Starting phenix.real_space_refine on Tue Sep 15 08:34:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5fmg_3231/09_2026/5fmg_3231.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fmg_3231/09_2026/5fmg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5fmg_3231/09_2026/5fmg_3231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fmg_3231/09_2026/5fmg_3231.map" model { file = "/net/cci-nas-00/data/ceres_data/5fmg_3231/09_2026/5fmg_3231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fmg_3231/09_2026/5fmg_3231.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5fmg_3231/09_2026/5fmg_3231.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5fmg_3231/09_2026/5fmg_3231.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 10.49, per 1000 atoms: 0.27 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: 3.55 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.62 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: 6.19 Time building geometry restraints manager: 4.66 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: 22918 19.99 - 39.98: 382 39.98 - 59.97: 60 59.97 - 79.97: 18 79.97 - 99.96: 8 Dihedral angle restraints: 23386 sinusoidal: 6802 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 23383 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 35.320 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.140 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 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 : 9.275 99.956 12670 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 are 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/Z covalent geometry : bond 0.01196 / 0.72 (39914) covalent geometry : angle 1.49552 / 0.97 (54552) SS BOND : bond 0.00366 / 0.17 ( 8) SS BOND : angle 2.51287 / 1.48 ( 16) hydrogen bonds : bond 0.12465 / 8.24 ( 1240) hydrogen bonds : angle 8.80299 / 6.20 ( 3720) Misc. bond : bond 0.65581 / 32.41 ( 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 : 1.491 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: 0.8998 (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: 0.8051 (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: 0.7217 (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: 0.2247 time to fit residues: 665.5314 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 : 1.597 ------------------------------------------------------------------------------- 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... 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** 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: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.154400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145429 restraints weight = 79673.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.147475 restraints weight = 45999.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148935 restraints weight = 29882.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.149954 restraints weight = 20965.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150619 restraints weight = 15626.446| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39926 Z= 0.181 Angle : 0.720 10.351 54568 Z= 0.384 Chirality : 0.045 0.305 6834 Planarity : 0.004 0.050 6918 Dihedral : 6.911 81.780 6012 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.43 % Favored : 96.43 % Rotamer: Outliers : 4.58 % Allowed : 14.48 % Favored : 80.94 % 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 are not related in a simple way. whole: -1.43 (0.11), residues: 5576 helix: -0.46 (0.11), residues: 1944 sheet: -2.05 (0.14), residues: 1062 loop : -0.64 (0.12), residues: 2570 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 0.023 0.002 PHE b 223 TRP 0.019 0.002 TRP Q 179 HIS 0.012 0.002 HIS W 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (39914) covalent geometry : angle 0.71834 / 0.38 (54552) SS BOND : bond 0.00627 / 0.32 ( 8) SS BOND : angle 2.55626 / 1.55 ( 16) hydrogen bonds : bond 0.04427 / 3.09 ( 1240) hydrogen bonds : angle 5.16156 / 3.67 ( 3720) Misc. bond : bond 0.00205 / 0.10 ( 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 1627 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1468 time to evaluate : 1.604 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 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 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: 0.6012 (OUTLIER) cc_final: 0.5484 (m-80) REVERT: A 128 ILE cc_start: 0.8371 (mt) cc_final: 0.7938 (mt) REVERT: A 180 GLU cc_start: 0.4768 (mp0) cc_final: 0.4499 (pt0) REVERT: C 133 SER cc_start: 0.8980 (m) cc_final: 0.8223 (t) REVERT: C 160 PHE cc_start: 0.6507 (m-80) cc_final: 0.6227 (m-80) REVERT: D 35 ILE cc_start: 0.8061 (mm) cc_final: 0.7666 (mm) REVERT: D 36 LYS cc_start: 0.6637 (ttpp) cc_final: 0.5982 (tttm) REVERT: D 84 VAL cc_start: 0.9461 (t) cc_final: 0.9214 (m) REVERT: D 116 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7472 (tm-30) REVERT: F 45 VAL cc_start: 0.8687 (t) cc_final: 0.8231 (m) REVERT: F 116 TYR cc_start: 0.7851 (m-80) cc_final: 0.7565 (m-80) REVERT: G 101 TYR cc_start: 0.7316 (t80) cc_final: 0.7087 (t80) REVERT: I 26 VAL cc_start: 0.9123 (m) cc_final: 0.8888 (p) REVERT: J 170 ASP cc_start: 0.6945 (m-30) cc_final: 0.6565 (m-30) REVERT: K 60 PHE cc_start: 0.8649 (t80) cc_final: 0.8435 (t80) REVERT: K 146 TYR cc_start: 0.6715 (m-80) cc_final: 0.6444 (m-80) REVERT: K 173 LEU cc_start: 0.7479 (tp) cc_final: 0.6842 (mp) REVERT: K 178 TYR cc_start: 0.6779 (m-80) cc_final: 0.6453 (m-80) REVERT: M 150 TYR cc_start: 0.8046 (m-80) cc_final: 0.7826 (m-80) REVERT: M 230 ILE cc_start: 0.8412 (mp) cc_final: 0.8128 (pt) REVERT: O 23 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.5491 (m-80) REVERT: O 128 ILE cc_start: 0.8413 (mt) cc_final: 0.8002 (mt) REVERT: O 180 GLU cc_start: 0.4550 (mp0) cc_final: 0.4314 (pt0) REVERT: P 41 LYS cc_start: 0.8274 (pttt) cc_final: 0.6650 (mptt) REVERT: Q 133 SER cc_start: 0.9040 (m) cc_final: 0.8281 (t) REVERT: R 36 LYS cc_start: 0.6296 (ttpp) cc_final: 0.6072 (tttt) REVERT: R 84 VAL cc_start: 0.9457 (t) cc_final: 0.9175 (m) REVERT: R 95 TYR cc_start: 0.8754 (t80) cc_final: 0.8420 (t80) REVERT: T 45 VAL cc_start: 0.8629 (t) cc_final: 0.8279 (m) REVERT: T 116 TYR cc_start: 0.7895 (m-80) cc_final: 0.7614 (m-80) REVERT: W 26 VAL cc_start: 0.9122 (m) cc_final: 0.8890 (p) REVERT: X 170 ASP cc_start: 0.6971 (m-30) cc_final: 0.6562 (m-30) REVERT: Y 60 PHE cc_start: 0.8631 (t80) cc_final: 0.8355 (t80) REVERT: a 150 TYR cc_start: 0.7992 (m-80) cc_final: 0.7791 (m-80) REVERT: a 230 ILE cc_start: 0.8428 (mp) cc_final: 0.8073 (pt) outliers start: 159 outliers final: 114 residues processed: 1534 average time/residue: 0.2085 time to fit residues: 551.4474 Evaluate side-chains 1402 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1286 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 THR 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 46 VAL 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 6 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 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 48 THR 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 87 THR 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 U residue 47 ILE Chi-restraints excluded: chain V residue 6 ILE 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 95 VAL 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: 6.9990 chunk 433 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 351 optimal weight: 0.0000 chunk 525 optimal weight: 1.9990 chunk 533 optimal weight: 2.9990 chunk 487 optimal weight: 0.9980 chunk 319 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN C 105 GLN C 119 GLN D 115 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 245 ASN I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN L 40 ASN L 146 ASN L 180 HIS M 179 ASN O 74 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 GLN R 115 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN U 89 ASN 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 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 a 179 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.147016 restraints weight = 79740.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.149175 restraints weight = 46063.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.150701 restraints weight = 29877.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151730 restraints weight = 20944.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.152470 restraints weight = 15661.448| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 39926 Z= 0.147 Angle : 0.634 10.688 54568 Z= 0.336 Chirality : 0.043 0.186 6834 Planarity : 0.004 0.045 6918 Dihedral : 6.083 80.430 6000 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 5.27 % Allowed : 18.74 % Favored : 75.99 % 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 are not related in a simple way. whole: -0.96 (0.11), residues: 5576 helix: 0.33 (0.11), residues: 1964 sheet: -1.91 (0.14), residues: 1100 loop : -0.65 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 170 TYR 0.025 0.002 TYR Z 136 PHE 0.025 0.002 PHE H 207 TRP 0.023 0.002 TRP Q 179 HIS 0.011 0.001 HIS Y 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (39914) covalent geometry : angle 0.63248 / 0.34 (54552) SS BOND : bond 0.01996 / 0.98 ( 8) SS BOND : angle 2.31334 / 1.39 ( 16) hydrogen bonds : bond 0.03864 / 2.69 ( 1240) hydrogen bonds : angle 4.60213 / 3.28 ( 3720) Misc. bond : bond 0.00172 / 0.08 ( 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 1568 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 1385 time to evaluate : 1.558 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. revert: symmetry clash 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: 0.5964 (OUTLIER) cc_final: 0.5216 (m-80) REVERT: A 130 VAL cc_start: 0.8738 (t) cc_final: 0.8537 (t) REVERT: B 41 LYS cc_start: 0.8383 (pttm) cc_final: 0.6420 (mptt) REVERT: C 133 SER cc_start: 0.8950 (m) cc_final: 0.8279 (t) REVERT: C 146 GLN cc_start: 0.6302 (mt0) cc_final: 0.6086 (mt0) REVERT: D 35 ILE cc_start: 0.8015 (mm) cc_final: 0.7672 (mm) REVERT: D 36 LYS cc_start: 0.6562 (ttpp) cc_final: 0.5913 (tttt) REVERT: D 84 VAL cc_start: 0.9433 (t) cc_final: 0.9192 (m) REVERT: D 95 TYR cc_start: 0.8789 (t80) cc_final: 0.8497 (t80) REVERT: D 116 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7397 (tm-30) REVERT: F 116 TYR cc_start: 0.7792 (m-80) cc_final: 0.7527 (m-80) REVERT: J 170 ASP cc_start: 0.6965 (m-30) cc_final: 0.6465 (m-30) REVERT: K 173 LEU cc_start: 0.7433 (tp) cc_final: 0.6863 (mp) REVERT: K 178 TYR cc_start: 0.6933 (m-80) cc_final: 0.6475 (m-80) REVERT: L 136 TYR cc_start: 0.6901 (t80) cc_final: 0.6689 (t80) REVERT: M 230 ILE cc_start: 0.8311 (mp) cc_final: 0.8094 (pt) REVERT: O 23 TYR cc_start: 0.6128 (OUTLIER) cc_final: 0.5587 (m-80) REVERT: Q 105 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7539 (tp40) REVERT: Q 133 SER cc_start: 0.9050 (m) cc_final: 0.8338 (t) REVERT: R 35 ILE cc_start: 0.7945 (mm) cc_final: 0.7639 (mm) REVERT: R 84 VAL cc_start: 0.9427 (t) cc_final: 0.9213 (m) REVERT: R 116 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7506 (tm-30) REVERT: T 116 TYR cc_start: 0.7806 (m-80) cc_final: 0.7561 (m-80) REVERT: V 195 ASP cc_start: 0.7906 (t70) cc_final: 0.7666 (t0) REVERT: W 26 VAL cc_start: 0.9052 (m) cc_final: 0.8776 (t) REVERT: X 170 ASP cc_start: 0.6955 (m-30) cc_final: 0.6438 (m-30) REVERT: Y 146 TYR cc_start: 0.6450 (m-80) cc_final: 0.6117 (m-80) REVERT: a 47 ASP cc_start: 0.8481 (p0) cc_final: 0.8225 (p0) outliers start: 183 outliers final: 122 residues processed: 1460 average time/residue: 0.2162 time to fit residues: 544.1655 Evaluate side-chains 1403 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1279 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 A residue 250 ASP 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 C residue 105 GLN 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 D residue 26 VAL Chi-restraints excluded: chain D residue 53 LEU 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 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 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 32 SER 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 120 CYS Chi-restraints excluded: chain I residue 160 CYS 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 151 VAL Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 119 ASP 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 110 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 182 ASN Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 15 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 23 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 115 VAL 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 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 26 VAL 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 31 ILE Chi-restraints excluded: chain S residue 46 VAL 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 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 V residue 244 VAL Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 32 SER 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 120 CYS 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 151 VAL Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 119 ASP 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 101 LEU Chi-restraints excluded: chain Z residue 110 ASN Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 182 ASN Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 15 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 520 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 507 optimal weight: 1.9990 chunk 517 optimal weight: 10.0000 chunk 178 optimal weight: 0.1980 chunk 496 optimal weight: 7.9990 chunk 516 optimal weight: 5.9990 chunk 387 optimal weight: 7.9990 chunk 360 optimal weight: 8.9990 chunk 311 optimal weight: 4.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 168 ASN ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 ASN O 74 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN R 115 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 108 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 109 GLN ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 ASN a 179 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143716 restraints weight = 80331.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145888 restraints weight = 46247.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.147429 restraints weight = 29870.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148417 restraints weight = 20772.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.149166 restraints weight = 15703.736| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 39926 Z= 0.206 Angle : 0.676 10.720 54568 Z= 0.356 Chirality : 0.044 0.178 6834 Planarity : 0.004 0.043 6918 Dihedral : 6.051 79.363 5996 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.09 % Rotamer: Outliers : 7.17 % Allowed : 19.46 % Favored : 73.37 % 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 are not related in a simple way. whole: -0.89 (0.11), residues: 5576 helix: 0.53 (0.11), residues: 1972 sheet: -1.87 (0.14), residues: 1110 loop : -0.75 (0.13), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 170 TYR 0.029 0.002 TYR X 98 PHE 0.026 0.002 PHE b 223 TRP 0.019 0.002 TRP Y 117 HIS 0.011 0.002 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (39914) covalent geometry : angle 0.67485 / 0.36 (54552) SS BOND : bond 0.00291 / 0.17 ( 8) SS BOND : angle 2.17537 / 1.28 ( 16) hydrogen bonds : bond 0.04014 / 2.80 ( 1240) hydrogen bonds : angle 4.57195 / 3.25 ( 3720) Misc. bond : bond 0.00065 / 0.03 ( 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 1549 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 1300 time to evaluate : 1.524 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: "CYS B 162 " (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: "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. 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: "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. 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: 0.6148 (OUTLIER) cc_final: 0.5517 (m-80) REVERT: B 41 LYS cc_start: 0.8440 (pttm) cc_final: 0.6420 (mptt) REVERT: C 133 SER cc_start: 0.9001 (m) cc_final: 0.8265 (t) REVERT: D 35 ILE cc_start: 0.7977 (mm) cc_final: 0.7616 (mm) REVERT: D 36 LYS cc_start: 0.6545 (ttpp) cc_final: 0.5956 (tttt) REVERT: D 84 VAL cc_start: 0.9433 (t) cc_final: 0.9172 (m) REVERT: D 116 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7407 (tm-30) REVERT: D 210 THR cc_start: 0.6839 (m) cc_final: 0.6595 (t) REVERT: F 116 TYR cc_start: 0.7920 (m-80) cc_final: 0.7343 (m-80) REVERT: F 132 LEU cc_start: 0.8455 (mt) cc_final: 0.8156 (mp) REVERT: F 172 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7076 (mm-30) REVERT: G 73 ASN cc_start: 0.7488 (t0) cc_final: 0.7262 (t0) REVERT: J 98 TYR cc_start: 0.7090 (t80) cc_final: 0.6850 (t80) REVERT: J 170 ASP cc_start: 0.6983 (m-30) cc_final: 0.6463 (m-30) REVERT: K 146 TYR cc_start: 0.6680 (m-80) cc_final: 0.6464 (m-80) REVERT: K 173 LEU cc_start: 0.7522 (tp) cc_final: 0.6894 (mp) REVERT: K 178 TYR cc_start: 0.6989 (m-80) cc_final: 0.6440 (m-80) REVERT: L 136 TYR cc_start: 0.7120 (t80) cc_final: 0.6907 (t80) REVERT: M 230 ILE cc_start: 0.8426 (mp) cc_final: 0.8165 (pt) REVERT: O 23 TYR cc_start: 0.6144 (OUTLIER) cc_final: 0.5646 (m-80) REVERT: P 41 LYS cc_start: 0.8348 (pttt) cc_final: 0.6714 (mptt) REVERT: Q 105 GLN cc_start: 0.8350 (tp-100) cc_final: 0.7709 (tp40) REVERT: Q 133 SER cc_start: 0.9091 (m) cc_final: 0.8318 (t) REVERT: Q 239 TYR cc_start: 0.4720 (OUTLIER) cc_final: 0.4473 (t80) REVERT: R 84 VAL cc_start: 0.9421 (t) cc_final: 0.9138 (m) REVERT: R 116 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7479 (tm-30) REVERT: T 116 TYR cc_start: 0.7945 (m-80) cc_final: 0.7412 (m-80) REVERT: T 132 LEU cc_start: 0.8455 (mt) cc_final: 0.8191 (mp) REVERT: V 153 PHE cc_start: 0.7232 (m-80) cc_final: 0.6961 (m-80) REVERT: V 195 ASP cc_start: 0.8022 (t70) cc_final: 0.7732 (t0) REVERT: W 26 VAL cc_start: 0.9049 (m) cc_final: 0.8803 (t) REVERT: X 98 TYR cc_start: 0.7149 (t80) cc_final: 0.6914 (t80) REVERT: X 170 ASP cc_start: 0.6981 (m-30) cc_final: 0.6429 (m-30) REVERT: Y 146 TYR cc_start: 0.6522 (m-80) cc_final: 0.6304 (m-80) outliers start: 249 outliers final: 199 residues processed: 1407 average time/residue: 0.2115 time to fit residues: 512.9720 Evaluate side-chains 1445 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 1243 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 119 THR 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 19 LEU 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 149 HIS 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 D residue 26 VAL Chi-restraints excluded: chain D residue 63 ILE 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 87 THR Chi-restraints excluded: chain E residue 89 ILE 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 75 SER Chi-restraints excluded: chain F residue 79 SER 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 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 41 LEU Chi-restraints excluded: chain H residue 43 VAL 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 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 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 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 94 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 151 VAL 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 119 ASP 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 58 TYR Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 105 LEU 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 50 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 69 THR 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 108 LEU Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 119 THR 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 19 LEU 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 189 LEU Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 239 TYR 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 89 ILE Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 241 ILE 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 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU 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 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 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 7 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 56 THR Chi-restraints excluded: chain W residue 80 VAL 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 94 SER 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 178 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 101 LEU Chi-restraints excluded: chain Z residue 110 ASN Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 138 LEU 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 50 THR Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 69 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 410 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 319 optimal weight: 0.8980 chunk 195 optimal weight: 8.9990 chunk 439 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 533 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 359 optimal weight: 5.9990 chunk 488 optimal weight: 1.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN M 179 ASN O 74 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** 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 ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 GLN a 179 ASN b 104 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144766 restraints weight = 80000.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146922 restraints weight = 46028.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.148448 restraints weight = 29739.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.149453 restraints weight = 20811.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.150217 restraints weight = 15698.607| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 39926 Z= 0.159 Angle : 0.623 13.733 54568 Z= 0.328 Chirality : 0.043 0.221 6834 Planarity : 0.004 0.041 6918 Dihedral : 5.813 79.333 5996 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.82 % Allowed : 20.61 % Favored : 72.57 % 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 are not related in a simple way. whole: -0.72 (0.11), residues: 5576 helix: 0.84 (0.12), residues: 1970 sheet: -1.87 (0.14), residues: 1144 loop : -0.74 (0.13), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 170 TYR 0.028 0.002 TYR Z 136 PHE 0.022 0.002 PHE b 223 TRP 0.020 0.002 TRP K 117 HIS 0.010 0.001 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (39914) covalent geometry : angle 0.62182 / 0.33 (54552) SS BOND : bond 0.00235 / 0.13 ( 8) SS BOND : angle 1.94065 / 1.14 ( 16) hydrogen bonds : bond 0.03684 / 2.58 ( 1240) hydrogen bonds : angle 4.31763 / 3.08 ( 3720) Misc. bond : bond 0.00066 / 0.03 ( 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 1565 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 1328 time to evaluate : 1.562 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. revert: symmetry clash 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. 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: "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. 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. 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 23 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.5463 (m-80) REVERT: B 41 LYS cc_start: 0.8510 (pttm) cc_final: 0.6302 (mptt) REVERT: C 133 SER cc_start: 0.8908 (m) cc_final: 0.8226 (t) REVERT: D 35 ILE cc_start: 0.7976 (mm) cc_final: 0.7577 (mm) REVERT: D 36 LYS cc_start: 0.6471 (ttpp) cc_final: 0.5905 (tttt) REVERT: D 84 VAL cc_start: 0.9347 (t) cc_final: 0.9098 (m) REVERT: D 116 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7407 (tm-30) REVERT: D 210 THR cc_start: 0.6546 (m) cc_final: 0.6300 (t) REVERT: E 234 THR cc_start: 0.6605 (m) cc_final: 0.6347 (p) REVERT: F 116 TYR cc_start: 0.7871 (m-80) cc_final: 0.7417 (m-80) REVERT: F 132 LEU cc_start: 0.8408 (mt) cc_final: 0.8155 (mp) REVERT: F 169 THR cc_start: 0.7754 (m) cc_final: 0.7507 (m) REVERT: F 172 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7128 (mm-30) REVERT: H 67 LYS cc_start: 0.8456 (tptp) cc_final: 0.8221 (ttpp) REVERT: H 195 ASP cc_start: 0.7837 (t0) cc_final: 0.7273 (t0) REVERT: J 98 TYR cc_start: 0.7118 (t80) cc_final: 0.6818 (t80) REVERT: J 170 ASP cc_start: 0.7079 (m-30) cc_final: 0.6532 (m-30) REVERT: K 173 LEU cc_start: 0.7492 (tp) cc_final: 0.6921 (mp) REVERT: K 178 TYR cc_start: 0.7021 (m-80) cc_final: 0.6554 (m-80) REVERT: L 99 ILE cc_start: 0.9092 (pt) cc_final: 0.8880 (pt) REVERT: L 136 TYR cc_start: 0.7086 (t80) cc_final: 0.6681 (t80) REVERT: M 230 ILE cc_start: 0.8422 (mp) cc_final: 0.8158 (pt) REVERT: N 49 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7493 (mttm) REVERT: O 23 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.5673 (m-80) REVERT: P 19 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7324 (mm) REVERT: P 41 LYS cc_start: 0.8369 (pttt) cc_final: 0.6737 (mptt) REVERT: Q 105 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7814 (tp40) REVERT: Q 133 SER cc_start: 0.9020 (m) cc_final: 0.8335 (t) REVERT: R 84 VAL cc_start: 0.9332 (t) cc_final: 0.9080 (m) REVERT: R 116 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7438 (tm-30) REVERT: S 234 THR cc_start: 0.6708 (m) cc_final: 0.6411 (p) REVERT: T 116 TYR cc_start: 0.7878 (m-80) cc_final: 0.7324 (m-80) REVERT: T 132 LEU cc_start: 0.8472 (mt) cc_final: 0.8214 (mp) REVERT: T 172 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6794 (mm-30) REVERT: V 192 TYR cc_start: 0.7609 (t80) cc_final: 0.7172 (t80) REVERT: W 26 VAL cc_start: 0.9008 (m) cc_final: 0.8764 (t) REVERT: X 98 TYR cc_start: 0.7159 (t80) cc_final: 0.6871 (t80) REVERT: X 170 ASP cc_start: 0.7112 (m-30) cc_final: 0.6549 (m-30) REVERT: Z 17 ASP cc_start: 0.7316 (p0) cc_final: 0.6639 (p0) REVERT: Z 149 LEU cc_start: 0.8021 (tp) cc_final: 0.7818 (tp) outliers start: 237 outliers final: 193 residues processed: 1424 average time/residue: 0.2162 time to fit residues: 529.9688 Evaluate side-chains 1443 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 1247 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 130 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 A residue 250 ASP 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 C residue 114 ILE 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 D residue 26 VAL Chi-restraints excluded: chain D residue 71 LEU 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 87 THR 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 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 84 ASP 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 43 VAL 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 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 H residue 244 VAL 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 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 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 119 ASP 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 58 TYR Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 184 TYR Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 105 LEU 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 50 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 67 LEU 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 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 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 19 LEU 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 164 ILE Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 235 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 141 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 241 ILE 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 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 84 ASP Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 238 THR 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 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 7 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 80 VAL 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 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 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 178 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 99 ILE Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 110 ASN Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 184 TYR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 9 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 461 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 524 optimal weight: 7.9990 chunk 512 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN ** 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 106 HIS ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 86 GLN M 179 ASN N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 ASN ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN V 219 HIS W 35 HIS ** W 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN W 109 GLN ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN a 179 ASN b 104 ASN b 170 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.141048 restraints weight = 81273.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143169 restraints weight = 46915.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144653 restraints weight = 30392.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145713 restraints weight = 21332.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146437 restraints weight = 15964.891| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 39926 Z= 0.275 Angle : 0.736 13.995 54568 Z= 0.385 Chirality : 0.046 0.185 6834 Planarity : 0.004 0.044 6918 Dihedral : 6.200 79.051 5996 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 8.29 % Allowed : 21.33 % Favored : 70.38 % 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 are not related in a simple way. whole: -1.06 (0.11), residues: 5576 helix: 0.63 (0.12), residues: 1942 sheet: -1.88 (0.14), residues: 1090 loop : -1.13 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 11 TYR 0.030 0.002 TYR E 103 PHE 0.031 0.002 PHE N 223 TRP 0.015 0.002 TRP K 117 HIS 0.010 0.002 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.28 (39914) covalent geometry : angle 0.73508 / 0.38 (54552) SS BOND : bond 0.00203 / 0.13 ( 8) SS BOND : angle 2.30050 / 1.35 ( 16) hydrogen bonds : bond 0.04232 / 2.96 ( 1240) hydrogen bonds : angle 4.66236 / 3.31 ( 3720) Misc. bond : bond 0.00072 / 0.04 ( 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 1531 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 288 poor density : 1243 time to evaluate : 1.522 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: "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: "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. 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. TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE S 241 " (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: "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: "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 23 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.5666 (m-80) REVERT: B 41 LYS cc_start: 0.8465 (pttm) cc_final: 0.6208 (mptt) REVERT: C 133 SER cc_start: 0.8972 (m) cc_final: 0.8272 (t) REVERT: D 36 LYS cc_start: 0.6592 (ttpp) cc_final: 0.5997 (tttt) REVERT: D 84 VAL cc_start: 0.9400 (t) cc_final: 0.9097 (m) REVERT: E 98 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.6922 (t-90) REVERT: F 84 LEU cc_start: 0.8928 (mt) cc_final: 0.8692 (mt) REVERT: F 116 TYR cc_start: 0.7975 (m-80) cc_final: 0.7526 (m-80) REVERT: F 132 LEU cc_start: 0.8468 (mt) cc_final: 0.8207 (mp) REVERT: F 169 THR cc_start: 0.7776 (m) cc_final: 0.7513 (m) REVERT: G 78 ILE cc_start: 0.8457 (mp) cc_final: 0.7966 (mm) REVERT: H 195 ASP cc_start: 0.8055 (t0) cc_final: 0.7732 (t0) REVERT: J 98 TYR cc_start: 0.7128 (t80) cc_final: 0.6689 (t80) REVERT: K 146 TYR cc_start: 0.6430 (m-80) cc_final: 0.6151 (m-80) REVERT: K 173 LEU cc_start: 0.7627 (tp) cc_final: 0.6971 (mp) REVERT: L 136 TYR cc_start: 0.7091 (t80) cc_final: 0.6711 (t80) REVERT: M 230 ILE cc_start: 0.8418 (mp) cc_final: 0.8157 (pt) REVERT: O 23 TYR cc_start: 0.6030 (m-80) cc_final: 0.5827 (m-80) REVERT: P 41 LYS cc_start: 0.8411 (pttt) cc_final: 0.6600 (mptt) REVERT: P 123 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: Q 133 SER cc_start: 0.9058 (m) cc_final: 0.8333 (t) REVERT: R 84 VAL cc_start: 0.9389 (t) cc_final: 0.9100 (m) REVERT: R 116 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7408 (tm-30) REVERT: S 103 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5821 (p90) REVERT: T 116 TYR cc_start: 0.7963 (m-80) cc_final: 0.7440 (m-80) REVERT: T 132 LEU cc_start: 0.8458 (mt) cc_final: 0.8186 (mp) REVERT: T 169 THR cc_start: 0.7759 (m) cc_final: 0.7490 (m) REVERT: V 192 TYR cc_start: 0.7902 (t80) cc_final: 0.7585 (t80) REVERT: W 26 VAL cc_start: 0.9031 (m) cc_final: 0.8794 (t) REVERT: X 98 TYR cc_start: 0.7157 (t80) cc_final: 0.6707 (t80) REVERT: Y 178 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: Z 17 ASP cc_start: 0.7784 (p0) cc_final: 0.7044 (p0) REVERT: b 225 GLN cc_start: 0.7827 (pt0) cc_final: 0.7625 (pt0) outliers start: 288 outliers final: 237 residues processed: 1375 average time/residue: 0.2077 time to fit residues: 494.2974 Evaluate side-chains 1437 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 1195 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 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 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 114 ILE 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 D residue 9 VAL 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 87 THR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 98 HIS 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 46 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 232 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 113 ILE 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 37 ILE 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 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 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 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 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 69 LEU 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 119 ASP 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 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 110 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 150 ASP 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 105 LEU 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 50 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 73 ILE 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 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 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 123 GLN 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 189 LEU Chi-restraints excluded: chain Q residue 235 LEU 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 103 TYR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 241 ILE 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 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 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 140 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 30 CYS Chi-restraints excluded: chain V residue 37 ILE 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 210 ILE 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 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 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 94 SER 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 128 ASN Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 178 TYR Chi-restraints excluded: chain Y residue 185 ASP 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 99 ILE Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 110 ASN Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 160 ILE 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 138 LEU Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 199 ILE 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 69 THR Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 170 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 427 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 chunk 413 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 331 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 500 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 392 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 115 GLN ** D 146 GLN ** 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** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 ASN N 104 ASN O 74 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 232 ASN ** W 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 ASN b 104 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.142996 restraints weight = 80769.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145171 restraints weight = 46370.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146682 restraints weight = 29751.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147733 restraints weight = 20746.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148494 restraints weight = 15473.708| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4076 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= 0.188 Angle : 0.657 13.723 54568 Z= 0.344 Chirality : 0.044 0.185 6834 Planarity : 0.004 0.043 6918 Dihedral : 5.978 79.550 5996 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 7.83 % Allowed : 23.34 % Favored : 68.83 % 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 are not related in a simple way. whole: -0.99 (0.11), residues: 5576 helix: 0.76 (0.12), residues: 1980 sheet: -1.89 (0.14), residues: 1118 loop : -1.14 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 11 TYR 0.031 0.002 TYR Z 136 PHE 0.025 0.002 PHE N 223 TRP 0.020 0.002 TRP Q 179 HIS 0.010 0.001 HIS Y 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (39914) covalent geometry : angle 0.65675 / 0.34 (54552) SS BOND : bond 0.00235 / 0.13 ( 8) SS BOND : angle 1.88243 / 1.10 ( 16) hydrogen bonds : bond 0.03812 / 2.67 ( 1240) hydrogen bonds : angle 4.38609 / 3.12 ( 3720) Misc. bond : bond 0.00057 / 0.03 ( 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 1529 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 1257 time to evaluate : 1.549 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: "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. revert: symmetry clash 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. 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. revert: symmetry clash 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: 0.6214 (mptt) REVERT: C 133 SER cc_start: 0.8886 (m) cc_final: 0.8218 (t) REVERT: D 36 LYS cc_start: 0.6561 (ttpp) cc_final: 0.5998 (tttt) REVERT: D 84 VAL cc_start: 0.9321 (t) cc_final: 0.9036 (m) REVERT: D 116 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7567 (tm-30) REVERT: D 210 THR cc_start: 0.6672 (m) cc_final: 0.6384 (t) REVERT: E 98 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.6994 (t-90) REVERT: E 234 THR cc_start: 0.6521 (m) cc_final: 0.6204 (p) REVERT: F 84 LEU cc_start: 0.8913 (mt) cc_final: 0.8697 (mt) REVERT: F 116 TYR cc_start: 0.7906 (m-80) cc_final: 0.7483 (m-80) REVERT: F 132 LEU cc_start: 0.8396 (mt) cc_final: 0.8149 (mp) REVERT: F 169 THR cc_start: 0.7810 (m) cc_final: 0.7563 (m) REVERT: H 195 ASP cc_start: 0.8036 (t0) cc_final: 0.7663 (t0) REVERT: J 98 TYR cc_start: 0.7058 (t80) cc_final: 0.6626 (t80) REVERT: J 170 ASP cc_start: 0.7056 (m-30) cc_final: 0.6535 (m-30) REVERT: K 146 TYR cc_start: 0.6312 (m-80) cc_final: 0.6054 (m-80) REVERT: K 173 LEU cc_start: 0.7563 (tp) cc_final: 0.6966 (mp) REVERT: L 13 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7953 (tt) REVERT: L 17 ASP cc_start: 0.7890 (p0) cc_final: 0.7007 (p0) REVERT: L 34 ILE cc_start: 0.7842 (mm) cc_final: 0.7600 (mm) REVERT: L 136 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6635 (t80) REVERT: M 48 TYR cc_start: 0.7375 (p90) cc_final: 0.7101 (p90) REVERT: M 230 ILE cc_start: 0.8444 (mp) cc_final: 0.8171 (pt) REVERT: N 49 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7528 (mttm) REVERT: P 123 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: Q 105 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7722 (tp40) REVERT: Q 133 SER cc_start: 0.9004 (m) cc_final: 0.8310 (t) REVERT: R 84 VAL cc_start: 0.9336 (t) cc_final: 0.9043 (m) REVERT: R 116 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7331 (tm-30) REVERT: S 103 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.5712 (p90) REVERT: T 39 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7476 (ttpp) REVERT: T 116 TYR cc_start: 0.7855 (m-80) cc_final: 0.7484 (m-80) REVERT: T 169 THR cc_start: 0.7834 (m) cc_final: 0.7585 (m) REVERT: U 10 LEU cc_start: 0.5745 (mt) cc_final: 0.5521 (mp) REVERT: U 104 ASN cc_start: 0.7579 (m-40) cc_final: 0.7259 (m-40) REVERT: V 192 TYR cc_start: 0.7708 (t80) cc_final: 0.7400 (t80) REVERT: X 15 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8152 (mmm) REVERT: X 98 TYR cc_start: 0.7075 (t80) cc_final: 0.6644 (t80) REVERT: X 170 ASP cc_start: 0.7079 (m-30) cc_final: 0.6578 (m-30) REVERT: Y 178 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: Z 13 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7667 (tt) REVERT: b 49 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7586 (mttm) outliers start: 272 outliers final: 234 residues processed: 1377 average time/residue: 0.2148 time to fit residues: 511.1569 Evaluate side-chains 1444 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 1202 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR 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 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 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 114 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 D residue 9 VAL Chi-restraints excluded: chain D residue 26 VAL 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 57 THR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 98 HIS 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 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 223 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain G residue 30 SER 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 37 ILE 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 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 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 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 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 69 LEU 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 119 ASP 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 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 64 LYS 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 184 TYR Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain M residue 234 THR 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 50 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 72 ASN 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 50 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 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 123 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 189 LEU Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 26 VAL 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 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 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 160 PHE Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain T residue 221 GLN 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 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 37 ILE 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 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 3 ILE Chi-restraints excluded: chain W residue 7 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 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 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 94 SER 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 178 TYR 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 99 ILE Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 110 ASN Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain Z residue 184 TYR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 SER 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 a residue 234 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 11 SER 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 72 ASN Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 170 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 292 optimal weight: 0.7980 chunk 370 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 227 optimal weight: 1.9990 chunk 547 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 304 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 349 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 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** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 115 GLN V 232 ASN W 109 GLN ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 ASN b 104 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 = 0.3890 r_free = 0.3890 target = 0.153378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144207 restraints weight = 80484.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146300 restraints weight = 45793.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147803 restraints weight = 29355.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.148801 restraints weight = 20358.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.149534 restraints weight = 15300.073| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39926 Z= 0.161 Angle : 0.639 14.465 54568 Z= 0.333 Chirality : 0.043 0.189 6834 Planarity : 0.004 0.052 6918 Dihedral : 5.771 80.028 5996 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 7.48 % Allowed : 24.47 % Favored : 68.05 % 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 are not related in a simple way. whole: -0.90 (0.11), residues: 5576 helix: 0.90 (0.12), residues: 1988 sheet: -1.91 (0.14), residues: 1130 loop : -1.11 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 170 TYR 0.026 0.002 TYR Z 136 PHE 0.023 0.002 PHE N 223 TRP 0.019 0.002 TRP Q 179 HIS 0.011 0.001 HIS Y 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (39914) covalent geometry : angle 0.63855 / 0.33 (54552) SS BOND : bond 0.00329 / 0.17 ( 8) SS BOND : angle 1.69176 / 0.98 ( 16) hydrogen bonds : bond 0.03667 / 2.56 ( 1240) hydrogen bonds : angle 4.30015 / 3.07 ( 3720) Misc. bond : bond 0.00056 / 0.03 ( 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 1510 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 1250 time to evaluate : 1.607 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. 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. 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. 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: "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: "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 19 LEU cc_start: 0.7406 (mt) cc_final: 0.7127 (mm) REVERT: B 41 LYS cc_start: 0.8407 (pttm) cc_final: 0.6217 (mptt) REVERT: C 133 SER cc_start: 0.8868 (m) cc_final: 0.8208 (t) REVERT: D 36 LYS cc_start: 0.6651 (ttpp) cc_final: 0.6234 (tttm) REVERT: D 84 VAL cc_start: 0.9311 (t) cc_final: 0.9012 (m) REVERT: D 116 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7502 (tm-30) REVERT: D 210 THR cc_start: 0.6635 (m) cc_final: 0.6356 (t) REVERT: E 98 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.6985 (t-90) REVERT: E 234 THR cc_start: 0.6580 (m) cc_final: 0.6253 (p) REVERT: F 84 LEU cc_start: 0.8917 (mt) cc_final: 0.8714 (mt) REVERT: F 116 TYR cc_start: 0.7958 (m-80) cc_final: 0.7528 (m-80) REVERT: F 132 LEU cc_start: 0.8410 (mt) cc_final: 0.8158 (mp) REVERT: F 169 THR cc_start: 0.7751 (m) cc_final: 0.7505 (m) REVERT: H 195 ASP cc_start: 0.8009 (t0) cc_final: 0.7552 (t0) REVERT: J 98 TYR cc_start: 0.7090 (t80) cc_final: 0.6566 (t80) REVERT: J 170 ASP cc_start: 0.6980 (m-30) cc_final: 0.6437 (m-30) REVERT: K 146 TYR cc_start: 0.6376 (m-80) cc_final: 0.6175 (m-80) REVERT: K 173 LEU cc_start: 0.7556 (tp) cc_final: 0.6967 (mp) REVERT: L 13 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7836 (tt) REVERT: L 136 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6576 (t80) REVERT: M 48 TYR cc_start: 0.7351 (p90) cc_final: 0.7079 (p90) REVERT: M 64 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: M 230 ILE cc_start: 0.8451 (mp) cc_final: 0.8175 (pt) REVERT: N 49 LYS cc_start: 0.7897 (mtpt) cc_final: 0.7586 (mttm) REVERT: N 112 ASN cc_start: 0.7861 (t0) cc_final: 0.7510 (t0) REVERT: P 123 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: Q 133 SER cc_start: 0.9016 (m) cc_final: 0.8324 (t) REVERT: R 116 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7357 (tm-30) REVERT: S 103 TYR cc_start: 0.6271 (OUTLIER) cc_final: 0.5810 (p90) REVERT: T 39 LYS cc_start: 0.7794 (ttpp) cc_final: 0.7585 (ttpp) REVERT: T 116 TYR cc_start: 0.7929 (m-80) cc_final: 0.7550 (m-80) REVERT: T 169 THR cc_start: 0.7797 (m) cc_final: 0.7566 (m) REVERT: V 192 TYR cc_start: 0.7729 (t80) cc_final: 0.7365 (t80) REVERT: X 15 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8085 (mmm) REVERT: X 98 TYR cc_start: 0.7072 (t80) cc_final: 0.6565 (t80) REVERT: X 170 ASP cc_start: 0.7034 (m-30) cc_final: 0.6553 (m-30) REVERT: Y 28 LEU cc_start: 0.7459 (mt) cc_final: 0.7242 (mm) REVERT: Y 178 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: Z 13 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7690 (tt) REVERT: Z 136 TYR cc_start: 0.6947 (t80) cc_final: 0.6699 (t80) REVERT: a 64 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: b 49 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7627 (mttm) outliers start: 260 outliers final: 230 residues processed: 1364 average time/residue: 0.2158 time to fit residues: 509.0474 Evaluate side-chains 1450 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 1210 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 50 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 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 114 ILE 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 D residue 9 VAL Chi-restraints excluded: chain D residue 26 VAL 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 57 THR Chi-restraints excluded: chain E residue 98 HIS 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 223 ILE 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 51 ILE Chi-restraints excluded: chain G residue 122 ILE 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 37 ILE 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 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 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 55 THR 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 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 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 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 155 GLU 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 64 LYS 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 184 TYR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 105 LEU 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 50 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 ASN 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 50 ILE Chi-restraints excluded: chain O residue 113 TYR 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 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 123 GLN 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 189 LEU Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 VAL 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 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 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 46 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 T residue 221 GLN 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 47 ILE 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 37 ILE 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 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 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 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 55 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 58 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 94 SER 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 119 ASP Chi-restraints excluded: chain Y residue 152 THR Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 178 TYR 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 87 LEU Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 110 ASN Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 184 TYR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 64 TYR 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 a residue 234 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 50 THR Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 72 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 280 optimal weight: 7.9990 chunk 304 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 487 optimal weight: 9.9990 chunk 440 optimal weight: 20.0000 chunk 410 optimal weight: 20.0000 chunk 446 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 275 optimal weight: 10.0000 chunk 376 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 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** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN W 109 GLN ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 ASN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 ASN b 104 ASN b 170 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.141430 restraints weight = 80949.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143568 restraints weight = 46579.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145060 restraints weight = 30116.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.145971 restraints weight = 21152.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146765 restraints weight = 16179.932| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 39926 Z= 0.231 Angle : 0.702 15.015 54568 Z= 0.366 Chirality : 0.045 0.205 6834 Planarity : 0.004 0.079 6918 Dihedral : 6.008 79.573 5996 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 8.03 % Allowed : 24.47 % Favored : 67.50 % 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 are not related in a simple way. whole: -1.08 (0.11), residues: 5576 helix: 0.74 (0.12), residues: 1978 sheet: -1.92 (0.15), residues: 1100 loop : -1.26 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 11 TYR 0.040 0.002 TYR B 24 PHE 0.027 0.002 PHE N 223 TRP 0.030 0.002 TRP W 42 HIS 0.011 0.002 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (39914) covalent geometry : angle 0.70090 / 0.37 (54552) SS BOND : bond 0.00238 / 0.14 ( 8) SS BOND : angle 1.84883 / 1.08 ( 16) hydrogen bonds : bond 0.04047 / 2.83 ( 1240) hydrogen bonds : angle 4.54616 / 3.24 ( 3720) Misc. bond : bond 0.00059 / 0.03 ( 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 1472 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 279 poor density : 1193 time to evaluate : 1.570 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: "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: "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. 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. 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: "TYR W 90 " (corrupted residue). Skipping it. revert: symmetry clash 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 231 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7644 (t) REVERT: B 41 LYS cc_start: 0.8430 (pttm) cc_final: 0.6215 (mptt) REVERT: C 133 SER cc_start: 0.8928 (m) cc_final: 0.8236 (t) REVERT: D 36 LYS cc_start: 0.6716 (ttpp) cc_final: 0.6137 (tttt) REVERT: D 116 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7502 (tm-30) REVERT: D 210 THR cc_start: 0.6980 (m) cc_final: 0.6670 (t) REVERT: E 98 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.6993 (t-90) REVERT: E 103 TYR cc_start: 0.6157 (OUTLIER) cc_final: 0.5334 (p90) REVERT: F 169 THR cc_start: 0.7753 (m) cc_final: 0.7515 (m) REVERT: G 89 ASN cc_start: 0.7329 (m-40) cc_final: 0.7041 (m110) REVERT: H 194 GLN cc_start: 0.7243 (pt0) cc_final: 0.6988 (pt0) REVERT: J 98 TYR cc_start: 0.7010 (t80) cc_final: 0.6487 (t80) REVERT: K 146 TYR cc_start: 0.6366 (m-80) cc_final: 0.6158 (m-80) REVERT: K 170 ARG cc_start: 0.6346 (mtm180) cc_final: 0.6059 (mtm-85) REVERT: K 173 LEU cc_start: 0.7611 (tp) cc_final: 0.6975 (mp) REVERT: L 13 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7977 (tt) REVERT: L 136 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6677 (t80) REVERT: M 48 TYR cc_start: 0.7291 (p90) cc_final: 0.7058 (p90) REVERT: M 64 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: M 230 ILE cc_start: 0.8447 (mp) cc_final: 0.8051 (pt) REVERT: N 112 ASN cc_start: 0.7940 (t0) cc_final: 0.7595 (t0) REVERT: O 231 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7659 (t) REVERT: P 123 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: Q 105 GLN cc_start: 0.8267 (tp40) cc_final: 0.7854 (tp40) REVERT: Q 133 SER cc_start: 0.9076 (m) cc_final: 0.8350 (t) REVERT: R 116 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7390 (tm-30) REVERT: S 103 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5788 (p90) REVERT: T 169 THR cc_start: 0.7744 (m) cc_final: 0.7514 (m) REVERT: V 194 GLN cc_start: 0.7160 (pt0) cc_final: 0.6808 (tm-30) REVERT: X 15 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8044 (mmm) REVERT: X 98 TYR cc_start: 0.7030 (t80) cc_final: 0.6501 (t80) REVERT: Y 178 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: Z 13 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7732 (tt) REVERT: a 64 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: b 112 ASN cc_start: 0.7861 (t0) cc_final: 0.7481 (t0) outliers start: 279 outliers final: 240 residues processed: 1322 average time/residue: 0.2067 time to fit residues: 473.6109 Evaluate side-chains 1421 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 1168 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 73 THR 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 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 114 ILE 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 D residue 9 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 VAL 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 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 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 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 G residue 30 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 51 ILE 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 37 ILE 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 210 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 220 ASN 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 41 ILE 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 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 69 LEU 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 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 155 GLU 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 64 LYS Chi-restraints excluded: chain L residue 87 LEU 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 M residue 60 SER Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain M residue 234 THR 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 50 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 ASN 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 50 ILE Chi-restraints excluded: chain O residue 113 TYR 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 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 123 GLN 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 189 LEU Chi-restraints excluded: chain Q residue 235 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 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 165 THR 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 46 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 51 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 37 ILE 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 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 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 41 ILE 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 58 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 97 LEU 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 119 ASP Chi-restraints excluded: chain Y residue 152 THR Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 178 TYR 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 87 LEU Chi-restraints excluded: chain Z residue 99 ILE 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 184 TYR Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 64 TYR 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 a residue 199 ILE Chi-restraints excluded: chain a residue 234 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 50 THR Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 72 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 294 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 512 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 497 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** 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** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 ASN b 104 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 = 0.3858 r_free = 0.3858 target = 0.150917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.141558 restraints weight = 80516.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143696 restraints weight = 46097.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145196 restraints weight = 29626.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.146232 restraints weight = 20646.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146903 restraints weight = 15412.399| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 39926 Z= 0.217 Angle : 0.770 59.199 54568 Z= 0.417 Chirality : 0.045 0.543 6834 Planarity : 0.004 0.093 6918 Dihedral : 6.014 79.610 5996 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.59 % Rotamer: Outliers : 7.57 % Allowed : 25.22 % Favored : 67.21 % 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 are not related in a simple way. whole: -1.07 (0.11), residues: 5576 helix: 0.78 (0.12), residues: 1966 sheet: -1.93 (0.15), residues: 1100 loop : -1.27 (0.12), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 11 TYR 0.034 0.002 TYR B 24 PHE 0.027 0.002 PHE N 223 TRP 0.028 0.002 TRP W 42 HIS 0.011 0.002 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (39914) covalent geometry : angle 0.76932 / 0.42 (54552) SS BOND : bond 0.00359 / 0.19 ( 8) SS BOND : angle 1.75415 / 1.02 ( 16) hydrogen bonds : bond 0.04019 / 2.80 ( 1240) hydrogen bonds : angle 4.54448 / 3.23 ( 3720) Misc. bond : bond 0.00045 / 0.02 ( 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 1443 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 1180 time to evaluate : 1.602 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: "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: "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. 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. 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: "TYR W 90 " (corrupted residue). Skipping it. revert: symmetry clash 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 231 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7640 (t) REVERT: B 41 LYS cc_start: 0.8438 (pttm) cc_final: 0.6214 (mptt) REVERT: C 133 SER cc_start: 0.8943 (m) cc_final: 0.8266 (t) REVERT: D 36 LYS cc_start: 0.6697 (ttpp) cc_final: 0.6265 (tttm) REVERT: D 84 VAL cc_start: 0.9334 (t) cc_final: 0.9020 (m) REVERT: D 116 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7522 (tm-30) REVERT: D 210 THR cc_start: 0.6976 (m) cc_final: 0.6667 (t) REVERT: E 98 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.6986 (t-90) REVERT: E 103 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5361 (p90) REVERT: F 169 THR cc_start: 0.7749 (m) cc_final: 0.7512 (m) REVERT: G 89 ASN cc_start: 0.7328 (m-40) cc_final: 0.7029 (m110) REVERT: H 194 GLN cc_start: 0.7247 (pt0) cc_final: 0.6982 (pt0) REVERT: J 98 TYR cc_start: 0.7005 (t80) cc_final: 0.6475 (t80) REVERT: K 146 TYR cc_start: 0.6382 (m-80) cc_final: 0.6161 (m-80) REVERT: K 173 LEU cc_start: 0.7624 (tp) cc_final: 0.6967 (mp) REVERT: L 13 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7976 (tt) REVERT: L 136 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6665 (t80) REVERT: M 64 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: M 230 ILE cc_start: 0.8435 (mp) cc_final: 0.8052 (pt) REVERT: N 112 ASN cc_start: 0.7928 (t0) cc_final: 0.7585 (t0) REVERT: O 231 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7655 (t) REVERT: P 123 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: Q 105 GLN cc_start: 0.8302 (tp40) cc_final: 0.7857 (tp40) REVERT: Q 133 SER cc_start: 0.9079 (m) cc_final: 0.8338 (t) REVERT: R 116 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7374 (tm-30) REVERT: S 103 TYR cc_start: 0.6334 (OUTLIER) cc_final: 0.5787 (p90) REVERT: T 169 THR cc_start: 0.7737 (m) cc_final: 0.7507 (m) REVERT: V 194 GLN cc_start: 0.7159 (pt0) cc_final: 0.6785 (tm-30) REVERT: X 15 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8040 (mmm) REVERT: X 98 TYR cc_start: 0.7003 (t80) cc_final: 0.6491 (t80) REVERT: X 139 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7240 (pp) REVERT: Y 178 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: Z 13 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7725 (tt) REVERT: a 64 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: b 112 ASN cc_start: 0.7849 (t0) cc_final: 0.7467 (t0) outliers start: 263 outliers final: 244 residues processed: 1301 average time/residue: 0.1990 time to fit residues: 449.4110 Evaluate side-chains 1430 residues out of total 4988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 258 poor density : 1172 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 73 THR 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 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 85 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 ILE 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 D residue 9 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 VAL 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 57 THR 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 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 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 G residue 30 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 51 ILE 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 37 ILE 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 210 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 220 ASN 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 41 ILE 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 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 69 LEU 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 119 ASP Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 152 THR 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 64 LYS Chi-restraints excluded: chain L residue 87 LEU 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 M residue 60 SER Chi-restraints excluded: chain M residue 64 TYR 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 198 ASP Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain M residue 234 THR 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 60 ASP Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 ASN 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 50 ILE Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 113 TYR 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 185 LEU 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 P residue 123 GLN 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 189 LEU Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 VAL 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 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 165 THR 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 46 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 51 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 37 ILE 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 210 ILE 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 41 ILE 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 58 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 94 SER 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 152 THR Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 178 TYR 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 87 LEU 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 a residue 60 SER Chi-restraints excluded: chain a residue 64 TYR 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 a residue 234 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 50 THR Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 72 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 455 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 548 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 373 optimal weight: 1.9990 chunk 439 optimal weight: 5.9990 chunk 459 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 479 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** 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** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 ASN b 104 ASN b 170 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141553 restraints weight = 81209.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143651 restraints weight = 46164.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145127 restraints weight = 29711.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146146 restraints weight = 20802.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146771 restraints weight = 15568.521| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 39926 Z= 0.217 Angle : 0.769 59.160 54568 Z= 0.416 Chirality : 0.045 0.538 6834 Planarity : 0.004 0.093 6918 Dihedral : 6.014 79.610 5996 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.59 % Rotamer: Outliers : 7.48 % Allowed : 25.42 % Favored : 67.10 % 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 are not related in a simple way. whole: -1.07 (0.11), residues: 5576 helix: 0.78 (0.12), residues: 1966 sheet: -1.93 (0.15), residues: 1100 loop : -1.27 (0.12), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 11 TYR 0.033 0.002 TYR B 24 PHE 0.027 0.002 PHE N 223 TRP 0.027 0.002 TRP W 42 HIS 0.010 0.002 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (39914) covalent geometry : angle 0.76895 / 0.42 (54552) SS BOND : bond 0.00358 / 0.19 ( 8) SS BOND : angle 1.75418 / 1.02 ( 16) hydrogen bonds : bond 0.04018 / 2.80 ( 1240) hydrogen bonds : angle 4.54447 / 3.23 ( 3720) Misc. bond : bond 0.00045 / 0.02 ( 4) =============================================================================== Job complete usr+sys time: 9070.36 seconds wall clock time: 156 minutes 40.45 seconds (9400.45 seconds total)