Starting phenix.real_space_refine on Tue Aug 26 13:56:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fmg_3231/08_2025/5fmg_3231.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fmg_3231/08_2025/5fmg_3231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5fmg_3231/08_2025/5fmg_3231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fmg_3231/08_2025/5fmg_3231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5fmg_3231/08_2025/5fmg_3231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fmg_3231/08_2025/5fmg_3231.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 192 5.16 5 C 25110 2.51 5 N 6640 2.21 5 O 7392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39334 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1440 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 11, 'GLU:plan': 12, 'GLN:plan1': 3, 'TYR:plan': 5, 'ARG:plan': 5, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 182 Chain: "B" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1381 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 12, 'ASN:plan1': 7, 'ARG:plan': 6, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASP:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 202 Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1527 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1409 Classifications: {'peptide': 215} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 74} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 2, 'GLN:plan1': 6, 'GLU:plan': 14, 'ASN:plan1': 5, 'ASP:plan': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 169 Chain: "E" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1440 Classifications: {'peptide': 217} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 59} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 12, 'ARG:plan': 7, 'PHE:plan': 2, 'ASP:plan': 8, 'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 152 Chain: "F" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1492 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 11, 'GLN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "G" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1542 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 5, 'GLU:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 7, 'PHE:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 185 Chain: "H" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1316 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'TRANS': 190} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'PHE:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 115 Chain: "I" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1241 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2, 'TRP:plan': 1, 'ARG:plan': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "J" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1273 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 5, 'PHE:plan': 7, 'TYR:plan': 5, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 8, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 175 Chain: "K" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1452 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 192} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 4, 'GLN:plan1': 3, 'GLU:plan': 4, 'TYR:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "L" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1355 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 188} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 5, 'TYR:plan': 3, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 82 Chain: "M" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1413 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'HIS:plan': 1, 'PHE:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 109 Chain: "N" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1337 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'HIS:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 146 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'7F1': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b Time building chain proxies: 8.73, per 1000 atoms: 0.22 Number of scatterers: 39334 At special positions: 0 Unit cell: (140.4, 169.52, 135.2, 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 192 16.00 O 7392 8.00 N 6640 7.00 C 25110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 48 " distance=2.02 Simple disulfide: pdb=" SG CYS J 163 " - pdb=" SG CYS J 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 52 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS S 96 " - pdb=" SG CYS S 112 " distance=2.03 Simple disulfide: pdb=" SG CYS U 39 " - pdb=" SG CYS U 48 " distance=2.02 Simple disulfide: pdb=" SG CYS X 163 " - pdb=" SG CYS X 183 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 52 " - pdb=" SG CYS Z 97 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 715.3 nanoseconds 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10692 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 0 sheets defined 35.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 10 through 12 No H-bonds generated for 'chain 'A' and resid 10 through 12' Processing helix chain 'A' and resid 23 through 34 Processing helix chain 'A' and resid 90 through 111 Processing helix chain 'A' and resid 117 through 133 removed outlier: 3.772A pdb=" N ASN A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.859A pdb=" N ARG A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.776A pdb=" N LEU A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 80 through 100 Processing helix chain 'B' and resid 107 through 123 removed outlier: 3.873A pdb=" N PHE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 4.683A pdb=" N SER B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLU B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 168 through 179' Processing helix chain 'B' and resid 184 through 195 removed outlier: 4.299A pdb=" N HIS B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.709A pdb=" N ASN C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 removed outlier: 4.507A pdb=" N ILE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 168 through 177 removed outlier: 4.105A pdb=" N VAL C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 196 removed outlier: 4.648A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 207 No H-bonds generated for 'chain 'C' and resid 204 through 207' Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.931A pdb=" N GLU C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 removed outlier: 4.125A pdb=" N GLU D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA D 25 " --> pdb=" O HIS D 21 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 98 removed outlier: 4.210A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 165 through 175 removed outlier: 3.564A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN D 175 " --> pdb=" O PHE D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 192 removed outlier: 3.868A pdb=" N PHE D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 232 removed outlier: 4.265A pdb=" N SER D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 33 removed outlier: 3.698A pdb=" N LEU E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 100 removed outlier: 4.698A pdb=" N LYS E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 121 Processing helix chain 'E' and resid 174 through 186 removed outlier: 4.768A pdb=" N GLY E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU E 183 " --> pdb=" O ALA E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 removed outlier: 3.885A pdb=" N VAL E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 240 Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.607A pdb=" N ALA F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN F 31 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 99 Processing helix chain 'F' and resid 105 through 121 Processing helix chain 'F' and resid 164 through 173 removed outlier: 3.959A pdb=" N GLU F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS F 173 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'F' and resid 226 through 235 removed outlier: 4.122A pdb=" N SER F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS F 234 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL F 235 " --> pdb=" O TYR F 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 33 removed outlier: 4.056A pdb=" N ILE G 27 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 127 removed outlier: 4.087A pdb=" N TYR G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU G 127 " --> pdb=" O HIS G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 176 Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 192 through 200 removed outlier: 3.963A pdb=" N LYS G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 225 No H-bonds generated for 'chain 'G' and resid 223 through 225' Processing helix chain 'G' and resid 234 through 243 Proline residue: G 239 - end of helix Processing helix chain 'H' and resid 49 through 69 Processing helix chain 'H' and resid 76 through 88 Processing helix chain 'H' and resid 184 through 196 removed outlier: 5.101A pdb=" N TYR H 188 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE H 189 " --> pdb=" O GLY H 185 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR H 192 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 removed outlier: 4.538A pdb=" N ASN H 208 " --> pdb=" O LYS H 204 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 69 Processing helix chain 'I' and resid 76 through 89 removed outlier: 3.661A pdb=" N VAL I 80 " --> pdb=" O VAL I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 141 removed outlier: 4.124A pdb=" N VAL I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS I 141 " --> pdb=" O VAL I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 165 removed outlier: 4.175A pdb=" N CYS I 156 " --> pdb=" O LYS I 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 79 Processing helix chain 'J' and resid 86 through 98 Processing helix chain 'J' and resid 156 through 166 removed outlier: 4.291A pdb=" N SER J 165 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 190 removed outlier: 4.018A pdb=" N ASP J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG J 190 " --> pdb=" O SER J 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 71 Processing helix chain 'K' and resid 78 through 91 Processing helix chain 'K' and resid 134 through 146 removed outlier: 4.770A pdb=" N LEU K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA K 141 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 165 Processing helix chain 'L' and resid 49 through 70 Processing helix chain 'L' and resid 76 through 88 removed outlier: 3.796A pdb=" N LEU L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR L 88 " --> pdb=" O SER L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 141 removed outlier: 3.757A pdb=" N ILE L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP L 140 " --> pdb=" O TYR L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 166 Processing helix chain 'M' and resid 86 through 107 Processing helix chain 'M' and resid 113 through 127 removed outlier: 3.826A pdb=" N ARG M 127 " --> pdb=" O ILE M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 178 Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 195 through 212 removed outlier: 3.839A pdb=" N GLU M 211 " --> pdb=" O THR M 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 73 Processing helix chain 'N' and resid 88 through 103 Processing helix chain 'N' and resid 180 through 192 removed outlier: 4.356A pdb=" N THR N 187 " --> pdb=" O TYR N 183 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU N 188 " --> pdb=" O PHE N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 216 removed outlier: 3.759A pdb=" N PHE N 215 " --> pdb=" O ARG N 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 12 No H-bonds generated for 'chain 'O' and resid 10 through 12' Processing helix chain 'O' and resid 23 through 34 Processing helix chain 'O' and resid 90 through 111 Processing helix chain 'O' and resid 117 through 133 removed outlier: 3.772A pdb=" N ASN O 123 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR O 131 " --> pdb=" O LYS O 127 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR O 132 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN O 133 " --> pdb=" O GLN O 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 187 removed outlier: 3.859A pdb=" N ARG O 187 " --> pdb=" O SER O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 216 removed outlier: 3.776A pdb=" N LEU O 211 " --> pdb=" O ASN O 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 31 Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 80 through 100 Processing helix chain 'P' and resid 107 through 123 removed outlier: 3.873A pdb=" N PHE P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR P 122 " --> pdb=" O VAL P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 179 removed outlier: 4.683A pdb=" N SER P 172 " --> pdb=" O GLN P 168 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE P 173 " --> pdb=" O ASN P 169 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU P 174 " --> pdb=" O ASN P 170 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLU P 175 " --> pdb=" O MET P 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS P 176 " --> pdb=" O SER P 172 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG P 177 " --> pdb=" O PHE P 173 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR P 178 " --> pdb=" O LEU P 174 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN P 179 " --> pdb=" O GLU P 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 168 through 179' Processing helix chain 'P' and resid 184 through 195 removed outlier: 4.299A pdb=" N HIS P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR P 190 " --> pdb=" O ASP P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 224 through 230 Processing helix chain 'Q' and resid 19 through 30 removed outlier: 3.709A pdb=" N ASN Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 101 removed outlier: 4.507A pdb=" N ILE Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 122 Processing helix chain 'Q' and resid 168 through 177 removed outlier: 4.105A pdb=" N VAL Q 174 " --> pdb=" O THR Q 170 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU Q 175 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 196 removed outlier: 4.648A pdb=" N LEU Q 190 " --> pdb=" O GLU Q 186 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR Q 195 " --> pdb=" O LEU Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 207 No H-bonds generated for 'chain 'Q' and resid 204 through 207' Processing helix chain 'Q' and resid 227 through 239 removed outlier: 3.931A pdb=" N GLU Q 231 " --> pdb=" O LEU Q 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE Q 232 " --> pdb=" O THR Q 228 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE Q 236 " --> pdb=" O ILE Q 232 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS Q 237 " --> pdb=" O GLU Q 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 27 removed outlier: 4.125A pdb=" N GLU R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA R 25 " --> pdb=" O HIS R 21 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 98 removed outlier: 4.210A pdb=" N VAL R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 120 Processing helix chain 'R' and resid 165 through 175 removed outlier: 3.564A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN R 175 " --> pdb=" O PHE R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 192 removed outlier: 3.868A pdb=" N PHE R 187 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU R 188 " --> pdb=" O ASP R 184 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA R 189 " --> pdb=" O CYS R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 232 removed outlier: 4.265A pdb=" N SER R 224 " --> pdb=" O GLN R 220 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET R 225 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP R 230 " --> pdb=" O VAL R 226 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 33 removed outlier: 3.698A pdb=" N LEU S 28 " --> pdb=" O VAL S 24 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA S 30 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS S 32 " --> pdb=" O LEU S 28 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU S 33 " --> pdb=" O GLY S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 100 removed outlier: 4.698A pdb=" N LYS S 100 " --> pdb=" O CYS S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 121 Processing helix chain 'S' and resid 174 through 186 removed outlier: 4.768A pdb=" N GLY S 178 " --> pdb=" O SER S 174 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU S 181 " --> pdb=" O GLU S 177 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU S 182 " --> pdb=" O GLY S 178 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU S 183 " --> pdb=" O ALA S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 207 removed outlier: 3.885A pdb=" N VAL S 207 " --> pdb=" O VAL S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 240 Processing helix chain 'T' and resid 20 through 31 removed outlier: 3.607A pdb=" N ALA T 25 " --> pdb=" O GLN T 21 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER T 26 " --> pdb=" O VAL T 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU T 27 " --> pdb=" O GLU T 23 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN T 31 " --> pdb=" O GLU T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 99 Processing helix chain 'T' and resid 105 through 121 Processing helix chain 'T' and resid 164 through 173 removed outlier: 3.959A pdb=" N GLU T 172 " --> pdb=" O LYS T 168 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS T 173 " --> pdb=" O THR T 169 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 194 Processing helix chain 'T' and resid 226 through 235 removed outlier: 4.122A pdb=" N SER T 233 " --> pdb=" O GLU T 229 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS T 234 " --> pdb=" O GLU T 230 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL T 235 " --> pdb=" O TYR T 231 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 33 removed outlier: 4.056A pdb=" N ILE U 27 " --> pdb=" O GLN U 23 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR U 28 " --> pdb=" O VAL U 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS U 29 " --> pdb=" O GLU U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 105 Processing helix chain 'U' and resid 111 through 127 removed outlier: 4.087A pdb=" N TYR U 125 " --> pdb=" O TYR U 121 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR U 126 " --> pdb=" O ILE U 122 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU U 127 " --> pdb=" O HIS U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 176 Processing helix chain 'U' and resid 182 through 187 Processing helix chain 'U' and resid 192 through 200 removed outlier: 3.963A pdb=" N LYS U 198 " --> pdb=" O GLU U 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 223 through 225 No H-bonds generated for 'chain 'U' and resid 223 through 225' Processing helix chain 'U' and resid 234 through 243 Proline residue: U 239 - end of helix Processing helix chain 'V' and resid 49 through 69 Processing helix chain 'V' and resid 76 through 88 Processing helix chain 'V' and resid 184 through 196 removed outlier: 5.101A pdb=" N TYR V 188 " --> pdb=" O SER V 184 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE V 189 " --> pdb=" O GLY V 185 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER V 191 " --> pdb=" O ILE V 187 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR V 192 " --> pdb=" O TYR V 188 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP V 195 " --> pdb=" O SER V 191 " (cutoff:3.500A) Processing helix chain 'V' and resid 203 through 216 removed outlier: 4.538A pdb=" N ASN V 208 " --> pdb=" O LYS V 204 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU V 209 " --> pdb=" O GLU V 205 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 69 Processing helix chain 'W' and resid 76 through 89 removed outlier: 3.661A pdb=" N VAL W 80 " --> pdb=" O VAL W 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 141 removed outlier: 4.124A pdb=" N VAL W 137 " --> pdb=" O ASN W 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS W 141 " --> pdb=" O VAL W 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 148 through 165 removed outlier: 4.175A pdb=" N CYS W 156 " --> pdb=" O LYS W 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 79 Processing helix chain 'X' and resid 86 through 98 Processing helix chain 'X' and resid 156 through 166 removed outlier: 4.291A pdb=" N SER X 165 " --> pdb=" O GLY X 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 173 through 190 removed outlier: 4.018A pdb=" N ASP X 189 " --> pdb=" O LEU X 185 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG X 190 " --> pdb=" O SER X 186 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 71 Processing helix chain 'Y' and resid 78 through 91 Processing helix chain 'Y' and resid 134 through 146 removed outlier: 4.770A pdb=" N LEU Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA Y 141 " --> pdb=" O TYR Y 137 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 165 Processing helix chain 'Z' and resid 49 through 70 Processing helix chain 'Z' and resid 76 through 88 removed outlier: 3.796A pdb=" N LEU Z 83 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR Z 88 " --> pdb=" O SER Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 141 removed outlier: 3.757A pdb=" N ILE Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP Z 140 " --> pdb=" O TYR Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 166 Processing helix chain 'a' and resid 86 through 107 Processing helix chain 'a' and resid 113 through 127 removed outlier: 3.826A pdb=" N ARG a 127 " --> pdb=" O ILE a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 178 Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 195 through 212 removed outlier: 3.839A pdb=" N GLU a 211 " --> pdb=" O THR a 207 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 73 Processing helix chain 'b' and resid 88 through 103 Processing helix chain 'b' and resid 180 through 192 removed outlier: 4.356A pdb=" N THR b 187 " --> pdb=" O TYR b 183 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU b 188 " --> pdb=" O PHE b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 199 through 216 removed outlier: 3.759A pdb=" N PHE b 215 " --> pdb=" O ARG b 211 " (cutoff:3.500A) 1240 hydrogen bonds defined for protein. 3720 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: 5.47 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6548 1.31 - 1.44: 10626 1.44 - 1.58: 22504 1.58 - 1.71: 2 1.71 - 1.85: 234 Bond restraints: 39914 Sorted by residual: bond pdb=" C THR W 1 " pdb=" N THR W 2 " ideal model delta sigma weight residual 1.331 1.688 -0.357 1.33e-02 5.65e+03 7.20e+02 bond pdb=" C THR I 1 " pdb=" N THR I 2 " ideal model delta sigma weight residual 1.331 1.688 -0.357 1.33e-02 5.65e+03 7.20e+02 bond pdb=" C02 7F1 I 300 " pdb=" C03 7F1 I 300 " ideal model delta sigma weight residual 1.325 1.551 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C02 7F1 W 300 " pdb=" C03 7F1 W 300 " ideal model delta sigma weight residual 1.325 1.551 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C14 7F1 W 300 " pdb=" N01 7F1 W 300 " ideal model delta sigma weight residual 1.345 1.493 -0.148 2.00e-02 2.50e+03 5.46e+01 ... (remaining 39909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 53448 4.24 - 8.47: 1044 8.47 - 12.71: 52 12.71 - 16.95: 4 16.95 - 21.19: 4 Bond angle restraints: 54552 Sorted by residual: angle pdb=" O THR I 1 " pdb=" C THR I 1 " pdb=" N THR I 2 " ideal model delta sigma weight residual 123.00 101.81 21.19 1.60e+00 3.91e-01 1.75e+02 angle pdb=" O THR W 1 " pdb=" C THR W 1 " pdb=" N THR W 2 " ideal model delta sigma weight residual 123.00 101.81 21.19 1.60e+00 3.91e-01 1.75e+02 angle pdb=" CA LYS L 33 " pdb=" C LYS L 33 " pdb=" N ILE L 34 " ideal model delta sigma weight residual 118.47 104.82 13.65 1.26e+00 6.30e-01 1.17e+02 angle pdb=" CA LYS Z 33 " pdb=" C LYS Z 33 " pdb=" N ILE Z 34 " ideal model delta sigma weight residual 118.47 104.82 13.65 1.26e+00 6.30e-01 1.17e+02 angle pdb=" O GLU Z 32 " pdb=" C GLU Z 32 " pdb=" N LYS Z 33 " ideal model delta sigma weight residual 123.27 111.73 11.54 1.18e+00 7.18e-01 9.57e+01 ... (remaining 54547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.99: 22938 19.99 - 39.98: 390 39.98 - 59.97: 72 59.97 - 79.97: 22 79.97 - 99.96: 8 Dihedral angle restraints: 23430 sinusoidal: 6846 harmonic: 16584 Sorted by residual: dihedral pdb=" CB CYS J 163 " pdb=" SG CYS J 163 " pdb=" SG CYS J 183 " pdb=" CB CYS J 183 " ideal model delta sinusoidal sigma weight residual 93.00 155.55 -62.55 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" CB CYS X 163 " pdb=" SG CYS X 163 " pdb=" SG CYS X 183 " pdb=" CB CYS X 183 " ideal model delta sinusoidal sigma weight residual 93.00 155.55 -62.55 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" CA PHE K 12 " pdb=" C PHE K 12 " pdb=" N VAL K 13 " pdb=" CA VAL K 13 " ideal model delta harmonic sigma weight residual 180.00 147.96 32.04 0 5.00e+00 4.00e-02 4.11e+01 ... (remaining 23427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5036 0.068 - 0.136: 1612 0.136 - 0.204: 170 0.204 - 0.272: 14 0.272 - 0.340: 2 Chirality restraints: 6834 Sorted by residual: chirality pdb=" C01 7F1 I 300 " pdb=" C02 7F1 I 300 " pdb=" C05 7F1 I 300 " pdb=" N01 7F1 I 300 " both_signs ideal model delta sigma weight residual False 2.33 2.67 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C01 7F1 W 300 " pdb=" C02 7F1 W 300 " pdb=" C05 7F1 W 300 " pdb=" N01 7F1 W 300 " both_signs ideal model delta sigma weight residual False 2.33 2.67 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA TYR M 152 " pdb=" N TYR M 152 " pdb=" C TYR M 152 " pdb=" CB TYR M 152 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 6831 not shown) Planarity restraints: 6918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7F1 W 300 " 0.191 2.00e-02 2.50e+03 1.72e-01 2.97e+02 pdb=" C02 7F1 W 300 " -0.209 2.00e-02 2.50e+03 pdb=" C03 7F1 W 300 " -0.130 2.00e-02 2.50e+03 pdb=" S01 7F1 W 300 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7F1 I 300 " -0.191 2.00e-02 2.50e+03 1.72e-01 2.97e+02 pdb=" C02 7F1 I 300 " 0.209 2.00e-02 2.50e+03 pdb=" C03 7F1 I 300 " 0.130 2.00e-02 2.50e+03 pdb=" S01 7F1 I 300 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR W 1 " -0.071 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C THR W 1 " 0.194 2.00e-02 2.50e+03 pdb=" O THR W 1 " -0.069 2.00e-02 2.50e+03 pdb=" N THR W 2 " -0.054 2.00e-02 2.50e+03 ... (remaining 6915 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1548 2.67 - 3.23: 43021 3.23 - 3.78: 61491 3.78 - 4.34: 84580 4.34 - 4.90: 136959 Nonbonded interactions: 327599 Sorted by model distance: nonbonded pdb=" OG SER H 31 " pdb=" NZ LYS H 33 " model vdw 2.110 3.120 nonbonded pdb=" OG SER V 31 " pdb=" NZ LYS V 33 " model vdw 2.110 3.120 nonbonded pdb=" OG SER B 9 " pdb=" O GLN B 123 " model vdw 2.116 3.040 nonbonded pdb=" OG SER P 9 " pdb=" O GLN P 123 " model vdw 2.116 3.040 nonbonded pdb=" ND1 HIS S 73 " pdb=" O GLN S 227 " model vdw 2.117 3.120 ... (remaining 327594 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 '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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.370 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 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 : 0.014 0.811 39926 Z= 0.975 Angle : 1.496 21.186 54568 Z= 0.975 Chirality : 0.062 0.340 6834 Planarity : 0.007 0.172 6918 Dihedral : 9.528 99.956 12714 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 1.11 % Allowed : 5.09 % Favored : 93.79 % Rotamer: Outliers : 0.29 % Allowed : 1.90 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.10), residues: 5576 helix: -2.52 (0.08), residues: 1882 sheet: -2.41 (0.14), residues: 1028 loop : -0.17 (0.13), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG L 166 TYR 0.036 0.004 TYR H 62 PHE 0.042 0.004 PHE R 118 TRP 0.027 0.004 TRP U 129 HIS 0.016 0.004 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.01196 (39914) covalent geometry : angle 1.49552 (54552) SS BOND : bond 0.00366 ( 8) SS BOND : angle 2.51287 ( 16) hydrogen bonds : bond 0.12465 ( 1240) hydrogen bonds : angle 8.80299 ( 3720) Misc. bond : bond 0.65581 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1754 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1744 time to evaluate : 1.542 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: A 10 ASP cc_start: 0.7149 (p0) cc_final: 0.6922 (p0) REVERT: A 73 THR cc_start: 0.7408 (t) cc_final: 0.7086 (m) REVERT: A 128 ILE cc_start: 0.8045 (mt) cc_final: 0.7797 (mt) REVERT: B 41 LYS cc_start: 0.7393 (pttt) cc_final: 0.5999 (mptt) REVERT: C 133 SER cc_start: 0.8635 (m) cc_final: 0.8331 (t) REVERT: C 134 PHE cc_start: 0.8535 (p90) cc_final: 0.8274 (p90) REVERT: E 106 ASN cc_start: 0.5825 (m-40) cc_final: 0.5588 (m-40) REVERT: G 71 HIS cc_start: 0.7349 (p-80) cc_final: 0.7139 (p90) REVERT: H 227 LEU cc_start: 0.8103 (tp) cc_final: 0.7826 (tp) REVERT: I 26 VAL cc_start: 0.8999 (m) cc_final: 0.8755 (t) REVERT: J 27 LEU cc_start: 0.7588 (mt) cc_final: 0.7359 (mt) REVERT: K 173 LEU cc_start: 0.7411 (tp) cc_final: 0.7048 (mp) REVERT: M 150 TYR cc_start: 0.7461 (m-80) cc_final: 0.7233 (m-80) REVERT: O 10 ASP cc_start: 0.7135 (p0) cc_final: 0.6630 (p0) REVERT: O 73 THR cc_start: 0.7464 (t) cc_final: 0.7138 (m) REVERT: O 128 ILE cc_start: 0.8067 (mt) cc_final: 0.7857 (mt) REVERT: P 41 LYS cc_start: 0.7352 (pttt) cc_final: 0.6032 (mptt) REVERT: Q 133 SER cc_start: 0.8718 (m) cc_final: 0.8495 (t) REVERT: S 164 ASN cc_start: 0.6924 (t0) cc_final: 0.6690 (t0) REVERT: T 108 LEU cc_start: 0.7492 (tp) cc_final: 0.7271 (tp) REVERT: T 223 ILE cc_start: 0.6922 (mm) cc_final: 0.6452 (mt) REVERT: U 71 HIS cc_start: 0.7309 (p-80) cc_final: 0.7076 (p90) REVERT: V 227 LEU cc_start: 0.8050 (tp) cc_final: 0.7745 (tp) REVERT: W 26 VAL cc_start: 0.8992 (m) cc_final: 0.8779 (t) REVERT: X 27 LEU cc_start: 0.7497 (mt) cc_final: 0.7253 (mt) REVERT: X 170 ASP cc_start: 0.6010 (m-30) cc_final: 0.5751 (m-30) REVERT: Z 76 VAL cc_start: 0.8916 (t) cc_final: 0.8696 (p) REVERT: a 150 TYR cc_start: 0.7425 (m-80) cc_final: 0.7218 (m-80) REVERT: a 191 THR cc_start: 0.6703 (p) cc_final: 0.6473 (p) REVERT: b 57 GLU cc_start: 0.7326 (tt0) cc_final: 0.7016 (tt0) REVERT: b 60 ASP cc_start: 0.7874 (m-30) cc_final: 0.7515 (m-30) outliers start: 10 outliers final: 10 residues processed: 1748 average time/residue: 0.2307 time to fit residues: 680.5937 Evaluate side-chains 1254 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1244 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 75 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 394 optimal weight: 0.6980 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 74 ASN B 71 HIS B 123 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 146 GLN ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN G 123 HIS G 130 HIS G 217 ASN G 231 ASN H 168 ASN H 219 HIS ** H 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN I 66 HIS I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 ASN L 148 ASN ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 86 GLN M 107 HIS M 179 ASN M 186 GLN M 231 ASN N 104 ASN N 170 ASN O 24 GLN O 74 ASN P 71 HIS P 123 GLN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 GLN ** Q 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN R 146 GLN ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 ASN S 164 ASN U 123 HIS U 130 HIS U 217 ASN U 231 ASN V 219 HIS ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 245 ASN W 66 HIS ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 ASN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 ASN Z 146 ASN Z 148 ASN ** Z 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN a 107 HIS a 179 ASN a 186 GLN a 231 ASN b 104 ASN b 170 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.154418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145434 restraints weight = 79644.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147580 restraints weight = 45663.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148944 restraints weight = 29379.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150012 restraints weight = 20797.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.150665 restraints weight = 15448.395| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 39926 Z= 0.180 Angle : 0.710 9.572 54568 Z= 0.378 Chirality : 0.045 0.294 6834 Planarity : 0.004 0.050 6918 Dihedral : 7.177 81.551 6056 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.32 % Favored : 96.54 % Rotamer: Outliers : 4.78 % Allowed : 14.57 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.11), residues: 5576 helix: -0.39 (0.11), residues: 1934 sheet: -2.04 (0.14), residues: 1084 loop : -0.60 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 170 TYR 0.032 0.002 TYR Z 136 PHE 0.022 0.002 PHE R 118 TRP 0.019 0.002 TRP Q 179 HIS 0.014 0.002 HIS W 66 Details of bonding type rmsd covalent geometry : bond 0.00398 (39914) covalent geometry : angle 0.70849 (54552) SS BOND : bond 0.00501 ( 8) SS BOND : angle 2.60635 ( 16) hydrogen bonds : bond 0.04345 ( 1240) hydrogen bonds : angle 5.10958 ( 3720) Misc. bond : bond 0.00247 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1639 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1473 time to evaluate : 1.465 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: A 23 TYR cc_start: 0.6085 (OUTLIER) cc_final: 0.5512 (m-80) REVERT: C 133 SER cc_start: 0.8988 (m) cc_final: 0.8238 (t) REVERT: C 160 PHE cc_start: 0.6571 (m-80) cc_final: 0.6298 (m-80) REVERT: D 35 ILE cc_start: 0.8065 (mm) cc_final: 0.7687 (mm) REVERT: D 36 LYS cc_start: 0.6688 (ttpp) cc_final: 0.6045 (tttm) REVERT: D 84 VAL cc_start: 0.9467 (t) cc_final: 0.9197 (m) REVERT: D 95 TYR cc_start: 0.8809 (t80) cc_final: 0.8487 (t80) REVERT: D 116 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7648 (tm-30) REVERT: F 45 VAL cc_start: 0.8706 (t) cc_final: 0.8291 (m) REVERT: F 116 TYR cc_start: 0.7826 (m-80) cc_final: 0.7562 (m-80) REVERT: I 19 ARG cc_start: 0.7178 (ttt180) cc_final: 0.6932 (ttt180) REVERT: I 26 VAL cc_start: 0.9118 (m) cc_final: 0.8875 (p) REVERT: J 170 ASP cc_start: 0.7038 (m-30) cc_final: 0.6654 (m-30) REVERT: K 146 TYR cc_start: 0.6735 (m-80) cc_final: 0.6467 (m-80) REVERT: K 173 LEU cc_start: 0.7441 (tp) cc_final: 0.6808 (mp) REVERT: K 178 TYR cc_start: 0.6756 (m-80) cc_final: 0.6427 (m-80) REVERT: M 150 TYR cc_start: 0.8099 (m-80) cc_final: 0.7883 (m-80) REVERT: M 230 ILE cc_start: 0.8454 (mp) cc_final: 0.8164 (pt) REVERT: O 23 TYR cc_start: 0.5942 (OUTLIER) cc_final: 0.5490 (m-80) REVERT: O 128 ILE cc_start: 0.8405 (mt) cc_final: 0.7992 (mt) REVERT: O 180 GLU cc_start: 0.4791 (mp0) cc_final: 0.4210 (pt0) REVERT: P 41 LYS cc_start: 0.8297 (pttt) cc_final: 0.6664 (mptt) REVERT: Q 133 SER cc_start: 0.9047 (m) cc_final: 0.8294 (t) REVERT: R 36 LYS cc_start: 0.6329 (ttpp) cc_final: 0.6116 (tttt) REVERT: R 84 VAL cc_start: 0.9465 (t) cc_final: 0.9160 (m) REVERT: R 95 TYR cc_start: 0.8789 (t80) cc_final: 0.8498 (t80) REVERT: R 116 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7650 (tm-30) REVERT: T 45 VAL cc_start: 0.8647 (t) cc_final: 0.8285 (m) REVERT: T 116 TYR cc_start: 0.7842 (m-80) cc_final: 0.7590 (m-80) REVERT: W 26 VAL cc_start: 0.9123 (m) cc_final: 0.8878 (p) REVERT: X 170 ASP cc_start: 0.7017 (m-30) cc_final: 0.6599 (m-30) REVERT: Y 60 PHE cc_start: 0.8674 (t80) cc_final: 0.8425 (t80) REVERT: a 150 TYR cc_start: 0.8047 (m-80) cc_final: 0.7838 (m-80) REVERT: a 230 ILE cc_start: 0.8442 (mp) cc_final: 0.8078 (pt) outliers start: 166 outliers final: 112 residues processed: 1544 average time/residue: 0.2154 time to fit residues: 569.3305 Evaluate side-chains 1396 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1282 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 23 TYR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 114 HIS Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 178 TYR Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 226 optimal weight: 8.9990 chunk 540 optimal weight: 9.9990 chunk 541 optimal weight: 8.9990 chunk 433 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 351 optimal weight: 0.3980 chunk 525 optimal weight: 0.9990 chunk 533 optimal weight: 0.7980 chunk 487 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 123 GLN C 105 GLN C 119 GLN D 115 GLN ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN G 89 ASN H 53 GLN ** H 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 ASN L 40 ASN L 146 ASN L 180 HIS L 182 ASN M 179 ASN O 12 HIS O 74 ASN Q 105 GLN Q 119 GLN ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN U 89 ASN U 144 ASN ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN W 109 GLN ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 ASN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 146 ASN Z 180 HIS Z 182 ASN a 179 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.149392 restraints weight = 79137.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151567 restraints weight = 45914.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.153093 restraints weight = 29774.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154169 restraints weight = 21000.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154902 restraints weight = 15605.709| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 39926 Z= 0.123 Angle : 0.608 10.805 54568 Z= 0.323 Chirality : 0.043 0.158 6834 Planarity : 0.004 0.046 6918 Dihedral : 6.128 81.523 6044 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 4.17 % Allowed : 19.34 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.11), residues: 5576 helix: 0.48 (0.11), residues: 1966 sheet: -1.82 (0.14), residues: 1126 loop : -0.54 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 170 TYR 0.025 0.002 TYR Z 136 PHE 0.027 0.002 PHE H 207 TRP 0.024 0.002 TRP Q 179 HIS 0.011 0.001 HIS Y 40 Details of bonding type rmsd covalent geometry : bond 0.00275 (39914) covalent geometry : angle 0.60699 (54552) SS BOND : bond 0.00638 ( 8) SS BOND : angle 2.14294 ( 16) hydrogen bonds : bond 0.03688 ( 1240) hydrogen bonds : angle 4.41610 ( 3720) Misc. bond : bond 0.00185 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1584 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1439 time to evaluate : 1.948 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU D 53 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU R 53 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: A 23 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.5280 (m-80) REVERT: A 129 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8094 (tm-30) REVERT: A 130 VAL cc_start: 0.8637 (t) cc_final: 0.8174 (t) REVERT: B 41 LYS cc_start: 0.8372 (pttm) cc_final: 0.6442 (mptt) REVERT: C 133 SER cc_start: 0.8916 (m) cc_final: 0.8276 (t) REVERT: C 235 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.4392 (pp) REVERT: D 35 ILE cc_start: 0.7959 (mm) cc_final: 0.7613 (mm) REVERT: D 36 LYS cc_start: 0.6454 (ttpp) cc_final: 0.5860 (tttt) REVERT: D 79 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6421 (t70) REVERT: D 116 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7369 (tm-30) REVERT: D 210 THR cc_start: 0.6441 (m) cc_final: 0.6210 (t) REVERT: F 116 TYR cc_start: 0.7709 (m-80) cc_final: 0.7390 (m-80) REVERT: I 19 ARG cc_start: 0.7197 (ttt180) cc_final: 0.6997 (ttt180) REVERT: J 170 ASP cc_start: 0.6910 (m-30) cc_final: 0.6364 (m-30) REVERT: K 60 PHE cc_start: 0.8530 (t80) cc_final: 0.8299 (t80) REVERT: K 146 TYR cc_start: 0.6540 (m-80) cc_final: 0.6222 (m-80) REVERT: K 173 LEU cc_start: 0.7395 (tp) cc_final: 0.6834 (mp) REVERT: K 178 TYR cc_start: 0.6896 (m-80) cc_final: 0.6468 (m-80) REVERT: L 51 ASP cc_start: 0.7425 (p0) cc_final: 0.6940 (p0) REVERT: L 136 TYR cc_start: 0.6935 (t80) cc_final: 0.6700 (t80) REVERT: M 39 THR cc_start: 0.7434 (m) cc_final: 0.7161 (m) REVERT: M 230 ILE cc_start: 0.8390 (mp) cc_final: 0.8136 (pt) REVERT: O 23 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5291 (m-80) REVERT: O 130 VAL cc_start: 0.8726 (t) cc_final: 0.8283 (t) REVERT: Q 105 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7372 (tp40) REVERT: Q 133 SER cc_start: 0.9012 (m) cc_final: 0.8327 (t) REVERT: Q 134 PHE cc_start: 0.8461 (p90) cc_final: 0.8194 (p90) REVERT: R 35 ILE cc_start: 0.7993 (mm) cc_final: 0.7714 (mm) REVERT: R 116 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7428 (tm-30) REVERT: T 116 TYR cc_start: 0.7774 (m-80) cc_final: 0.7532 (m-80) REVERT: V 195 ASP cc_start: 0.7868 (t70) cc_final: 0.7582 (t0) REVERT: X 170 ASP cc_start: 0.6829 (m-30) cc_final: 0.6320 (m-30) REVERT: Y 146 TYR cc_start: 0.6432 (m-80) cc_final: 0.6029 (m-80) REVERT: Z 51 ASP cc_start: 0.7431 (p0) cc_final: 0.6978 (p0) REVERT: a 47 ASP cc_start: 0.8478 (p0) cc_final: 0.8234 (p0) REVERT: b 49 LYS cc_start: 0.7738 (mtpt) cc_final: 0.7409 (mttm) outliers start: 145 outliers final: 95 residues processed: 1497 average time/residue: 0.2008 time to fit residues: 515.3414 Evaluate side-chains 1391 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1291 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 23 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 178 TYR Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 520 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 352 optimal weight: 8.9990 chunk 507 optimal weight: 1.9990 chunk 517 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 496 optimal weight: 0.0870 chunk 516 optimal weight: 5.9990 chunk 387 optimal weight: 5.9990 chunk 360 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN H 168 ASN ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 182 ASN M 179 ASN N 89 GLN N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 35 HIS W 109 GLN ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 ASN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 ASN Z 182 ASN a 179 ASN b 170 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.154892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145434 restraints weight = 79888.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147630 restraints weight = 46317.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.149064 restraints weight = 29848.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.150204 restraints weight = 21149.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150912 restraints weight = 15719.333| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39926 Z= 0.173 Angle : 0.640 9.419 54568 Z= 0.336 Chirality : 0.043 0.169 6834 Planarity : 0.004 0.041 6918 Dihedral : 6.070 81.019 6040 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 6.42 % Allowed : 20.41 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.11), residues: 5576 helix: 0.78 (0.11), residues: 1968 sheet: -1.70 (0.14), residues: 1124 loop : -0.66 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 170 TYR 0.029 0.002 TYR Z 136 PHE 0.026 0.002 PHE b 223 TRP 0.020 0.002 TRP Y 117 HIS 0.011 0.002 HIS K 40 Details of bonding type rmsd covalent geometry : bond 0.00389 (39914) covalent geometry : angle 0.63932 (54552) SS BOND : bond 0.00635 ( 8) SS BOND : angle 2.13041 ( 16) hydrogen bonds : bond 0.03762 ( 1240) hydrogen bonds : angle 4.35788 ( 3720) Misc. bond : bond 0.00042 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1540 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 1317 time to evaluate : 1.526 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: A 23 TYR cc_start: 0.6007 (OUTLIER) cc_final: 0.5402 (m-80) REVERT: B 41 LYS cc_start: 0.8416 (pttm) cc_final: 0.6419 (mptt) REVERT: C 133 SER cc_start: 0.8990 (m) cc_final: 0.8260 (t) REVERT: C 239 TYR cc_start: 0.4699 (OUTLIER) cc_final: 0.4429 (t80) REVERT: D 35 ILE cc_start: 0.7917 (mm) cc_final: 0.7565 (mm) REVERT: D 36 LYS cc_start: 0.6427 (ttpp) cc_final: 0.5894 (tttt) REVERT: D 79 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6350 (t70) REVERT: D 116 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7392 (tm-30) REVERT: D 210 THR cc_start: 0.6511 (m) cc_final: 0.6251 (t) REVERT: E 234 THR cc_start: 0.6774 (m) cc_final: 0.6429 (p) REVERT: F 116 TYR cc_start: 0.7775 (m-80) cc_final: 0.7494 (m-80) REVERT: F 172 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7005 (mm-30) REVERT: J 98 TYR cc_start: 0.7057 (t80) cc_final: 0.6725 (t80) REVERT: J 170 ASP cc_start: 0.6982 (m-30) cc_final: 0.6456 (m-30) REVERT: K 111 ASP cc_start: 0.5833 (p0) cc_final: 0.5540 (p0) REVERT: K 146 TYR cc_start: 0.6527 (m-80) cc_final: 0.6311 (m-80) REVERT: K 173 LEU cc_start: 0.7536 (tp) cc_final: 0.6935 (mp) REVERT: K 178 TYR cc_start: 0.6988 (m-80) cc_final: 0.6475 (m-80) REVERT: L 29 GLN cc_start: 0.7782 (mt0) cc_final: 0.7358 (tt0) REVERT: L 105 ASP cc_start: 0.4456 (p0) cc_final: 0.4175 (p0) REVERT: L 136 TYR cc_start: 0.7098 (t80) cc_final: 0.6824 (t80) REVERT: M 230 ILE cc_start: 0.8412 (mp) cc_final: 0.8119 (pt) REVERT: O 23 TYR cc_start: 0.6045 (OUTLIER) cc_final: 0.5531 (m-80) REVERT: Q 133 SER cc_start: 0.9057 (m) cc_final: 0.8331 (t) REVERT: R 210 THR cc_start: 0.6491 (m) cc_final: 0.6253 (t) REVERT: S 234 THR cc_start: 0.6710 (m) cc_final: 0.6358 (p) REVERT: T 116 TYR cc_start: 0.7889 (m-80) cc_final: 0.7524 (m-80) REVERT: V 195 ASP cc_start: 0.7863 (t70) cc_final: 0.7602 (t0) REVERT: X 98 TYR cc_start: 0.7044 (t80) cc_final: 0.6735 (t80) REVERT: X 170 ASP cc_start: 0.7028 (m-30) cc_final: 0.6477 (m-30) REVERT: Y 64 ASN cc_start: 0.8361 (m110) cc_final: 0.7902 (m110) REVERT: Y 146 TYR cc_start: 0.6401 (m-80) cc_final: 0.6158 (m-80) REVERT: Z 29 GLN cc_start: 0.7731 (mt0) cc_final: 0.7349 (tt0) outliers start: 223 outliers final: 157 residues processed: 1419 average time/residue: 0.2107 time to fit residues: 513.1008 Evaluate side-chains 1398 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1237 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 154 ASP Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 23 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 178 TYR Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 410 optimal weight: 10.0000 chunk 235 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 439 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 533 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 359 optimal weight: 0.0070 chunk 488 optimal weight: 0.9980 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN ** H 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 ASN ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN L 106 HIS N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN U 144 ASN ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN W 114 HIS Y 11 ASN Y 42 ASN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.158357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.148912 restraints weight = 79200.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151137 restraints weight = 45436.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.152690 restraints weight = 29179.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153597 restraints weight = 20300.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.154372 restraints weight = 15544.286| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39926 Z= 0.113 Angle : 0.576 12.668 54568 Z= 0.302 Chirality : 0.042 0.176 6834 Planarity : 0.003 0.041 6918 Dihedral : 5.658 80.594 6040 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.01 % Allowed : 22.65 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.11), residues: 5576 helix: 1.12 (0.12), residues: 1992 sheet: -1.55 (0.14), residues: 1110 loop : -0.67 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 86 TYR 0.027 0.002 TYR Z 136 PHE 0.019 0.001 PHE b 223 TRP 0.017 0.002 TRP Q 179 HIS 0.009 0.001 HIS Y 40 Details of bonding type rmsd covalent geometry : bond 0.00254 (39914) covalent geometry : angle 0.57556 (54552) SS BOND : bond 0.00208 ( 8) SS BOND : angle 1.67958 ( 16) hydrogen bonds : bond 0.03278 ( 1240) hydrogen bonds : angle 3.99968 ( 3720) Misc. bond : bond 0.00037 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 1362 time to evaluate : 1.736 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU D 53 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU R 53 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE Y 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: A 23 TYR cc_start: 0.5894 (OUTLIER) cc_final: 0.5438 (m-80) REVERT: A 129 GLN cc_start: 0.8290 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 41 LYS cc_start: 0.8419 (pttm) cc_final: 0.6446 (mptt) REVERT: C 133 SER cc_start: 0.8852 (m) cc_final: 0.8191 (t) REVERT: D 35 ILE cc_start: 0.7982 (mm) cc_final: 0.7600 (mm) REVERT: D 36 LYS cc_start: 0.6408 (ttpp) cc_final: 0.6176 (tmtt) REVERT: D 79 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6160 (t70) REVERT: E 145 ILE cc_start: 0.8080 (mp) cc_final: 0.7843 (mp) REVERT: F 116 TYR cc_start: 0.7726 (m-80) cc_final: 0.7519 (m-80) REVERT: F 169 THR cc_start: 0.7819 (m) cc_final: 0.7577 (m) REVERT: F 172 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7102 (mm-30) REVERT: F 209 THR cc_start: 0.5465 (OUTLIER) cc_final: 0.4979 (m) REVERT: H 78 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7081 (mm-30) REVERT: H 242 THR cc_start: 0.4391 (OUTLIER) cc_final: 0.3775 (m) REVERT: I 62 ASN cc_start: 0.7574 (m-40) cc_final: 0.7365 (m-40) REVERT: J 98 TYR cc_start: 0.6892 (t80) cc_final: 0.6594 (t80) REVERT: J 149 PHE cc_start: 0.7651 (p90) cc_final: 0.7294 (p90) REVERT: J 170 ASP cc_start: 0.6804 (m-30) cc_final: 0.6311 (m-30) REVERT: J 188 LEU cc_start: 0.9069 (mp) cc_final: 0.8850 (mp) REVERT: K 111 ASP cc_start: 0.6006 (p0) cc_final: 0.5672 (p0) REVERT: K 114 GLN cc_start: 0.5618 (mt0) cc_final: 0.5408 (mt0) REVERT: K 160 PHE cc_start: 0.7135 (m-80) cc_final: 0.6891 (m-80) REVERT: K 173 LEU cc_start: 0.7369 (tp) cc_final: 0.6842 (mp) REVERT: K 178 TYR cc_start: 0.6923 (m-80) cc_final: 0.6520 (m-80) REVERT: L 112 PHE cc_start: 0.7252 (m-80) cc_final: 0.7030 (m-80) REVERT: L 136 TYR cc_start: 0.7063 (t80) cc_final: 0.6618 (t80) REVERT: N 49 LYS cc_start: 0.7725 (mtpt) cc_final: 0.7384 (mttm) REVERT: Q 105 GLN cc_start: 0.8194 (tp40) cc_final: 0.7988 (tp40) REVERT: Q 133 SER cc_start: 0.8958 (m) cc_final: 0.8263 (t) REVERT: R 35 ILE cc_start: 0.7961 (mm) cc_final: 0.7588 (mm) REVERT: T 116 TYR cc_start: 0.7785 (m-80) cc_final: 0.7515 (m-80) REVERT: T 169 THR cc_start: 0.7834 (m) cc_final: 0.7569 (m) REVERT: T 209 THR cc_start: 0.5628 (OUTLIER) cc_final: 0.5072 (m) REVERT: X 98 TYR cc_start: 0.6926 (t80) cc_final: 0.6566 (t80) REVERT: X 149 PHE cc_start: 0.7698 (p90) cc_final: 0.7336 (p90) REVERT: X 170 ASP cc_start: 0.6845 (m-30) cc_final: 0.6300 (m-30) REVERT: Y 64 ASN cc_start: 0.8333 (m110) cc_final: 0.7865 (m110) REVERT: Y 160 PHE cc_start: 0.7214 (m-80) cc_final: 0.6973 (m-80) REVERT: Y 164 PHE cc_start: 0.7403 (m-10) cc_final: 0.7184 (m-10) REVERT: Z 17 ASP cc_start: 0.7313 (p0) cc_final: 0.6568 (p0) REVERT: a 48 TYR cc_start: 0.7210 (p90) cc_final: 0.6841 (p90) REVERT: b 49 LYS cc_start: 0.7734 (mtpt) cc_final: 0.7409 (mttm) REVERT: b 112 ASN cc_start: 0.7599 (t0) cc_final: 0.7336 (t0) outliers start: 174 outliers final: 122 residues processed: 1449 average time/residue: 0.2219 time to fit residues: 550.0172 Evaluate side-chains 1373 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 1246 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 185 GLU Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 178 TYR Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 58 TYR Chi-restraints excluded: chain Z residue 64 LYS Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 9 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 461 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 524 optimal weight: 9.9990 chunk 512 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 119 GLN C 123 GLN E 227 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN H 194 GLN I 35 HIS ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN L 158 ASN M 179 ASN M 231 ASN N 167 HIS N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 ASN Q 119 GLN ** R 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN ** U 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 194 GLN V 219 HIS ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN W 109 GLN Y 42 ASN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 GLN Z 40 ASN Z 158 ASN a 179 ASN b 167 HIS b 170 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139559 restraints weight = 81610.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141563 restraints weight = 47510.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143026 restraints weight = 31386.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.144090 restraints weight = 22120.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144808 restraints weight = 16533.376| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 39926 Z= 0.372 Angle : 0.845 14.658 54568 Z= 0.444 Chirality : 0.050 0.196 6834 Planarity : 0.005 0.061 6918 Dihedral : 6.702 79.765 6040 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 8.64 % Allowed : 22.11 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.11), residues: 5576 helix: 0.42 (0.11), residues: 1940 sheet: -1.84 (0.14), residues: 1118 loop : -1.23 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 170 TYR 0.048 0.003 TYR T 231 PHE 0.036 0.003 PHE N 223 TRP 0.013 0.003 TRP Y 117 HIS 0.011 0.002 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00830 (39914) covalent geometry : angle 0.84412 (54552) SS BOND : bond 0.00309 ( 8) SS BOND : angle 2.42002 ( 16) hydrogen bonds : bond 0.04721 ( 1240) hydrogen bonds : angle 4.94280 ( 3720) Misc. bond : bond 0.00082 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1527 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 300 poor density : 1227 time to evaluate : 1.637 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: B 41 LYS cc_start: 0.8500 (pttm) cc_final: 0.6271 (mptt) REVERT: C 133 SER cc_start: 0.8968 (m) cc_final: 0.8225 (t) REVERT: D 36 LYS cc_start: 0.6793 (ttpp) cc_final: 0.6313 (tttm) REVERT: D 79 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.6162 (t70) REVERT: D 210 THR cc_start: 0.6859 (m) cc_final: 0.6548 (t) REVERT: E 98 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.6974 (t-90) REVERT: E 103 TYR cc_start: 0.6451 (OUTLIER) cc_final: 0.6189 (p90) REVERT: F 116 TYR cc_start: 0.8050 (m-80) cc_final: 0.7520 (m-80) REVERT: F 132 LEU cc_start: 0.8451 (mt) cc_final: 0.8207 (mp) REVERT: F 169 THR cc_start: 0.7798 (m) cc_final: 0.7552 (m) REVERT: H 13 MET cc_start: 0.7878 (mtt) cc_final: 0.7310 (mtt) REVERT: J 98 TYR cc_start: 0.7254 (t80) cc_final: 0.6605 (t80) REVERT: K 173 LEU cc_start: 0.7607 (tp) cc_final: 0.6971 (mp) REVERT: L 13 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7837 (tt) REVERT: L 51 ASP cc_start: 0.7096 (p0) cc_final: 0.6837 (p0) REVERT: L 99 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9039 (pt) REVERT: L 136 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6804 (t80) REVERT: P 41 LYS cc_start: 0.8501 (pttt) cc_final: 0.6589 (mptt) REVERT: Q 133 SER cc_start: 0.9062 (m) cc_final: 0.8357 (t) REVERT: R 210 THR cc_start: 0.6865 (m) cc_final: 0.6557 (t) REVERT: S 103 TYR cc_start: 0.6443 (OUTLIER) cc_final: 0.6125 (p90) REVERT: T 169 THR cc_start: 0.7858 (m) cc_final: 0.7623 (m) REVERT: V 195 ASP cc_start: 0.7892 (t70) cc_final: 0.7631 (t0) REVERT: X 98 TYR cc_start: 0.7278 (t80) cc_final: 0.6645 (t80) REVERT: Y 23 ASN cc_start: 0.8255 (t0) cc_final: 0.8031 (m-40) REVERT: Y 111 ASP cc_start: 0.6913 (p0) cc_final: 0.6664 (p0) REVERT: Z 139 LEU cc_start: 0.7258 (mt) cc_final: 0.7006 (mt) REVERT: Z 184 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.6345 (p90) REVERT: b 225 GLN cc_start: 0.7951 (pt0) cc_final: 0.7736 (pt0) outliers start: 300 outliers final: 235 residues processed: 1368 average time/residue: 0.2179 time to fit residues: 514.0373 Evaluate side-chains 1410 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 1167 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 98 HIS Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 170 ASN Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 151 ASP Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 239 TYR Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 16 GLU Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 142 CYS Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 15 MET Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 185 ASP Chi-restraints excluded: chain Y residue 192 TYR Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 58 TYR Chi-restraints excluded: chain Z residue 64 LYS Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 110 ASN Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 158 ASN Chi-restraints excluded: chain Z residue 184 TYR Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain a residue 98 LYS Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 166 MET Chi-restraints excluded: chain b residue 170 ASN Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 187 THR Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 427 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 chunk 413 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 331 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 500 optimal weight: 8.9990 chunk 196 optimal weight: 8.9990 chunk 392 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 ASN M 231 ASN N 104 ASN ** N 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 232 ASN ** W 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN ** Y 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 ASN Z 158 ASN a 179 ASN b 104 ASN b 170 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142470 restraints weight = 80531.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144502 restraints weight = 46438.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145948 restraints weight = 30452.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146957 restraints weight = 21563.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147585 restraints weight = 16133.809| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 39926 Z= 0.214 Angle : 0.695 13.644 54568 Z= 0.364 Chirality : 0.045 0.193 6834 Planarity : 0.004 0.072 6918 Dihedral : 6.360 81.148 6040 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 7.25 % Allowed : 25.01 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.11), residues: 5576 helix: 0.66 (0.12), residues: 1950 sheet: -1.92 (0.15), residues: 1070 loop : -1.26 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 170 TYR 0.038 0.002 TYR Z 136 PHE 0.027 0.002 PHE N 223 TRP 0.020 0.002 TRP Q 179 HIS 0.010 0.001 HIS K 40 Details of bonding type rmsd covalent geometry : bond 0.00488 (39914) covalent geometry : angle 0.69441 (54552) SS BOND : bond 0.00264 ( 8) SS BOND : angle 1.65336 ( 16) hydrogen bonds : bond 0.03983 ( 1240) hydrogen bonds : angle 4.59534 ( 3720) Misc. bond : bond 0.00043 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1486 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 1234 time to evaluate : 1.654 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: B 41 LYS cc_start: 0.8407 (pttm) cc_final: 0.6206 (mptt) REVERT: C 133 SER cc_start: 0.8976 (m) cc_final: 0.8292 (t) REVERT: D 36 LYS cc_start: 0.6653 (ttpp) cc_final: 0.6082 (tttt) REVERT: D 79 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6298 (t70) REVERT: D 210 THR cc_start: 0.6695 (m) cc_final: 0.6380 (t) REVERT: E 103 TYR cc_start: 0.6366 (OUTLIER) cc_final: 0.6062 (p90) REVERT: F 116 TYR cc_start: 0.7897 (m-80) cc_final: 0.7483 (m-80) REVERT: F 169 THR cc_start: 0.7835 (m) cc_final: 0.7608 (m) REVERT: H 168 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7389 (p0) REVERT: J 98 TYR cc_start: 0.7113 (t80) cc_final: 0.6570 (t80) REVERT: J 170 ASP cc_start: 0.7149 (m-30) cc_final: 0.6668 (m-30) REVERT: K 173 LEU cc_start: 0.7503 (tp) cc_final: 0.6957 (mp) REVERT: L 17 ASP cc_start: 0.7850 (p0) cc_final: 0.6825 (p0) REVERT: L 136 TYR cc_start: 0.7200 (t80) cc_final: 0.6711 (t80) REVERT: L 139 LEU cc_start: 0.7364 (mt) cc_final: 0.7152 (mt) REVERT: M 48 TYR cc_start: 0.7340 (p90) cc_final: 0.7109 (p90) REVERT: N 49 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7541 (mttm) REVERT: Q 133 SER cc_start: 0.8989 (m) cc_final: 0.8331 (t) REVERT: R 210 THR cc_start: 0.6889 (m) cc_final: 0.6562 (t) REVERT: S 103 TYR cc_start: 0.6396 (OUTLIER) cc_final: 0.5949 (p90) REVERT: T 169 THR cc_start: 0.7858 (m) cc_final: 0.7627 (m) REVERT: U 10 LEU cc_start: 0.5641 (mt) cc_final: 0.5418 (mp) REVERT: U 74 ASN cc_start: 0.7932 (t0) cc_final: 0.7420 (t0) REVERT: V 13 MET cc_start: 0.7617 (mtt) cc_final: 0.7384 (mtt) REVERT: X 98 TYR cc_start: 0.7122 (t80) cc_final: 0.6577 (t80) REVERT: X 170 ASP cc_start: 0.7146 (m-30) cc_final: 0.6702 (m-30) REVERT: Z 139 LEU cc_start: 0.6916 (mt) cc_final: 0.6714 (mt) REVERT: b 49 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7547 (mttm) outliers start: 252 outliers final: 209 residues processed: 1348 average time/residue: 0.2275 time to fit residues: 527.5040 Evaluate side-chains 1410 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 1197 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 168 ASN Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 184 TYR Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 151 ASP Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 239 TYR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 7 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 15 MET Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 192 TYR Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 58 TYR Chi-restraints excluded: chain Z residue 64 LYS Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 98 LYS Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 292 optimal weight: 0.9990 chunk 370 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 227 optimal weight: 0.3980 chunk 547 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 chunk 304 optimal weight: 10.0000 chunk 271 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 349 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN E 227 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 ASN M 179 ASN N 104 ASN ** N 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN W 109 GLN ** Y 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 ASN a 179 ASN b 170 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.155285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145973 restraints weight = 79986.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148101 restraints weight = 45483.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149648 restraints weight = 29177.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150698 restraints weight = 20221.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.151365 restraints weight = 15013.420| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39926 Z= 0.121 Angle : 0.615 14.429 54568 Z= 0.320 Chirality : 0.043 0.200 6834 Planarity : 0.004 0.051 6918 Dihedral : 5.808 82.391 6040 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.53 % Allowed : 27.00 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.11), residues: 5576 helix: 0.97 (0.12), residues: 1986 sheet: -1.75 (0.15), residues: 1070 loop : -1.19 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 170 TYR 0.029 0.002 TYR T 231 PHE 0.020 0.002 PHE N 223 TRP 0.025 0.002 TRP C 179 HIS 0.011 0.001 HIS K 40 Details of bonding type rmsd covalent geometry : bond 0.00275 (39914) covalent geometry : angle 0.61494 (54552) SS BOND : bond 0.00453 ( 8) SS BOND : angle 1.21359 ( 16) hydrogen bonds : bond 0.03401 ( 1240) hydrogen bonds : angle 4.19841 ( 3720) Misc. bond : bond 0.00040 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1279 time to evaluate : 1.639 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS B 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: B 41 LYS cc_start: 0.8419 (pttm) cc_final: 0.6249 (mptt) REVERT: C 133 SER cc_start: 0.8911 (m) cc_final: 0.8252 (t) REVERT: D 36 LYS cc_start: 0.6604 (ttpp) cc_final: 0.6208 (tttm) REVERT: D 79 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6258 (t70) REVERT: E 98 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.6952 (t-90) REVERT: E 234 THR cc_start: 0.6376 (m) cc_final: 0.6101 (p) REVERT: F 116 TYR cc_start: 0.7758 (m-80) cc_final: 0.7417 (m-80) REVERT: F 169 THR cc_start: 0.7765 (m) cc_final: 0.7532 (m) REVERT: J 98 TYR cc_start: 0.6894 (t80) cc_final: 0.6378 (t80) REVERT: J 149 PHE cc_start: 0.7482 (p90) cc_final: 0.7108 (p90) REVERT: J 170 ASP cc_start: 0.7040 (m-30) cc_final: 0.6537 (m-30) REVERT: K 173 LEU cc_start: 0.7475 (tp) cc_final: 0.6919 (mp) REVERT: L 34 ILE cc_start: 0.7758 (mm) cc_final: 0.7479 (mm) REVERT: L 136 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6641 (t80) REVERT: N 112 ASN cc_start: 0.7793 (t0) cc_final: 0.7464 (t0) REVERT: Q 133 SER cc_start: 0.8950 (m) cc_final: 0.8279 (t) REVERT: R 35 ILE cc_start: 0.7916 (mm) cc_final: 0.7570 (mm) REVERT: T 116 TYR cc_start: 0.7810 (m-80) cc_final: 0.7405 (m-80) REVERT: T 169 THR cc_start: 0.7801 (m) cc_final: 0.7575 (m) REVERT: U 74 ASN cc_start: 0.8087 (t0) cc_final: 0.7419 (t0) REVERT: X 98 TYR cc_start: 0.6859 (t80) cc_final: 0.6380 (t80) REVERT: X 170 ASP cc_start: 0.6904 (m-30) cc_final: 0.6367 (m-30) REVERT: Y 194 THR cc_start: 0.7396 (m) cc_final: 0.7177 (m) REVERT: Z 136 TYR cc_start: 0.6846 (t80) cc_final: 0.6638 (t80) REVERT: b 112 ASN cc_start: 0.7816 (t0) cc_final: 0.7549 (t0) REVERT: b 235 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.5768 (mp0) outliers start: 192 outliers final: 158 residues processed: 1364 average time/residue: 0.2187 time to fit residues: 512.6057 Evaluate side-chains 1380 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1218 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 98 HIS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 239 TYR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 7 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 15 MET Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 84 MET Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 192 TYR Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 58 TYR Chi-restraints excluded: chain Z residue 64 LYS Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain b residue 235 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 280 optimal weight: 1.9990 chunk 304 optimal weight: 7.9990 chunk 40 optimal weight: 0.0370 chunk 487 optimal weight: 9.9990 chunk 440 optimal weight: 6.9990 chunk 410 optimal weight: 20.0000 chunk 446 optimal weight: 5.9990 chunk 203 optimal weight: 0.0030 chunk 275 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 2.6074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN E 97 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 ASN M 231 ASN N 89 GLN N 104 ASN ** N 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 ASN S 186 ASN V 220 ASN ** W 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 ASN Z 158 ASN a 179 ASN b 170 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145742 restraints weight = 79843.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147894 restraints weight = 45859.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.149374 restraints weight = 29689.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.150406 restraints weight = 20857.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151128 restraints weight = 15576.809| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39926 Z= 0.152 Angle : 0.639 15.251 54568 Z= 0.330 Chirality : 0.043 0.260 6834 Planarity : 0.004 0.049 6918 Dihedral : 5.757 81.905 6040 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 6.04 % Allowed : 27.35 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.11), residues: 5576 helix: 1.03 (0.12), residues: 1986 sheet: -1.71 (0.15), residues: 1086 loop : -1.18 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 170 TYR 0.043 0.002 TYR P 24 PHE 0.021 0.002 PHE b 223 TRP 0.016 0.002 TRP C 179 HIS 0.011 0.001 HIS K 40 Details of bonding type rmsd covalent geometry : bond 0.00351 (39914) covalent geometry : angle 0.63916 (54552) SS BOND : bond 0.00227 ( 8) SS BOND : angle 1.28812 ( 16) hydrogen bonds : bond 0.03541 ( 1240) hydrogen bonds : angle 4.26442 ( 3720) Misc. bond : bond 0.00027 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 1210 time to evaluate : 1.637 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS B 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: B 41 LYS cc_start: 0.8414 (pttm) cc_final: 0.6257 (mptt) REVERT: C 133 SER cc_start: 0.8937 (m) cc_final: 0.8276 (t) REVERT: C 134 PHE cc_start: 0.8451 (p90) cc_final: 0.8238 (p90) REVERT: D 36 LYS cc_start: 0.6646 (ttpp) cc_final: 0.6310 (tmtt) REVERT: D 79 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6182 (t70) REVERT: E 98 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.6998 (t-90) REVERT: E 234 THR cc_start: 0.6442 (m) cc_final: 0.6130 (p) REVERT: F 116 TYR cc_start: 0.7838 (m-80) cc_final: 0.7497 (m-80) REVERT: F 169 THR cc_start: 0.7787 (m) cc_final: 0.7552 (m) REVERT: J 98 TYR cc_start: 0.6872 (t80) cc_final: 0.6411 (t80) REVERT: J 170 ASP cc_start: 0.6897 (m-30) cc_final: 0.6363 (m-30) REVERT: K 173 LEU cc_start: 0.7438 (tp) cc_final: 0.6887 (mp) REVERT: L 34 ILE cc_start: 0.7712 (mm) cc_final: 0.7448 (mm) REVERT: L 136 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6615 (t80) REVERT: P 41 LYS cc_start: 0.8339 (pttt) cc_final: 0.6567 (mptt) REVERT: Q 133 SER cc_start: 0.8976 (m) cc_final: 0.8306 (t) REVERT: S 234 THR cc_start: 0.6330 (m) cc_final: 0.6041 (p) REVERT: T 116 TYR cc_start: 0.7837 (m-80) cc_final: 0.7461 (m-80) REVERT: T 169 THR cc_start: 0.7776 (m) cc_final: 0.7562 (m) REVERT: U 74 ASN cc_start: 0.7943 (t0) cc_final: 0.7429 (t0) REVERT: X 98 TYR cc_start: 0.7096 (t80) cc_final: 0.6633 (t80) REVERT: X 170 ASP cc_start: 0.6927 (m-30) cc_final: 0.6385 (m-30) REVERT: Y 194 THR cc_start: 0.7468 (m) cc_final: 0.7201 (m) REVERT: Z 17 ASP cc_start: 0.7540 (p0) cc_final: 0.6713 (p0) REVERT: Z 136 TYR cc_start: 0.6922 (t80) cc_final: 0.6638 (t80) outliers start: 210 outliers final: 181 residues processed: 1308 average time/residue: 0.2194 time to fit residues: 492.4409 Evaluate side-chains 1365 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 1181 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 98 HIS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 154 ASP Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 239 TYR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 34 ASN Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain V residue 220 ASN Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 15 MET Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 192 TYR Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 58 TYR Chi-restraints excluded: chain Z residue 64 LYS Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 158 ASN Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 136 ASN Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 198 ASP Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 294 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 512 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 497 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 231 ASN N 104 ASN ** N 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 232 ASN ** W 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN W 109 GLN ** Y 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 ASN b 112 ASN b 170 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.154751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145659 restraints weight = 79751.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.147808 restraints weight = 46116.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.149303 restraints weight = 29897.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150303 restraints weight = 20980.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150959 restraints weight = 15788.102| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.322 39926 Z= 0.203 Angle : 0.834 59.200 54568 Z= 0.472 Chirality : 0.045 1.023 6834 Planarity : 0.004 0.068 6918 Dihedral : 5.758 81.908 6040 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 5.81 % Allowed : 27.63 % Favored : 66.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.11), residues: 5576 helix: 0.99 (0.12), residues: 1998 sheet: -1.70 (0.15), residues: 1086 loop : -1.18 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 86 TYR 0.038 0.002 TYR B 24 PHE 0.021 0.002 PHE b 223 TRP 0.015 0.002 TRP W 42 HIS 0.011 0.001 HIS K 40 Details of bonding type rmsd covalent geometry : bond 0.00497 (39914) covalent geometry : angle 0.83356 (54552) SS BOND : bond 0.00281 ( 8) SS BOND : angle 1.25226 ( 16) hydrogen bonds : bond 0.03568 ( 1240) hydrogen bonds : angle 4.28859 ( 3720) Misc. bond : bond 0.00026 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 1186 time to evaluate : 1.695 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS B 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: B 41 LYS cc_start: 0.8414 (pttm) cc_final: 0.6254 (mptt) REVERT: C 133 SER cc_start: 0.8919 (m) cc_final: 0.8262 (t) REVERT: C 134 PHE cc_start: 0.8422 (p90) cc_final: 0.8207 (p90) REVERT: D 36 LYS cc_start: 0.6604 (ttpp) cc_final: 0.6285 (tmtt) REVERT: D 79 ASP cc_start: 0.6581 (OUTLIER) cc_final: 0.6146 (t70) REVERT: E 98 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.6938 (t-90) REVERT: E 234 THR cc_start: 0.6405 (m) cc_final: 0.6097 (p) REVERT: F 116 TYR cc_start: 0.7805 (m-80) cc_final: 0.7478 (m-80) REVERT: F 169 THR cc_start: 0.7766 (m) cc_final: 0.7525 (m) REVERT: J 98 TYR cc_start: 0.6820 (t80) cc_final: 0.6350 (t80) REVERT: J 170 ASP cc_start: 0.6852 (m-30) cc_final: 0.6320 (m-30) REVERT: K 173 LEU cc_start: 0.7463 (tp) cc_final: 0.6914 (mp) REVERT: L 34 ILE cc_start: 0.7695 (mm) cc_final: 0.7439 (mm) REVERT: L 136 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6572 (t80) REVERT: N 112 ASN cc_start: 0.7690 (t0) cc_final: 0.7450 (t0) REVERT: P 41 LYS cc_start: 0.8327 (pttt) cc_final: 0.6561 (mptt) REVERT: Q 133 SER cc_start: 0.8970 (m) cc_final: 0.8297 (t) REVERT: S 234 THR cc_start: 0.6309 (m) cc_final: 0.6017 (p) REVERT: T 116 TYR cc_start: 0.7814 (m-80) cc_final: 0.7443 (m-80) REVERT: T 169 THR cc_start: 0.7763 (m) cc_final: 0.7543 (m) REVERT: U 74 ASN cc_start: 0.8020 (t0) cc_final: 0.7431 (t0) REVERT: X 98 TYR cc_start: 0.7070 (t80) cc_final: 0.6594 (t80) REVERT: X 139 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7236 (pp) REVERT: X 170 ASP cc_start: 0.6870 (m-30) cc_final: 0.6332 (m-30) REVERT: Y 194 THR cc_start: 0.7415 (m) cc_final: 0.7141 (m) REVERT: Z 136 TYR cc_start: 0.6864 (t80) cc_final: 0.6606 (t80) outliers start: 202 outliers final: 188 residues processed: 1275 average time/residue: 0.2200 time to fit residues: 482.0721 Evaluate side-chains 1373 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1181 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 98 HIS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 154 ASP Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 184 TYR Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 151 ASP Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 239 TYR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 16 GLU Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 34 ASN Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain V residue 220 ASN Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 15 MET Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 192 TYR Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 58 TYR Chi-restraints excluded: chain Z residue 64 LYS Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 136 ASN Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 198 ASP Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 455 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 548 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 373 optimal weight: 5.9990 chunk 439 optimal weight: 8.9990 chunk 459 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 479 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 231 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** N 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN W 109 GLN ** Y 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 ASN b 170 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.154731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145580 restraints weight = 80327.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.147759 restraints weight = 46481.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149241 restraints weight = 30036.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150281 restraints weight = 21217.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150921 restraints weight = 15848.005| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.322 39926 Z= 0.203 Angle : 0.834 59.200 54568 Z= 0.472 Chirality : 0.045 1.023 6834 Planarity : 0.004 0.068 6918 Dihedral : 5.758 81.908 6040 Min Nonbonded Distance : 1.226 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 5.64 % Allowed : 27.81 % Favored : 66.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.11), residues: 5576 helix: 0.99 (0.12), residues: 1998 sheet: -1.70 (0.15), residues: 1086 loop : -1.18 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 86 TYR 0.038 0.002 TYR B 24 PHE 0.021 0.002 PHE b 223 TRP 0.015 0.002 TRP W 42 HIS 0.011 0.001 HIS K 40 Details of bonding type rmsd covalent geometry : bond 0.00497 (39914) covalent geometry : angle 0.83356 (54552) SS BOND : bond 0.00281 ( 8) SS BOND : angle 1.25226 ( 16) hydrogen bonds : bond 0.03568 ( 1240) hydrogen bonds : angle 4.28859 ( 3720) Misc. bond : bond 0.00026 ( 4) =============================================================================== Job complete usr+sys time: 9178.06 seconds wall clock time: 158 minutes 48.26 seconds (9528.26 seconds total)