Starting phenix.real_space_refine on Fri Jul 3 11:13:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7upt_26675/07_2026/7upt_26675.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upt_26675/07_2026/7upt_26675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7upt_26675/07_2026/7upt_26675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upt_26675/07_2026/7upt_26675.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7upt_26675/07_2026/7upt_26675.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7upt_26675/07_2026/7upt_26675.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upt_26675/07_2026/7upt_26675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upt_26675/07_2026/7upt_26675.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.052 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: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 93 5.16 5 C 8512 2.51 5 N 2386 2.21 5 O 2554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13567 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2148 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2343 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "C" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2357 Classifications: {'peptide': 299} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 286} Chain breaks: 1 Chain: "D" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2318 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2311 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Chain breaks: 1 Chain: "F" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1853 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 4 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.32, per 1000 atoms: 0.17 Number of scatterers: 13567 At special positions: 0 Unit cell: (96.512, 130.624, 138.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 93 16.00 P 17 15.00 Mg 5 11.99 O 2554 8.00 N 2386 7.00 C 8512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 417.7 milliseconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3266 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 8 sheets defined 58.5% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 96 through 107 removed outlier: 4.304A pdb=" N ILE A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.512A pdb=" N ILE A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.702A pdb=" N GLU A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 4.265A pdb=" N LYS A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.684A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'A' and resid 263 through 274 removed outlier: 4.158A pdb=" N ALA A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 295 through 316 removed outlier: 3.551A pdb=" N LYS A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.664A pdb=" N GLN B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 158 through 163 removed outlier: 4.215A pdb=" N LEU B 162 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 184 removed outlier: 3.887A pdb=" N PHE B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.951A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 222 removed outlier: 3.694A pdb=" N ASP B 221 " --> pdb=" O MET B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.902A pdb=" N ASP B 242 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.699A pdb=" N ARG B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 273 Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.863A pdb=" N VAL B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 315 Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.868A pdb=" N LYS B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.689A pdb=" N ALA C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.815A pdb=" N ALA C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.748A pdb=" N PHE C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 206 through 222 removed outlier: 3.616A pdb=" N ASP C 221 " --> pdb=" O MET C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.511A pdb=" N ASP C 242 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 261 through 273 Processing helix chain 'C' and resid 283 through 291 removed outlier: 3.545A pdb=" N THR C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 317 removed outlier: 3.941A pdb=" N GLU C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR C 314 " --> pdb=" O CYS C 310 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 348 removed outlier: 3.540A pdb=" N GLU C 341 " --> pdb=" O HIS C 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 4.076A pdb=" N LYS D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 78 removed outlier: 3.584A pdb=" N ALA D 78 " --> pdb=" O MET D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 96 through 112 removed outlier: 3.737A pdb=" N ILE D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.512A pdb=" N LEU D 116 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 168 through 184 removed outlier: 3.585A pdb=" N LYS D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.009A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 222 removed outlier: 3.537A pdb=" N MET D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 removed outlier: 3.692A pdb=" N ARG D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 removed outlier: 3.517A pdb=" N LEU D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 291 removed outlier: 3.832A pdb=" N GLU D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 313 removed outlier: 3.513A pdb=" N LEU D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 350 removed outlier: 3.787A pdb=" N HIS D 337 " --> pdb=" O GLN D 333 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 62 Processing helix chain 'E' and resid 71 through 78 removed outlier: 3.615A pdb=" N ALA E 78 " --> pdb=" O MET E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 112 removed outlier: 3.596A pdb=" N ILE E 100 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.941A pdb=" N PHE E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'E' and resid 158 through 163 removed outlier: 4.169A pdb=" N LEU E 162 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 158 through 163' Processing helix chain 'E' and resid 168 through 184 removed outlier: 3.866A pdb=" N PHE E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 Processing helix chain 'E' and resid 206 through 222 removed outlier: 3.534A pdb=" N LYS E 213 " --> pdb=" O THR E 209 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP E 221 " --> pdb=" O MET E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 283 through 291 removed outlier: 3.561A pdb=" N VAL E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 313 removed outlier: 3.701A pdb=" N GLU E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 347 Processing helix chain 'F' and resid 71 through 78 Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.776A pdb=" N ILE F 100 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 removed outlier: 3.659A pdb=" N ILE F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 158 through 162 Processing helix chain 'F' and resid 169 through 184 removed outlier: 4.125A pdb=" N PHE F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 184 " --> pdb=" O LEU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 220 Processing helix chain 'F' and resid 245 through 251 removed outlier: 3.889A pdb=" N ARG F 249 " --> pdb=" O SER F 245 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 245 through 251' Processing helix chain 'F' and resid 261 through 273 removed outlier: 3.637A pdb=" N LEU F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 272 " --> pdb=" O ILE F 268 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 295 through 316 removed outlier: 3.529A pdb=" N CYS F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 348 removed outlier: 3.645A pdb=" N LYS F 345 " --> pdb=" O GLU F 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 156 removed outlier: 7.248A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 129 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 130 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 156 removed outlier: 6.811A pdb=" N SER B 187 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N MET B 234 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 189 " --> pdb=" O MET B 234 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA B 236 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 191 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 129 through 132 Processing sheet with id=AA4, first strand: chain 'C' and resid 155 through 156 removed outlier: 6.736A pdb=" N SER C 187 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET C 234 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE C 189 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA C 236 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 191 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 130 through 132 removed outlier: 6.682A pdb=" N LEU D 130 " --> pdb=" O PHE D 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 154 through 156 removed outlier: 6.016A pdb=" N ILE D 189 " --> pdb=" O MET D 234 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA D 236 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE D 191 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 154 through 156 removed outlier: 6.321A pdb=" N SER E 187 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N MET E 234 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE E 189 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA E 236 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE E 191 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 155 through 156 removed outlier: 7.271A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ASP F 192 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE F 189 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA F 236 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE F 191 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 235 " --> pdb=" O VAL F 129 " (cutoff:3.500A) 581 hydrogen bonds defined for protein. 1665 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: 1.58 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4468 1.34 - 1.46: 2690 1.46 - 1.58: 6445 1.58 - 1.70: 28 1.70 - 1.81: 157 Bond restraints: 13788 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.48e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.41e+01 bond pdb=" C4 ATP F 602 " pdb=" C5 ATP F 602 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.41e+01 ... (remaining 13783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 18480 4.04 - 8.08: 98 8.08 - 12.12: 31 12.12 - 16.17: 3 16.17 - 20.21: 7 Bond angle restraints: 18619 Sorted by residual: angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 119.66 20.21 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 119.75 20.12 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 119.77 20.10 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 119.98 19.89 1.00e+00 1.00e+00 3.95e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 120.00 19.87 1.00e+00 1.00e+00 3.95e+02 ... (remaining 18614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 7409 21.67 - 43.34: 818 43.34 - 65.02: 237 65.02 - 86.69: 34 86.69 - 108.36: 5 Dihedral angle restraints: 8503 sinusoidal: 3527 harmonic: 4976 Sorted by residual: dihedral pdb=" CA HIS C 227 " pdb=" C HIS C 227 " pdb=" N SER C 228 " pdb=" CA SER C 228 " ideal model delta harmonic sigma weight residual 180.00 147.88 32.12 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" C2' ADP A 501 " pdb=" C1' ADP A 501 " pdb=" N9 ADP A 501 " pdb=" C4 ADP A 501 " ideal model delta sinusoidal sigma weight residual 91.55 -16.81 108.36 1 2.00e+01 2.50e-03 3.16e+01 dihedral pdb=" CA CYS D 137 " pdb=" C CYS D 137 " pdb=" N GLY D 138 " pdb=" CA GLY D 138 " ideal model delta harmonic sigma weight residual 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 8500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 2114 0.344 - 0.688: 0 0.688 - 1.032: 0 1.032 - 1.376: 0 1.376 - 1.720: 13 Chirality restraints: 2127 Sorted by residual: chirality pdb=" CG LEU F 243 " pdb=" CB LEU F 243 " pdb=" CD1 LEU F 243 " pdb=" CD2 LEU F 243 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.39e+01 chirality pdb=" CG LEU F 271 " pdb=" CB LEU F 271 " pdb=" CD1 LEU F 271 " pdb=" CD2 LEU F 271 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 chirality pdb=" CG LEU C 141 " pdb=" CB LEU C 141 " pdb=" CD1 LEU C 141 " pdb=" CD2 LEU C 141 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.26e+01 ... (remaining 2124 not shown) Planarity restraints: 2349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 56 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C GLU D 56 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU D 56 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS D 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 109 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO B 110 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 109 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO F 110 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO F 110 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 110 " -0.021 5.00e-02 4.00e+02 ... (remaining 2346 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 161 2.54 - 3.13: 11721 3.13 - 3.72: 21980 3.72 - 4.31: 28297 4.31 - 4.90: 46581 Nonbonded interactions: 108740 Sorted by model distance: nonbonded pdb=" O LEU E 184 " pdb=" OG SER E 187 " model vdw 1.944 3.040 nonbonded pdb="MG MG C 601 " pdb=" O3B ATP C 602 " model vdw 1.953 2.170 nonbonded pdb=" OG1 THR C 140 " pdb="MG MG C 601 " model vdw 1.953 2.170 nonbonded pdb=" OG1 THR F 140 " pdb="MG MG F 601 " model vdw 1.955 2.170 nonbonded pdb=" OG1 THR E 140 " pdb="MG MG E 502 " model vdw 1.964 2.170 ... (remaining 108735 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' and (resid 69 through 112 or resid 128 through 197 or resid 210 throu \ gh 220 or resid 230 through 314 or resid 328 through 351)) selection = (chain 'B' and (resid 69 through 112 or resid 128 through 197 or resid 210 throu \ gh 220 or resid 230 through 314 or resid 328 through 351)) selection = (chain 'C' and (resid 69 through 112 or resid 128 through 197 or resid 210 throu \ gh 220 or resid 230 through 314 or resid 328 through 351)) selection = (chain 'D' and (resid 69 through 112 or resid 128 through 197 or resid 210 throu \ gh 220 or resid 230 through 314 or resid 328 through 351)) selection = (chain 'E' and (resid 69 through 112 or resid 128 through 197 or resid 210 throu \ gh 220 or resid 230 through 351)) selection = (chain 'F' and (resid 69 through 314 or resid 328 through 351)) } 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: 1.960 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.060 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.004 0.080 13789 Z= 0.319 Angle : 0.949 20.207 18619 Z= 0.655 Chirality : 0.132 1.720 2127 Planarity : 0.003 0.041 2349 Dihedral : 19.196 108.360 5237 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.34 % Favored : 92.60 % Rotamer: Outliers : 11.28 % Allowed : 22.89 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.18), residues: 1662 helix: -1.62 (0.16), residues: 804 sheet: -2.39 (0.38), residues: 154 loop : -2.27 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 254 TYR 0.004 0.000 TYR F 132 PHE 0.009 0.001 PHE B 154 TRP 0.004 0.001 TRP D 220 HIS 0.003 0.000 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.32 (13788) covalent geometry : angle 0.94886 / 0.66 (18619) hydrogen bonds : bond 0.19766 / 13.38 ( 581) hydrogen bonds : angle 7.24064 / 4.97 ( 1665) Misc. bond : bond 0.00384 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 253 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7847 (m-70) cc_final: 0.7441 (m170) REVERT: A 92 ASP cc_start: 0.8167 (m-30) cc_final: 0.7726 (t70) REVERT: A 157 LEU cc_start: 0.8957 (tp) cc_final: 0.8591 (tt) REVERT: A 184 LEU cc_start: 0.9263 (tp) cc_final: 0.8939 (tp) REVERT: A 258 ASN cc_start: 0.7451 (t0) cc_final: 0.6555 (p0) REVERT: A 298 ASP cc_start: 0.8412 (m-30) cc_final: 0.8126 (m-30) REVERT: B 54 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8599 (tm-30) REVERT: B 66 ASN cc_start: 0.8495 (m110) cc_final: 0.8242 (t0) REVERT: B 71 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7836 (tp30) REVERT: B 312 ARG cc_start: 0.8785 (tmt90) cc_final: 0.8402 (tmm-80) REVERT: C 59 MET cc_start: 0.8651 (ttp) cc_final: 0.8381 (tmm) REVERT: C 220 TRP cc_start: 0.8307 (t60) cc_final: 0.8085 (t60) REVERT: C 343 MET cc_start: 0.8794 (tpt) cc_final: 0.8525 (tpp) REVERT: D 47 GLN cc_start: 0.5978 (OUTLIER) cc_final: 0.5435 (pp30) REVERT: E 61 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8721 (tm-30) REVERT: E 132 TYR cc_start: 0.8351 (p90) cc_final: 0.7769 (p90) REVERT: E 203 SER cc_start: 0.8190 (t) cc_final: 0.7875 (p) REVERT: F 85 ASN cc_start: 0.9531 (m-40) cc_final: 0.9266 (m-40) REVERT: F 248 MET cc_start: 0.8175 (ttt) cc_final: 0.7972 (ttt) REVERT: F 249 ARG cc_start: 0.8346 (mmp80) cc_final: 0.8137 (mtt-85) REVERT: F 280 ARG cc_start: 0.8780 (tpp-160) cc_final: 0.8099 (tpm170) REVERT: F 281 HIS cc_start: 0.8272 (m170) cc_final: 0.7436 (t70) REVERT: F 311 VAL cc_start: 0.9332 (t) cc_final: 0.9078 (t) REVERT: F 342 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7794 (tmtt) outliers start: 166 outliers final: 107 residues processed: 404 average time/residue: 0.1171 time to fit residues: 65.6468 Evaluate side-chains 290 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 181 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 335 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN A 289 GLN B 66 ASN B 206 HIS B 238 ASN B 334 GLN C 54 GLN D 193 GLN D 227 HIS E 61 GLN E 215 GLN E 238 ASN E 264 GLN F 85 ASN F 193 GLN F 332 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.101125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074801 restraints weight = 39444.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077835 restraints weight = 17227.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.079854 restraints weight = 10435.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.081110 restraints weight = 7615.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081914 restraints weight = 6284.612| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13789 Z= 0.149 Angle : 0.719 13.998 18619 Z= 0.355 Chirality : 0.043 0.272 2127 Planarity : 0.005 0.048 2349 Dihedral : 13.035 116.051 2090 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 9.99 % Allowed : 23.98 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.60 (0.20), residues: 1662 helix: -0.42 (0.17), residues: 840 sheet: -1.87 (0.38), residues: 166 loop : -1.55 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 304 TYR 0.011 0.001 TYR C 72 PHE 0.019 0.001 PHE D 154 TRP 0.023 0.001 TRP A 90 HIS 0.004 0.001 HIS B 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13788) covalent geometry : angle 0.71914 / 0.35 (18619) hydrogen bonds : bond 0.04637 / 3.20 ( 581) hydrogen bonds : angle 5.47396 / 3.77 ( 1665) Misc. bond : bond 0.00394 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 207 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.8060 (m-30) cc_final: 0.7793 (t0) REVERT: A 139 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6811 (mttp) REVERT: A 184 LEU cc_start: 0.9010 (tp) cc_final: 0.8493 (tp) REVERT: A 224 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: A 258 ASN cc_start: 0.7434 (t0) cc_final: 0.6636 (p0) REVERT: A 263 LYS cc_start: 0.9228 (tppt) cc_final: 0.8957 (mmtm) REVERT: B 65 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6147 (pttm) REVERT: B 66 ASN cc_start: 0.8393 (m-40) cc_final: 0.8161 (t0) REVERT: B 71 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7747 (tp30) REVERT: B 96 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7885 (pp) REVERT: B 121 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8300 (ttp-170) REVERT: B 248 MET cc_start: 0.8797 (tpp) cc_final: 0.8480 (tpp) REVERT: C 59 MET cc_start: 0.8644 (ttp) cc_final: 0.8293 (tmm) REVERT: C 220 TRP cc_start: 0.8367 (t60) cc_final: 0.7950 (t60) REVERT: C 248 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7795 (tpp) REVERT: D 47 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.5681 (pp30) REVERT: D 96 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7647 (pp) REVERT: D 250 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7808 (ttm170) REVERT: D 344 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8369 (mtmt) REVERT: E 132 TYR cc_start: 0.8292 (p90) cc_final: 0.7860 (p90) REVERT: E 341 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8587 (mm-30) REVERT: E 343 MET cc_start: 0.8213 (mmm) cc_final: 0.7767 (mmt) REVERT: F 72 TYR cc_start: 0.8498 (m-80) cc_final: 0.7606 (m-10) REVERT: F 249 ARG cc_start: 0.8343 (mmp80) cc_final: 0.7981 (mtm-85) REVERT: F 280 ARG cc_start: 0.8771 (tpp-160) cc_final: 0.8032 (tpm170) REVERT: F 281 HIS cc_start: 0.8237 (m170) cc_final: 0.7435 (t70) REVERT: F 312 ARG cc_start: 0.8125 (tmm-80) cc_final: 0.7677 (ttp80) REVERT: F 342 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7773 (tmtt) outliers start: 147 outliers final: 94 residues processed: 335 average time/residue: 0.1109 time to fit residues: 53.1693 Evaluate side-chains 284 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 180 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 303 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 138 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 HIS ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN C 52 GLN C 193 GLN C 230 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS E 256 HIS F 158 GLN F 332 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.092820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.065536 restraints weight = 40030.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068159 restraints weight = 18260.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.069938 restraints weight = 11456.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071049 restraints weight = 8575.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071795 restraints weight = 7182.490| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13789 Z= 0.257 Angle : 0.752 12.046 18619 Z= 0.373 Chirality : 0.045 0.218 2127 Planarity : 0.005 0.050 2349 Dihedral : 11.836 124.896 2017 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 9.99 % Allowed : 24.46 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.21), residues: 1662 helix: -0.16 (0.17), residues: 856 sheet: -1.65 (0.39), residues: 178 loop : -1.34 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 338 TYR 0.017 0.002 TYR F 72 PHE 0.022 0.002 PHE D 154 TRP 0.018 0.002 TRP B 220 HIS 0.007 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.26 (13788) covalent geometry : angle 0.75207 / 0.37 (18619) hydrogen bonds : bond 0.04720 / 3.25 ( 581) hydrogen bonds : angle 5.26152 / 3.64 ( 1665) Misc. bond : bond 0.00216 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 163 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7071 (ttmm) REVERT: A 258 ASN cc_start: 0.7689 (t0) cc_final: 0.6887 (p0) REVERT: A 263 LYS cc_start: 0.9260 (tppt) cc_final: 0.9056 (mptt) REVERT: B 65 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6037 (pttm) REVERT: B 66 ASN cc_start: 0.8393 (m-40) cc_final: 0.8155 (t0) REVERT: B 71 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8204 (tp30) REVERT: B 96 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8126 (pp) REVERT: B 121 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8336 (ttp-170) REVERT: B 153 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7167 (mmt90) REVERT: B 275 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.7605 (t0) REVERT: C 59 MET cc_start: 0.8691 (ttp) cc_final: 0.8381 (tmm) REVERT: C 248 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7691 (tpt) REVERT: D 47 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.5789 (pp30) REVERT: D 96 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8021 (pp) REVERT: D 248 MET cc_start: 0.8723 (tpp) cc_final: 0.8294 (tpp) REVERT: E 73 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: E 109 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8253 (mm) REVERT: E 190 PHE cc_start: 0.9010 (t80) cc_final: 0.8614 (t80) REVERT: E 341 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8553 (mm-30) REVERT: F 248 MET cc_start: 0.8409 (ttt) cc_final: 0.7998 (ttt) REVERT: F 249 ARG cc_start: 0.8293 (mmp80) cc_final: 0.7865 (mtm-85) REVERT: F 342 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7895 (tttp) outliers start: 147 outliers final: 101 residues processed: 297 average time/residue: 0.0941 time to fit residues: 41.1663 Evaluate side-chains 263 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 150 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 145 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 140 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 230 GLN A 238 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 333 GLN D 333 GLN F 79 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.097478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.070496 restraints weight = 39379.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073336 restraints weight = 17510.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075260 restraints weight = 10750.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076456 restraints weight = 7938.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.077116 restraints weight = 6604.983| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13789 Z= 0.129 Angle : 0.672 13.523 18619 Z= 0.325 Chirality : 0.043 0.209 2127 Planarity : 0.004 0.052 2349 Dihedral : 11.376 122.555 1999 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 8.90 % Allowed : 26.22 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.82 (0.21), residues: 1662 helix: 0.16 (0.18), residues: 857 sheet: -1.43 (0.40), residues: 173 loop : -1.11 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 312 TYR 0.007 0.001 TYR C 72 PHE 0.016 0.001 PHE A 178 TRP 0.009 0.001 TRP A 90 HIS 0.004 0.001 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (13788) covalent geometry : angle 0.67241 / 0.33 (18619) hydrogen bonds : bond 0.03790 / 2.59 ( 581) hydrogen bonds : angle 4.99595 / 3.44 ( 1665) Misc. bond : bond 0.00290 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 182 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.8161 (m-70) cc_final: 0.7865 (m170) REVERT: A 139 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6857 (ttmm) REVERT: A 224 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: A 258 ASN cc_start: 0.7684 (t0) cc_final: 0.6998 (p0) REVERT: A 263 LYS cc_start: 0.9266 (tppt) cc_final: 0.9000 (mmtm) REVERT: B 50 GLU cc_start: 0.8123 (mp0) cc_final: 0.7810 (pm20) REVERT: B 71 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7780 (tp30) REVERT: B 72 TYR cc_start: 0.8024 (m-10) cc_final: 0.7335 (m-10) REVERT: B 96 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7897 (pp) REVERT: B 121 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8272 (ttp-170) REVERT: B 153 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7160 (mmt90) REVERT: B 248 MET cc_start: 0.8755 (tpp) cc_final: 0.7925 (tpp) REVERT: C 59 MET cc_start: 0.8655 (ttp) cc_final: 0.8384 (tmm) REVERT: C 248 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7698 (tpt) REVERT: D 47 GLN cc_start: 0.6808 (OUTLIER) cc_final: 0.6028 (pp30) REVERT: D 96 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7795 (pp) REVERT: D 197 PHE cc_start: 0.8687 (t80) cc_final: 0.8414 (t80) REVERT: D 248 MET cc_start: 0.8479 (tpp) cc_final: 0.8235 (ttp) REVERT: D 333 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: E 109 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8200 (mm) REVERT: E 266 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8441 (tm-30) REVERT: E 341 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8652 (mm-30) REVERT: F 248 MET cc_start: 0.8359 (ttt) cc_final: 0.7933 (ttt) REVERT: F 249 ARG cc_start: 0.8360 (mmp80) cc_final: 0.7840 (mtm-85) REVERT: F 281 HIS cc_start: 0.8354 (m90) cc_final: 0.7348 (t70) REVERT: F 342 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7800 (tmtt) outliers start: 131 outliers final: 88 residues processed: 299 average time/residue: 0.0998 time to fit residues: 44.0443 Evaluate side-chains 269 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 169 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 124 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 chunk 49 optimal weight: 3.9990 chunk 75 optimal weight: 0.0170 chunk 166 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS D 333 GLN E 124 GLN F 79 HIS F 85 ASN F 238 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.097929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071027 restraints weight = 39221.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073826 restraints weight = 17751.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075698 restraints weight = 11044.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.076886 restraints weight = 8218.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077550 restraints weight = 6839.445| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13789 Z= 0.121 Angle : 0.664 13.558 18619 Z= 0.317 Chirality : 0.042 0.152 2127 Planarity : 0.004 0.052 2349 Dihedral : 10.673 123.022 1978 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 8.36 % Allowed : 26.49 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.21), residues: 1662 helix: 0.21 (0.18), residues: 857 sheet: -1.30 (0.42), residues: 173 loop : -1.10 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 312 TYR 0.009 0.001 TYR A 72 PHE 0.016 0.001 PHE D 154 TRP 0.008 0.001 TRP A 90 HIS 0.003 0.000 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (13788) covalent geometry : angle 0.66356 / 0.32 (18619) hydrogen bonds : bond 0.03601 / 2.45 ( 581) hydrogen bonds : angle 4.86162 / 3.37 ( 1665) Misc. bond : bond 0.00291 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 171 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.8071 (m-70) cc_final: 0.7750 (m170) REVERT: A 171 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8222 (mm110) REVERT: A 211 MET cc_start: 0.8871 (ttt) cc_final: 0.8155 (tmm) REVERT: A 213 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7460 (mtmm) REVERT: A 224 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: A 258 ASN cc_start: 0.7646 (t0) cc_final: 0.7019 (p0) REVERT: B 71 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7793 (tp30) REVERT: B 72 TYR cc_start: 0.7999 (m-10) cc_final: 0.7435 (m-10) REVERT: B 96 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7916 (pp) REVERT: B 121 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8209 (ttp-170) REVERT: B 153 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7637 (mmt90) REVERT: C 248 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7766 (tpt) REVERT: D 47 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6312 (pp30) REVERT: D 96 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7606 (pp) REVERT: D 197 PHE cc_start: 0.8654 (t80) cc_final: 0.8409 (t80) REVERT: D 333 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7523 (tp40) REVERT: D 338 ARG cc_start: 0.8744 (tmm-80) cc_final: 0.8523 (tmm-80) REVERT: E 341 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8635 (mm-30) REVERT: F 87 HIS cc_start: 0.7630 (m90) cc_final: 0.6564 (t-170) REVERT: F 281 HIS cc_start: 0.8349 (m90) cc_final: 0.7383 (t70) REVERT: F 342 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7896 (tttp) REVERT: F 343 MET cc_start: 0.7950 (tpt) cc_final: 0.7667 (tpp) outliers start: 123 outliers final: 87 residues processed: 277 average time/residue: 0.0929 time to fit residues: 37.9345 Evaluate side-chains 257 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 159 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 215 GLN Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 301 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 113 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN D 333 GLN F 79 HIS F 238 ASN F 275 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.094745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.067756 restraints weight = 39881.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.070427 restraints weight = 18232.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072237 restraints weight = 11464.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073382 restraints weight = 8585.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.074009 restraints weight = 7194.708| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13789 Z= 0.210 Angle : 0.695 12.384 18619 Z= 0.337 Chirality : 0.043 0.156 2127 Planarity : 0.004 0.050 2349 Dihedral : 10.280 126.881 1954 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 8.83 % Allowed : 27.24 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.21), residues: 1662 helix: 0.21 (0.18), residues: 868 sheet: -1.22 (0.41), residues: 173 loop : -1.11 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.024 0.001 TYR C 132 PHE 0.023 0.002 PHE C 197 TRP 0.013 0.002 TRP B 220 HIS 0.003 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (13788) covalent geometry : angle 0.69514 / 0.34 (18619) hydrogen bonds : bond 0.03895 / 2.65 ( 581) hydrogen bonds : angle 4.88071 / 3.37 ( 1665) Misc. bond : bond 0.00240 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 155 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ASN cc_start: 0.7786 (t0) cc_final: 0.7034 (p0) REVERT: A 343 MET cc_start: 0.2974 (OUTLIER) cc_final: 0.2426 (mmm) REVERT: B 96 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7988 (pp) REVERT: B 121 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8162 (ttp-170) REVERT: B 153 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7415 (mmt90) REVERT: B 248 MET cc_start: 0.8738 (tpp) cc_final: 0.8039 (tpp) REVERT: C 207 GLU cc_start: 0.8772 (pp20) cc_final: 0.8468 (pp20) REVERT: C 248 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7685 (tpt) REVERT: C 343 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8685 (tpp) REVERT: D 47 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6299 (pp30) REVERT: D 74 MET cc_start: 0.8477 (tpp) cc_final: 0.8248 (mpp) REVERT: D 96 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7906 (pp) REVERT: D 251 MET cc_start: 0.9203 (mtt) cc_final: 0.8856 (mtt) REVERT: E 266 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8498 (tm-30) REVERT: E 341 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8672 (mm-30) REVERT: F 249 ARG cc_start: 0.8292 (mmp80) cc_final: 0.7784 (mtm-85) REVERT: F 281 HIS cc_start: 0.8358 (m90) cc_final: 0.7326 (t70) REVERT: F 342 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7920 (tttp) REVERT: F 343 MET cc_start: 0.7938 (tpt) cc_final: 0.7678 (tpp) outliers start: 130 outliers final: 95 residues processed: 265 average time/residue: 0.0859 time to fit residues: 34.4169 Evaluate side-chains 251 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 146 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 215 GLN Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 301 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 112 optimal weight: 0.2980 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN D 333 GLN F 79 HIS F 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.095632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068561 restraints weight = 39197.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.071283 restraints weight = 17865.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.073054 restraints weight = 11194.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074220 restraints weight = 8387.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074964 restraints weight = 7004.750| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13789 Z= 0.156 Angle : 0.688 15.226 18619 Z= 0.327 Chirality : 0.043 0.162 2127 Planarity : 0.004 0.052 2349 Dihedral : 9.953 126.744 1948 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 8.29 % Allowed : 28.12 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1662 helix: 0.32 (0.18), residues: 865 sheet: -1.20 (0.41), residues: 177 loop : -1.00 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.022 0.001 TYR C 132 PHE 0.020 0.002 PHE D 154 TRP 0.010 0.001 TRP B 220 HIS 0.004 0.001 HIS F 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (13788) covalent geometry : angle 0.68751 / 0.33 (18619) hydrogen bonds : bond 0.03640 / 2.47 ( 581) hydrogen bonds : angle 4.79361 / 3.30 ( 1665) Misc. bond : bond 0.00293 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 159 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.8099 (m-70) cc_final: 0.7768 (m170) REVERT: A 171 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8078 (mm110) REVERT: A 182 ILE cc_start: 0.9263 (pp) cc_final: 0.9053 (pp) REVERT: A 211 MET cc_start: 0.9021 (ttt) cc_final: 0.8098 (tmm) REVERT: A 224 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: A 258 ASN cc_start: 0.7726 (t0) cc_final: 0.7097 (p0) REVERT: A 343 MET cc_start: 0.3096 (OUTLIER) cc_final: 0.2523 (mmm) REVERT: B 96 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.7964 (pp) REVERT: B 153 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7840 (mmt90) REVERT: B 248 MET cc_start: 0.8747 (tpp) cc_final: 0.7982 (tpp) REVERT: C 248 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7685 (tpt) REVERT: C 343 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8662 (tpp) REVERT: D 47 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6396 (pp30) REVERT: D 74 MET cc_start: 0.8490 (tpp) cc_final: 0.8267 (tpp) REVERT: D 96 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7878 (pp) REVERT: D 117 PHE cc_start: 0.8223 (m-80) cc_final: 0.7989 (m-80) REVERT: D 184 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8862 (pp) REVERT: D 197 PHE cc_start: 0.8639 (t80) cc_final: 0.8411 (t80) REVERT: E 266 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: E 341 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8645 (mm-30) REVERT: F 249 ARG cc_start: 0.8266 (mmp80) cc_final: 0.7879 (mtm-85) REVERT: F 281 HIS cc_start: 0.8399 (m90) cc_final: 0.7396 (t70) REVERT: F 342 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7909 (tttp) REVERT: F 343 MET cc_start: 0.7992 (tpt) cc_final: 0.7717 (tpp) outliers start: 122 outliers final: 91 residues processed: 263 average time/residue: 0.0867 time to fit residues: 34.5679 Evaluate side-chains 251 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 148 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 215 GLN Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 301 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 92 optimal weight: 0.0470 chunk 9 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN F 238 ASN F 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.096564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.069611 restraints weight = 39227.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072312 restraints weight = 18079.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074109 restraints weight = 11370.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075281 restraints weight = 8526.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.075912 restraints weight = 7138.223| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13789 Z= 0.138 Angle : 0.697 14.592 18619 Z= 0.329 Chirality : 0.042 0.185 2127 Planarity : 0.004 0.051 2349 Dihedral : 9.627 126.593 1940 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 7.88 % Allowed : 28.60 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1662 helix: 0.40 (0.18), residues: 868 sheet: -1.16 (0.41), residues: 178 loop : -0.93 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 250 TYR 0.014 0.001 TYR F 72 PHE 0.018 0.001 PHE D 154 TRP 0.008 0.001 TRP A 166 HIS 0.002 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13788) covalent geometry : angle 0.69703 / 0.33 (18619) hydrogen bonds : bond 0.03487 / 2.37 ( 581) hydrogen bonds : angle 4.76569 / 3.29 ( 1665) Misc. bond : bond 0.00263 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 157 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.8153 (m-70) cc_final: 0.7835 (m170) REVERT: A 171 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8052 (mm110) REVERT: A 211 MET cc_start: 0.9019 (ttt) cc_final: 0.8089 (tmm) REVERT: A 224 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: A 258 ASN cc_start: 0.7757 (t0) cc_final: 0.7165 (p0) REVERT: A 343 MET cc_start: 0.2965 (OUTLIER) cc_final: 0.2439 (mmm) REVERT: B 73 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: B 96 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7934 (pp) REVERT: B 153 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7653 (mmt90) REVERT: B 248 MET cc_start: 0.8743 (tpp) cc_final: 0.7941 (tpp) REVERT: B 302 MET cc_start: 0.7964 (ttp) cc_final: 0.7407 (tmm) REVERT: C 197 PHE cc_start: 0.8399 (t80) cc_final: 0.8149 (t80) REVERT: C 248 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7725 (tpt) REVERT: C 343 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8681 (tpp) REVERT: D 47 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6462 (pp30) REVERT: D 96 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7828 (pp) REVERT: D 197 PHE cc_start: 0.8609 (t80) cc_final: 0.8349 (t80) REVERT: E 266 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8456 (tm-30) REVERT: F 166 TRP cc_start: 0.6471 (t-100) cc_final: 0.6182 (t-100) REVERT: F 249 ARG cc_start: 0.8221 (mmp80) cc_final: 0.7840 (mtm-85) REVERT: F 251 MET cc_start: 0.8157 (ttm) cc_final: 0.6387 (tpp) REVERT: F 281 HIS cc_start: 0.8451 (m90) cc_final: 0.7422 (t70) REVERT: F 342 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7880 (tttp) REVERT: F 343 MET cc_start: 0.7912 (tpt) cc_final: 0.7646 (tpp) outliers start: 116 outliers final: 90 residues processed: 252 average time/residue: 0.0985 time to fit residues: 37.1786 Evaluate side-chains 252 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 151 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 215 GLN Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 301 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 93 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN F 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.096740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069708 restraints weight = 39176.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.072439 restraints weight = 17864.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074258 restraints weight = 11169.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075437 restraints weight = 8313.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076192 restraints weight = 6937.254| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13789 Z= 0.139 Angle : 0.710 14.265 18619 Z= 0.333 Chirality : 0.042 0.147 2127 Planarity : 0.004 0.050 2349 Dihedral : 9.063 125.631 1925 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 7.47 % Allowed : 29.08 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.22), residues: 1662 helix: 0.45 (0.18), residues: 868 sheet: -1.09 (0.41), residues: 178 loop : -0.92 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 239 TYR 0.007 0.001 TYR F 72 PHE 0.019 0.001 PHE D 154 TRP 0.008 0.001 TRP A 166 HIS 0.002 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (13788) covalent geometry : angle 0.71043 / 0.33 (18619) hydrogen bonds : bond 0.03446 / 2.34 ( 581) hydrogen bonds : angle 4.75791 / 3.29 ( 1665) Misc. bond : bond 0.00257 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 155 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8086 (mm110) REVERT: A 211 MET cc_start: 0.8988 (ttt) cc_final: 0.8101 (tmm) REVERT: A 224 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: A 258 ASN cc_start: 0.7629 (t0) cc_final: 0.7145 (p0) REVERT: B 72 TYR cc_start: 0.7865 (m-10) cc_final: 0.7337 (m-10) REVERT: B 73 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: B 96 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.7978 (pp) REVERT: B 153 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7836 (mmt90) REVERT: B 248 MET cc_start: 0.8726 (tpp) cc_final: 0.7927 (tpp) REVERT: B 302 MET cc_start: 0.7949 (ttp) cc_final: 0.7395 (tmm) REVERT: C 248 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7751 (tpt) REVERT: C 343 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8665 (tpp) REVERT: D 74 MET cc_start: 0.8479 (tpp) cc_final: 0.8238 (mpp) REVERT: D 96 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7820 (pp) REVERT: D 117 PHE cc_start: 0.8100 (m-80) cc_final: 0.7854 (m-80) REVERT: D 197 PHE cc_start: 0.8614 (t80) cc_final: 0.8365 (t80) REVERT: E 266 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8488 (tm-30) REVERT: F 166 TRP cc_start: 0.6435 (t-100) cc_final: 0.6177 (t-100) REVERT: F 249 ARG cc_start: 0.8222 (mmp80) cc_final: 0.7827 (mtm-85) REVERT: F 251 MET cc_start: 0.8175 (ttm) cc_final: 0.6420 (tpp) REVERT: F 281 HIS cc_start: 0.8410 (m90) cc_final: 0.7417 (t70) REVERT: F 342 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7893 (tttp) REVERT: F 343 MET cc_start: 0.7957 (tpt) cc_final: 0.7685 (tpp) outliers start: 110 outliers final: 91 residues processed: 243 average time/residue: 0.0863 time to fit residues: 31.9155 Evaluate side-chains 250 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 150 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 215 GLN Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 301 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN F 85 ASN F 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.097330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.070243 restraints weight = 39231.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.072992 restraints weight = 17881.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074817 restraints weight = 11186.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075961 restraints weight = 8363.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076723 restraints weight = 6999.391| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13789 Z= 0.130 Angle : 0.707 14.001 18619 Z= 0.330 Chirality : 0.042 0.147 2127 Planarity : 0.004 0.047 2349 Dihedral : 8.878 124.551 1920 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 7.34 % Allowed : 29.28 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1662 helix: 0.53 (0.18), residues: 864 sheet: -0.90 (0.42), residues: 173 loop : -0.93 (0.27), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 250 TYR 0.005 0.001 TYR E 72 PHE 0.018 0.001 PHE D 154 TRP 0.010 0.001 TRP F 90 HIS 0.003 0.000 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13788) covalent geometry : angle 0.70720 / 0.33 (18619) hydrogen bonds : bond 0.03353 / 2.28 ( 581) hydrogen bonds : angle 4.71226 / 3.26 ( 1665) Misc. bond : bond 0.00258 / 0.14 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 162 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8031 (mm110) REVERT: A 211 MET cc_start: 0.8934 (ttt) cc_final: 0.8045 (tmm) REVERT: A 213 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7412 (mtmm) REVERT: A 224 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: A 258 ASN cc_start: 0.7663 (t0) cc_final: 0.7249 (p0) REVERT: B 72 TYR cc_start: 0.7849 (m-10) cc_final: 0.7329 (m-10) REVERT: B 73 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: B 96 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.7970 (pp) REVERT: B 153 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7582 (mmt90) REVERT: B 248 MET cc_start: 0.8718 (tpp) cc_final: 0.7831 (tpp) REVERT: B 302 MET cc_start: 0.7942 (ttp) cc_final: 0.7402 (tmm) REVERT: C 248 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7793 (tpt) REVERT: C 343 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8649 (tpp) REVERT: D 74 MET cc_start: 0.8488 (tpp) cc_final: 0.8252 (mpp) REVERT: D 96 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7778 (pp) REVERT: D 117 PHE cc_start: 0.8061 (m-80) cc_final: 0.7822 (m-80) REVERT: D 197 PHE cc_start: 0.8613 (t80) cc_final: 0.8367 (t80) REVERT: D 251 MET cc_start: 0.9046 (mtt) cc_final: 0.8472 (mmm) REVERT: E 266 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: E 302 MET cc_start: 0.8896 (tmm) cc_final: 0.8623 (tmm) REVERT: F 166 TRP cc_start: 0.6448 (t-100) cc_final: 0.6191 (t-100) REVERT: F 249 ARG cc_start: 0.8229 (mmp80) cc_final: 0.7829 (mtm-85) REVERT: F 251 MET cc_start: 0.8231 (ttm) cc_final: 0.6492 (tpp) REVERT: F 281 HIS cc_start: 0.8451 (m90) cc_final: 0.7454 (t70) REVERT: F 342 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7885 (tttp) REVERT: F 343 MET cc_start: 0.7987 (tpt) cc_final: 0.7710 (tpp) outliers start: 108 outliers final: 90 residues processed: 248 average time/residue: 0.0886 time to fit residues: 33.3687 Evaluate side-chains 255 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 155 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 215 GLN Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 TYR Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 301 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 121 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.0470 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.097420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.070527 restraints weight = 39782.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073308 restraints weight = 17926.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075172 restraints weight = 11151.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076392 restraints weight = 8279.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077067 restraints weight = 6874.300| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 13789 Z= 0.227 Angle : 1.063 59.199 18619 Z= 0.609 Chirality : 0.051 0.872 2127 Planarity : 0.005 0.060 2349 Dihedral : 8.809 124.553 1906 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.00 % Favored : 91.94 % Rotamer: Outliers : 7.07 % Allowed : 29.28 % Favored : 63.65 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.33 (0.22), residues: 1662 helix: 0.54 (0.18), residues: 864 sheet: -0.88 (0.42), residues: 173 loop : -0.97 (0.27), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 250 TYR 0.005 0.001 TYR E 72 PHE 0.018 0.001 PHE D 154 TRP 0.009 0.001 TRP F 90 HIS 0.002 0.000 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (13788) covalent geometry : angle 1.06290 / 0.61 (18619) hydrogen bonds : bond 0.03757 / 2.35 ( 581) hydrogen bonds : angle 4.71124 / 3.26 ( 1665) Misc. bond : bond 0.00250 / 0.13 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.21 seconds wall clock time: 44 minutes 46.20 seconds (2686.20 seconds total)