cc_final: 0.7431 (p0) REVERT: N 102 MET cc_start: 0.8550 (mmt) cc_final: 0.8146 (mmt) REVERT: N 106 ASP cc_start: 0.7732 (m-30) cc_final: 0.7383 (m-30) REVERT: N 140 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: N 142 GLU cc_start: 0.7964 (tp30) cc_final: 0.7746 (pm20) REVERT: N 193 ARG cc_start: 0.8358 (mtt-85) cc_final: 0.8084 (mtp85) REVERT: O 33 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8500 (tm) REVERT: O 48 LEU cc_start: 0.8613 (mm) cc_final: 0.7920 (pp) REVERT: O 149 TYR cc_start: 0.9030 (p90) cc_final: 0.8634 (p90) REVERT: O 200 ASP cc_start: 0.7891 (t0) cc_final: 0.7221 (t0) REVERT: O 207 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7604 (mp10) REVERT: P 91 ASP cc_start: 0.8401 (t0) cc_final: 0.8083 (t0) REVERT: P 183 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7092 (mtmm) REVERT: P 197 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7266 (ptpp) REVERT: Q 20 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6586 (mm-30) REVERT: Q 24 GLN cc_start: 0.7608 (tt0) cc_final: 0.6941 (tt0) REVERT: Q 64 ASP cc_start: 0.7509 (t0) cc_final: 0.7253 (t0) REVERT: Q 66 ASP cc_start: 0.7330 (p0) cc_final: 0.6932 (p0) REVERT: Q 143 TYR cc_start: 0.8697 (m-80) cc_final: 0.7993 (m-80) REVERT: R 50 LYS cc_start: 0.7542 (ttpt) cc_final: 0.7302 (tttt) REVERT: R 111 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: R 174 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7581 (mm-30) REVERT: S 30 GLN cc_start: 0.8055 (mt0) cc_final: 0.7810 (mt0) REVERT: S 38 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8319 (mp) REVERT: S 43 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.6223 (p90) REVERT: S 163 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7920 (mtt90) REVERT: T 50 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: T 100 MET cc_start: 0.8732 (mtt) cc_final: 0.8274 (mtm) REVERT: U 186 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: V 97 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8223 (mm110) REVERT: V 154 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6766 (tp30) REVERT: V 190 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7880 (mmt) REVERT: V 196 LYS cc_start: 0.6379 (tptt) cc_final: 0.5350 (mppt) REVERT: W 183 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5879 (tpp) REVERT: W 189 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8896 (tp) REVERT: W 195 TYR cc_start: 0.9358 (p90) cc_final: 0.8907 (p90) REVERT: X 95 HIS cc_start: 0.7405 (m90) cc_final: 0.6675 (m-70) REVERT: X 183 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8233 (ptmm) REVERT: Y 98 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8361 (tm-30) REVERT: Z 137 ASP cc_start: 0.7649 (m-30) cc_final: 0.7379 (m-30) REVERT: Z 141 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8117 (m) REVERT: Z 164 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: Z 246 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6221 (tt0) REVERT: a 98 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: b 86 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7430 (tpt-90) REVERT: b 102 MET cc_start: 0.8563 (mmt) cc_final: 0.8314 (mmt) REVERT: b 106 ASP cc_start: 0.7850 (m-30) cc_final: 0.7587 (m-30) REVERT: b 140 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7615 (tp30) outliers start: 178 outliers final: 78 residues processed: 788 average time/residue: 1.2865 time to fit residues: 1261.5365 Evaluate side-chains 769 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 648 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 128 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 167 CYS Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 192 ARG Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 133 CYS Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 161 GLN Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 241 LYS Chi-restraints excluded: chain L residue 249 GLU Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 197 LYS Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain U residue 149 SER Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 190 MET Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 183 MET Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 67 ARG Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 133 CYS Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 148 ASN Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 5.9990 chunk 555 optimal weight: 1.9990 chunk 507 optimal weight: 0.5980 chunk 540 optimal weight: 5.9990 chunk 325 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 424 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 488 optimal weight: 0.6980 chunk 511 optimal weight: 0.0060 chunk 538 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 112 GLN B 114 ASN E 27 ASN G 52 HIS G 59 GLN H 48 GLN H 94 HIS I 79 ASN K 124 GLN N 203 GLN P 112 GLN R 208 ASN U 52 HIS U 92 HIS U 120 GLN V 201 ASN W 79 ASN Y 124 GLN ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 49140 Z= 0.167 Angle : 0.538 21.654 66254 Z= 0.288 Chirality : 0.044 0.199 7400 Planarity : 0.004 0.057 8522 Dihedral : 5.118 56.547 6701 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.15 % Allowed : 20.54 % Favored : 77.31 % 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: 1.04 (0.11), residues: 6092 helix: 2.01 (0.11), residues: 2188 sheet: 0.66 (0.14), residues: 1374 loop : -0.44 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 280 HIS 0.005 0.001 HIS U 92 PHE 0.029 0.001 PHE E 94 TYR 0.024 0.001 TYR C 21 ARG 0.013 0.001 ARG b 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 721 time to evaluate : 4.637 Fit side-chains revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8046 (ttmt) REVERT: 3 140 ASP cc_start: 0.5799 (t0) cc_final: 0.5234 (p0) REVERT: 3 141 ASP cc_start: 0.5619 (OUTLIER) cc_final: 0.5030 (t0) REVERT: 4 135 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8045 (ttmt) REVERT: 4 140 ASP cc_start: 0.6372 (p0) cc_final: 0.6149 (t0) REVERT: A 61 LYS cc_start: 0.7677 (mttm) cc_final: 0.7434 (mtmt) REVERT: A 80 ASP cc_start: 0.8649 (m-30) cc_final: 0.8352 (m-30) REVERT: A 118 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: A 149 TYR cc_start: 0.8851 (p90) cc_final: 0.8439 (p90) REVERT: A 210 ARG cc_start: 0.8482 (ptm-80) cc_final: 0.8202 (ttp80) REVERT: B 8 GLU cc_start: 0.8007 (tp30) cc_final: 0.7538 (tp30) REVERT: B 73 MET cc_start: 0.8356 (mmm) cc_final: 0.8048 (mmp) REVERT: C 24 GLN cc_start: 0.7603 (tt0) cc_final: 0.6751 (tt0) REVERT: C 28 GLN cc_start: 0.6121 (OUTLIER) cc_final: 0.5816 (mp10) REVERT: C 153 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6994 (tm-30) REVERT: E 43 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.6186 (p90) REVERT: E 48 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7157 (t) REVERT: E 49 TYR cc_start: 0.7814 (t80) cc_final: 0.7558 (t80) REVERT: F 70 PHE cc_start: 0.8095 (p90) cc_final: 0.7574 (p90) REVERT: G 6 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7599 (mp0) REVERT: G 92 HIS cc_start: 0.8748 (OUTLIER) cc_final: 0.8274 (t70) REVERT: G 214 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: H 97 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8216 (mm110) REVERT: H 196 LYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5242 (mppt) REVERT: I 116 ASP cc_start: 0.7362 (t70) cc_final: 0.7092 (t0) REVERT: I 195 TYR cc_start: 0.9370 (p90) cc_final: 0.8874 (p90) REVERT: K 75 THR cc_start: 0.8741 (m) cc_final: 0.8527 (p) REVERT: K 98 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8540 (tm-30) REVERT: K 175 ARG cc_start: 0.8385 (mtm110) cc_final: 0.8085 (mtp-110) REVERT: L 137 ASP cc_start: 0.7741 (m-30) cc_final: 0.7459 (m-30) REVERT: L 161 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: L 164 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7172 (tp30) REVERT: L 249 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: L 257 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6939 (m-30) REVERT: L 268 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: L 290 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7789 (mm-30) REVERT: M 96 ARG cc_start: 0.8179 (mtt90) cc_final: 0.7819 (mtm-85) REVERT: M 148 ASN cc_start: 0.7733 (p0) cc_final: 0.7349 (p0) REVERT: N 102 MET cc_start: 0.8498 (mmt) cc_final: 0.8133 (mmt) REVERT: N 106 ASP cc_start: 0.7734 (m-30) cc_final: 0.7395 (m-30) REVERT: N 140 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: N 142 GLU cc_start: 0.7977 (tp30) cc_final: 0.7723 (pm20) REVERT: N 193 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.8012 (mtp85) REVERT: O 33 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8434 (tm) REVERT: O 48 LEU cc_start: 0.8593 (mm) cc_final: 0.7827 (pp) REVERT: O 149 TYR cc_start: 0.8936 (p90) cc_final: 0.8388 (p90) REVERT: O 200 ASP cc_start: 0.7868 (t0) cc_final: 0.7154 (t0) REVERT: O 207 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7656 (mp10) REVERT: P 91 ASP cc_start: 0.8314 (t0) cc_final: 0.7991 (t0) REVERT: P 183 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7322 (mtmm) REVERT: P 197 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7217 (ptpp) REVERT: Q 20 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6588 (mm-30) REVERT: Q 24 GLN cc_start: 0.7540 (tt0) cc_final: 0.7031 (tt0) REVERT: Q 64 ASP cc_start: 0.7466 (t0) cc_final: 0.7248 (t0) REVERT: Q 66 ASP cc_start: 0.7310 (p0) cc_final: 0.6941 (p0) REVERT: R 50 LYS cc_start: 0.7583 (ttpt) cc_final: 0.7256 (tmmt) REVERT: R 111 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: R 174 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7533 (mm-30) REVERT: R 208 ASN cc_start: 0.6741 (OUTLIER) cc_final: 0.6443 (m-40) REVERT: S 10 TYR cc_start: 0.8863 (p90) cc_final: 0.8553 (p90) REVERT: S 30 GLN cc_start: 0.7956 (mt0) cc_final: 0.7678 (mt0) REVERT: S 38 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8092 (mp) REVERT: S 43 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6222 (p90) REVERT: S 163 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7804 (mtt90) REVERT: S 206 LYS cc_start: 0.7785 (pttt) cc_final: 0.7473 (mtpt) REVERT: T 100 MET cc_start: 0.8736 (mtt) cc_final: 0.8410 (mtm) REVERT: U 145 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7840 (ppp) REVERT: U 177 GLU cc_start: 0.7041 (mp0) cc_final: 0.6692 (mt-10) REVERT: U 186 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: V 97 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8166 (mm110) REVERT: V 154 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6629 (tp30) REVERT: W 183 MET cc_start: 0.5828 (mmm) cc_final: 0.5560 (tpp) REVERT: W 189 LEU cc_start: 0.9081 (tm) cc_final: 0.8857 (tp) REVERT: W 195 TYR cc_start: 0.9335 (p90) cc_final: 0.8819 (p90) REVERT: X 95 HIS cc_start: 0.7115 (m90) cc_final: 0.6564 (m-70) REVERT: X 124 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: X 147 LYS cc_start: 0.9008 (mmtp) cc_final: 0.8766 (mmtm) REVERT: Y 98 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8405 (tm-30) REVERT: Z 137 ASP cc_start: 0.7677 (m-30) cc_final: 0.7404 (m-30) REVERT: Z 164 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: a 98 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6408 (tm-30) REVERT: b 86 ARG cc_start: 0.7850 (ttt-90) cc_final: 0.7473 (tpt-90) REVERT: b 106 ASP cc_start: 0.7806 (m-30) cc_final: 0.7537 (m-30) outliers start: 114 outliers final: 52 residues processed: 791 average time/residue: 1.2719 time to fit residues: 1255.0513 Evaluate side-chains 753 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 671 time to evaluate : 4.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 167 CYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 133 CYS Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 161 GLN Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 249 GLU Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain N residue 172 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 197 LYS Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 208 ASN Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Z residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 0.9990 chunk 571 optimal weight: 0.0370 chunk 348 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 chunk 397 optimal weight: 9.9990 chunk 599 optimal weight: 3.9990 chunk 551 optimal weight: 0.9980 chunk 477 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 368 optimal weight: 30.0000 chunk 292 optimal weight: 8.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 79 ASN A 117 GLN B 112 GLN E 27 ASN G 52 HIS G 59 GLN G 120 GLN H 77 ASN I 79 ASN K 124 GLN P 112 GLN Q 39 ASN R 208 ASN U 52 HIS U 92 HIS U 120 GLN V 201 ASN ** W 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 124 GLN ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 87 GLN a 148 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.360 49140 Z= 0.259 Angle : 0.672 62.097 66254 Z= 0.361 Chirality : 0.044 0.479 7400 Planarity : 0.004 0.140 8522 Dihedral : 5.119 56.545 6701 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.85 % Allowed : 21.44 % Favored : 76.71 % 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: 1.04 (0.11), residues: 6092 helix: 2.02 (0.11), residues: 2188 sheet: 0.67 (0.14), residues: 1374 loop : -0.44 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 280 HIS 0.005 0.001 HIS U 92 PHE 0.028 0.001 PHE A 81 TYR 0.042 0.001 TYR G 202 ARG 0.012 0.001 ARG O 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 672 time to evaluate : 4.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8046 (ttmt) REVERT: 3 140 ASP cc_start: 0.5786 (t0) cc_final: 0.5235 (p0) REVERT: 3 141 ASP cc_start: 0.5614 (OUTLIER) cc_final: 0.5032 (t0) REVERT: 4 135 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8042 (ttmt) REVERT: A 61 LYS cc_start: 0.7669 (mttm) cc_final: 0.7435 (mtmt) REVERT: A 80 ASP cc_start: 0.8649 (m-30) cc_final: 0.8353 (m-30) REVERT: A 118 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6897 (pt0) REVERT: A 149 TYR cc_start: 0.8852 (p90) cc_final: 0.8435 (p90) REVERT: A 210 ARG cc_start: 0.8483 (ptm-80) cc_final: 0.8193 (ttp80) REVERT: B 8 GLU cc_start: 0.7995 (tp30) cc_final: 0.7536 (tp30) REVERT: B 73 MET cc_start: 0.8359 (mmm) cc_final: 0.8046 (mmp) REVERT: C 24 GLN cc_start: 0.7608 (tt0) cc_final: 0.6751 (tt0) REVERT: C 28 GLN cc_start: 0.6125 (OUTLIER) cc_final: 0.5816 (mp10) REVERT: C 153 GLU cc_start: 0.7615 (mt-10) cc_final: 0.6994 (tm-30) REVERT: E 43 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.6187 (p90) REVERT: E 48 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.7159 (t) REVERT: E 49 TYR cc_start: 0.7814 (t80) cc_final: 0.7570 (t80) REVERT: F 70 PHE cc_start: 0.8074 (p90) cc_final: 0.7532 (p90) REVERT: G 6 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7598 (mp0) REVERT: G 92 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.8372 (t-90) REVERT: G 214 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: H 97 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8215 (mm110) REVERT: H 151 MET cc_start: 0.8689 (mtm) cc_final: 0.8432 (mtm) REVERT: H 196 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5243 (mppt) REVERT: I 116 ASP cc_start: 0.7361 (t70) cc_final: 0.7087 (t70) REVERT: I 195 TYR cc_start: 0.9369 (p90) cc_final: 0.8875 (p90) REVERT: J 124 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: K 75 THR cc_start: 0.8746 (m) cc_final: 0.8530 (p) REVERT: K 98 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8541 (tm-30) REVERT: K 175 ARG cc_start: 0.8383 (mtm110) cc_final: 0.8085 (mtp-110) REVERT: L 137 ASP cc_start: 0.7742 (m-30) cc_final: 0.7459 (m-30) REVERT: L 161 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: L 164 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7173 (tp30) REVERT: L 249 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: L 257 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: L 268 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: L 290 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7789 (mm-30) REVERT: M 96 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7804 (mtm-85) REVERT: M 148 ASN cc_start: 0.7732 (p0) cc_final: 0.7348 (p0) REVERT: N 142 GLU cc_start: 0.7978 (tp30) cc_final: 0.7736 (pm20) REVERT: N 193 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.8005 (mtp85) REVERT: O 33 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8431 (tm) REVERT: O 48 LEU cc_start: 0.8593 (mm) cc_final: 0.7828 (pp) REVERT: O 149 TYR cc_start: 0.8929 (p90) cc_final: 0.8382 (p90) REVERT: O 200 ASP cc_start: 0.7871 (t0) cc_final: 0.7156 (t0) REVERT: O 207 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7656 (mp10) REVERT: P 91 ASP cc_start: 0.8310 (t0) cc_final: 0.7990 (t0) REVERT: P 183 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7323 (mtmm) REVERT: Q 20 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6587 (mm-30) REVERT: Q 24 GLN cc_start: 0.7544 (tt0) cc_final: 0.7030 (tt0) REVERT: Q 66 ASP cc_start: 0.7308 (p0) cc_final: 0.6951 (p0) REVERT: R 50 LYS cc_start: 0.7583 (ttpt) cc_final: 0.7256 (tmmt) REVERT: R 111 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: R 174 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7531 (mm-30) REVERT: R 208 ASN cc_start: 0.6789 (OUTLIER) cc_final: 0.6171 (p0) REVERT: S 10 TYR cc_start: 0.8865 (p90) cc_final: 0.8540 (p90) REVERT: S 30 GLN cc_start: 0.7959 (mt0) cc_final: 0.7678 (mt0) REVERT: S 38 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8091 (mp) REVERT: S 43 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.6223 (p90) REVERT: S 163 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7803 (mtt90) REVERT: S 206 LYS cc_start: 0.7785 (pttt) cc_final: 0.7473 (mtpt) REVERT: T 100 MET cc_start: 0.8737 (mtt) cc_final: 0.8410 (mtm) REVERT: U 145 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7842 (ppp) REVERT: U 177 GLU cc_start: 0.7040 (mp0) cc_final: 0.6708 (mt-10) REVERT: U 186 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: V 97 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8166 (mm110) REVERT: V 154 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6630 (tp30) REVERT: W 183 MET cc_start: 0.5832 (mmm) cc_final: 0.5557 (tpp) REVERT: W 189 LEU cc_start: 0.9082 (tm) cc_final: 0.8858 (tp) REVERT: W 195 TYR cc_start: 0.9335 (p90) cc_final: 0.8816 (p90) REVERT: X 95 HIS cc_start: 0.7119 (m90) cc_final: 0.6563 (m-70) REVERT: X 124 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: X 147 LYS cc_start: 0.9004 (mmtp) cc_final: 0.8766 (mmtm) REVERT: Y 98 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8404 (tm-30) REVERT: Z 137 ASP cc_start: 0.7679 (m-30) cc_final: 0.7404 (m-30) REVERT: Z 164 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: a 98 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6383 (tm-30) REVERT: b 86 ARG cc_start: 0.7845 (ttt-90) cc_final: 0.7472 (tpt-90) REVERT: b 106 ASP cc_start: 0.7805 (m-30) cc_final: 0.7538 (m-30) outliers start: 98 outliers final: 60 residues processed: 730 average time/residue: 1.2897 time to fit residues: 1174.2421 Evaluate side-chains 753 residues out of total 5450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 664 time to evaluate : 5.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 167 CYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 133 CYS Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 161 GLN Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 249 GLU Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 172 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 208 ASN Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain U residue 149 SER Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 191 ASN Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Z residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 10.0000 chunk 508 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 440 optimal weight: 0.0470 chunk 70 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 478 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 491 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 79 ASN B 112 GLN E 27 ASN G 52 HIS G 59 GLN H 77 ASN I 79 ASN K 124 GLN P 112 GLN Q 39 ASN ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 HIS U 92 HIS U 120 GLN V 201 ASN ** W 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 124 GLN ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113077 restraints weight = 65073.047| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.81 r_work: 0.3332 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.360 49140 Z= 0.263 Angle : 0.664 62.095 66254 Z= 0.363 Chirality : 0.044 0.529 7400 Planarity : 0.004 0.140 8522 Dihedral : 5.119 56.545 6701 Min Nonbonded Distance : 1.357 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.76 % Allowed : 21.48 % Favored : 76.76 % 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: 1.04 (0.11), residues: 6092 helix: 2.02 (0.11), residues: 2188 sheet: 0.67 (0.14), residues: 1374 loop : -0.44 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 280 HIS 0.005 0.001 HIS U 92 PHE 0.028 0.001 PHE A 81 TYR 0.042 0.001 TYR G 202 ARG 0.012 0.001 ARG O 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17329.08 seconds wall clock time: 300 minutes 33.06 seconds (18033.06 seconds total)