Starting phenix.real_space_refine on Thu Jul 31 21:27:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upt_26675/07_2025/7upt_26675.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upt_26675/07_2025/7upt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7upt_26675/07_2025/7upt_26675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upt_26675/07_2025/7upt_26675.map" model { file = "/net/cci-nas-00/data/ceres_data/7upt_26675/07_2025/7upt_26675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upt_26675/07_2025/7upt_26675.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.45, per 1000 atoms: 0.62 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: 3.32 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.47 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: 3.57 Time building geometry restraints manager: 3.88 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: 7471 21.67 - 43.34: 886 43.34 - 65.02: 262 65.02 - 86.69: 34 86.69 - 108.36: 5 Dihedral angle restraints: 8658 sinusoidal: 3682 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 8655 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: 2.560 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.990 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 19.591 108.360 5392 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (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 TRP 0.004 0.001 TRP D 220 HIS 0.003 0.000 HIS D 227 PHE 0.009 0.001 PHE B 154 TYR 0.004 0.000 TYR F 132 ARG 0.003 0.000 ARG C 254 Details of bonding type rmsd hydrogen bonds : bond 0.19766 ( 581) hydrogen bonds : angle 7.24064 ( 1665) covalent geometry : bond 0.00425 (13788) covalent geometry : angle 0.94886 (18619) Misc. bond : bond 0.00384 ( 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 : 1.535 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: 0.9262 (tp) cc_final: 0.8939 (tp) REVERT: A 258 ASN cc_start: 0.7451 (t0) cc_final: 0.6554 (p0) REVERT: A 298 ASP cc_start: 0.8412 (m-30) cc_final: 0.8091 (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: 0.8342 (mm-30) cc_final: 0.7796 (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: 0.8526 (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: 0.9077 (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: 0.3224 time to fit residues: 177.9170 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 : 1.513 ------------------------------------------------------------------------------- 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 141 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 289 GLN A 337 HIS B 66 ASN B 206 HIS ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN 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 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.098344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.071635 restraints weight = 39414.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074537 restraints weight = 17487.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076495 restraints weight = 10728.015| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13789 Z= 0.180 Angle : 0.724 13.169 18619 Z= 0.360 Chirality : 0.044 0.268 2127 Planarity : 0.005 0.050 2349 Dihedral : 14.986 116.837 2245 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 10.46 % Allowed : 24.32 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.20), residues: 1662 helix: -0.44 (0.17), residues: 841 sheet: -1.93 (0.38), residues: 165 loop : -1.54 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 90 HIS 0.004 0.001 HIS B 79 PHE 0.020 0.002 PHE D 154 TYR 0.011 0.001 TYR C 72 ARG 0.006 0.001 ARG C 254 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 581) hydrogen bonds : angle 5.49648 ( 1665) covalent geometry : bond 0.00419 (13788) covalent geometry : angle 0.72414 (18619) Misc. bond : bond 0.00340 ( 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 351 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 197 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7760 (m-70) cc_final: 0.6614 (m170) REVERT: A 92 ASP cc_start: 0.8179 (m-30) cc_final: 0.7855 (t0) REVERT: A 139 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6864 (mttp) REVERT: A 158 GLN cc_start: 0.8330 (mt0) cc_final: 0.7557 (mt0) REVERT: A 224 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: A 258 ASN cc_start: 0.7561 (t0) cc_final: 0.6710 (p0) REVERT: A 263 LYS cc_start: 0.9228 (tppt) cc_final: 0.8961 (mmtm) REVERT: B 65 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6239 (pttm) REVERT: B 66 ASN cc_start: 0.8469 (m-40) cc_final: 0.8198 (t0) REVERT: B 71 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7794 (tp30) REVERT: B 96 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8027 (pp) REVERT: B 121 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8295 (ttp-170) REVERT: B 248 MET cc_start: 0.8849 (tpp) cc_final: 0.8434 (tpp) REVERT: B 312 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8533 (tmm-80) REVERT: C 343 MET cc_start: 0.8936 (tpt) cc_final: 0.8697 (tpp) REVERT: D 47 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.5487 (pp30) REVERT: D 74 MET cc_start: 0.8228 (tpp) cc_final: 0.8021 (tpp) REVERT: D 96 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7864 (pp) REVERT: D 274 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8981 (mtpp) REVERT: D 294 PHE cc_start: 0.8696 (m-80) cc_final: 0.8480 (m-80) REVERT: E 53 LYS cc_start: 0.9248 (mmmt) cc_final: 0.9041 (mmtt) REVERT: E 61 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8894 (tm-30) REVERT: E 343 MET cc_start: 0.8237 (mmm) cc_final: 0.7846 (mmt) REVERT: F 72 TYR cc_start: 0.8451 (m-80) cc_final: 0.7626 (m-10) REVERT: F 249 ARG cc_start: 0.8360 (mmp80) cc_final: 0.7984 (mtm-85) REVERT: F 280 ARG cc_start: 0.8783 (tpp-160) cc_final: 0.8058 (tpm170) REVERT: F 281 HIS cc_start: 0.8317 (m170) cc_final: 0.7410 (t70) REVERT: F 312 ARG cc_start: 0.8150 (tmm-80) cc_final: 0.7663 (ttp80) REVERT: F 342 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7789 (tmtt) outliers start: 154 outliers final: 99 residues processed: 331 average time/residue: 0.3126 time to fit residues: 148.3505 Evaluate side-chains 276 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 167 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 211 MET 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 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 287 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 312 ARG 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 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 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 E residue 61 GLN 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 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 107 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.0050 chunk 101 optimal weight: 0.8980 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN C 52 GLN C 230 GLN F 79 HIS F 158 GLN F 238 ASN F 332 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.096809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.069767 restraints weight = 39127.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072528 restraints weight = 17612.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.074405 restraints weight = 10885.595| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13789 Z= 0.149 Angle : 0.681 12.908 18619 Z= 0.336 Chirality : 0.043 0.219 2127 Planarity : 0.004 0.050 2349 Dihedral : 13.971 120.067 2175 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 9.17 % Allowed : 25.07 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.21), residues: 1662 helix: -0.03 (0.17), residues: 849 sheet: -1.67 (0.39), residues: 176 loop : -1.25 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 90 HIS 0.003 0.001 HIS B 79 PHE 0.016 0.001 PHE D 154 TYR 0.020 0.001 TYR F 72 ARG 0.006 0.000 ARG C 153 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 581) hydrogen bonds : angle 5.13314 ( 1665) covalent geometry : bond 0.00337 (13788) covalent geometry : angle 0.68095 (18619) Misc. bond : bond 0.00287 ( 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 312 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 177 time to evaluate : 1.716 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: 0.7786 (m-70) cc_final: 0.6547 (m-70) REVERT: A 139 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6851 (mttp) REVERT: A 158 GLN cc_start: 0.8338 (mt0) cc_final: 0.7829 (mt0) REVERT: A 224 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: A 258 ASN cc_start: 0.7629 (t0) cc_final: 0.6761 (p0) REVERT: A 263 LYS cc_start: 0.9255 (tppt) cc_final: 0.8998 (mmtm) REVERT: B 65 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6109 (pttm) REVERT: B 66 ASN cc_start: 0.8504 (m-40) cc_final: 0.8243 (t0) REVERT: B 71 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7706 (tp30) REVERT: B 96 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.7931 (pp) REVERT: B 121 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8343 (ttp-170) REVERT: C 52 GLN cc_start: 0.8644 (tt0) cc_final: 0.8051 (tm-30) REVERT: C 248 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7870 (tpp) REVERT: D 47 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.5726 (pp30) REVERT: D 96 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7787 (pp) REVERT: D 234 MET cc_start: 0.8080 (ptm) cc_final: 0.7854 (ptm) REVERT: D 248 MET cc_start: 0.8641 (tpp) cc_final: 0.8193 (tpp) REVERT: D 302 MET cc_start: 0.8272 (ttp) cc_final: 0.8058 (ppp) REVERT: E 61 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8887 (tm-30) REVERT: E 86 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8046 (pmm) REVERT: E 109 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8242 (mm) REVERT: E 343 MET cc_start: 0.8323 (mmm) cc_final: 0.8108 (mmt) REVERT: F 248 MET cc_start: 0.8362 (ttt) cc_final: 0.7849 (ttt) REVERT: F 249 ARG cc_start: 0.8333 (mmp80) cc_final: 0.7862 (mtm-85) REVERT: F 281 HIS cc_start: 0.8287 (m170) cc_final: 0.7428 (t70) REVERT: F 309 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8297 (mm) REVERT: F 312 ARG cc_start: 0.8145 (tmm-80) cc_final: 0.7694 (ttp80) REVERT: F 342 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7768 (tmtt) outliers start: 135 outliers final: 92 residues processed: 293 average time/residue: 0.3422 time to fit residues: 143.1594 Evaluate side-chains 263 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 159 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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 211 MET 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 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 158 GLN Chi-restraints excluded: chain B residue 165 LYS 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 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 112 LYS 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 192 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS 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 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 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 67 VAL 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 105 ASP 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 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 F residue 131 LEU Chi-restraints excluded: chain F residue 149 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 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 309 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 102 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN B 241 GLN C 54 GLN D 333 GLN F 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.097737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.070738 restraints weight = 39171.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073529 restraints weight = 17805.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075396 restraints weight = 11100.484| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13789 Z= 0.138 Angle : 0.658 12.895 18619 Z= 0.322 Chirality : 0.042 0.208 2127 Planarity : 0.004 0.051 2349 Dihedral : 13.441 122.646 2152 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 9.58 % Allowed : 25.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1662 helix: 0.21 (0.18), residues: 849 sheet: -1.52 (0.40), residues: 176 loop : -1.13 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 90 HIS 0.003 0.001 HIS F 87 PHE 0.016 0.001 PHE D 154 TYR 0.009 0.001 TYR A 72 ARG 0.003 0.000 ARG C 265 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 581) hydrogen bonds : angle 4.93869 ( 1665) covalent geometry : bond 0.00315 (13788) covalent geometry : angle 0.65786 (18619) Misc. bond : bond 0.00276 ( 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 312 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 171 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6861 (ttmm) REVERT: A 224 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: A 258 ASN cc_start: 0.7751 (t0) cc_final: 0.7016 (p0) REVERT: A 263 LYS cc_start: 0.9266 (tppt) cc_final: 0.9064 (mptt) REVERT: B 71 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7763 (tp30) REVERT: B 96 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7931 (pp) REVERT: B 121 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8255 (ttp-170) REVERT: B 122 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7491 (pt) REVERT: B 153 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7295 (mmt90) REVERT: B 248 MET cc_start: 0.8768 (tpp) cc_final: 0.8024 (tpp) REVERT: C 112 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8493 (mmtm) REVERT: C 248 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7713 (tpt) REVERT: D 47 GLN cc_start: 0.6667 (OUTLIER) cc_final: 0.5873 (pp30) REVERT: D 96 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7775 (pp) REVERT: D 197 PHE cc_start: 0.8700 (t80) cc_final: 0.8452 (t80) REVERT: D 248 MET cc_start: 0.8555 (tpp) cc_final: 0.8158 (tpp) REVERT: D 333 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8197 (tp40) REVERT: D 338 ARG cc_start: 0.8752 (tmm-80) cc_final: 0.8534 (tmm-80) REVERT: E 61 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8860 (tm-30) REVERT: E 86 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7955 (pmm) REVERT: E 109 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8216 (mm) REVERT: E 343 MET cc_start: 0.8413 (mmm) cc_final: 0.8199 (mmt) REVERT: F 248 MET cc_start: 0.8344 (ttt) cc_final: 0.7954 (ttt) REVERT: F 249 ARG cc_start: 0.8302 (mmp80) cc_final: 0.7870 (mtm-85) REVERT: F 281 HIS cc_start: 0.8353 (m170) cc_final: 0.7440 (t70) REVERT: F 342 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7857 (tttp) outliers start: 141 outliers final: 92 residues processed: 293 average time/residue: 0.3338 time to fit residues: 143.2015 Evaluate side-chains 266 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 160 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 211 MET 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 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 122 LEU 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 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 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 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 C residue 340 ILE 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 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 300 LYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 67 VAL 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 105 ASP 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 180 LEU 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 F residue 149 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 152 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN F 79 HIS F 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.098035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071140 restraints weight = 39109.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.073937 restraints weight = 17822.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.075807 restraints weight = 11076.520| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3481 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= 0.128 Angle : 0.669 12.988 18619 Z= 0.320 Chirality : 0.043 0.242 2127 Planarity : 0.004 0.051 2349 Dihedral : 13.120 123.022 2140 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 8.56 % Allowed : 26.22 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1662 helix: 0.23 (0.18), residues: 858 sheet: -1.38 (0.41), residues: 174 loop : -1.08 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 90 HIS 0.003 0.000 HIS C 115 PHE 0.017 0.001 PHE D 154 TYR 0.011 0.001 TYR A 72 ARG 0.007 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 581) hydrogen bonds : angle 4.81549 ( 1665) covalent geometry : bond 0.00287 (13788) covalent geometry : angle 0.66863 (18619) Misc. bond : bond 0.00279 ( 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 297 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 171 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7988 (m-70) cc_final: 0.7771 (m-70) REVERT: A 139 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6838 (ttmm) REVERT: A 213 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7362 (mttp) REVERT: A 224 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: A 258 ASN cc_start: 0.7760 (t0) cc_final: 0.7093 (p0) REVERT: B 50 GLU cc_start: 0.7747 (pm20) cc_final: 0.6759 (pm20) REVERT: B 71 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7823 (tp30) REVERT: B 72 TYR cc_start: 0.8108 (m-10) cc_final: 0.7474 (m-10) REVERT: B 96 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7904 (pp) REVERT: B 121 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8293 (ttp-170) REVERT: B 153 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7404 (mmt90) REVERT: B 275 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.7751 (t0) REVERT: C 112 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8495 (mmtm) REVERT: C 197 PHE cc_start: 0.8423 (t80) cc_final: 0.8192 (t80) REVERT: C 248 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7762 (tpt) REVERT: D 47 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6113 (pp30) REVERT: D 96 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7622 (pp) REVERT: D 197 PHE cc_start: 0.8665 (t80) cc_final: 0.8459 (t80) REVERT: D 338 ARG cc_start: 0.8720 (tmm-80) cc_final: 0.8506 (tmm-80) REVERT: E 61 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8844 (tm-30) REVERT: E 86 MET cc_start: 0.8232 (ptt) cc_final: 0.7936 (pmm) REVERT: E 190 PHE cc_start: 0.8884 (t80) cc_final: 0.8631 (t80) REVERT: F 85 ASN cc_start: 0.9585 (m110) cc_final: 0.9370 (m110) REVERT: F 86 MET cc_start: 0.9109 (ptp) cc_final: 0.8633 (ttp) REVERT: F 87 HIS cc_start: 0.7747 (m90) cc_final: 0.6668 (t-170) REVERT: F 154 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6977 (t80) REVERT: F 248 MET cc_start: 0.8390 (ttt) cc_final: 0.8090 (ttt) REVERT: F 249 ARG cc_start: 0.8301 (mmp80) cc_final: 0.7854 (mtm-85) REVERT: F 281 HIS cc_start: 0.8353 (m170) cc_final: 0.7436 (t70) REVERT: F 342 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7875 (tttp) REVERT: F 343 MET cc_start: 0.7867 (tpt) cc_final: 0.7616 (tpp) outliers start: 126 outliers final: 92 residues processed: 282 average time/residue: 0.3038 time to fit residues: 125.3602 Evaluate side-chains 260 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 155 time to evaluate : 2.830 ------------------------------------------------------------------------------- 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 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 211 MET 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 302 MET 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 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 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 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 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LYS 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 232 ILE 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 340 ILE 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 155 ILE 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 247 ILE Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain E residue 61 GLN 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 131 LEU Chi-restraints excluded: chain E residue 155 ILE 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 310 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain F residue 149 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 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 7 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 91 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 HIS D 238 ASN E 124 GLN F 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.098270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.071284 restraints weight = 39466.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074068 restraints weight = 18069.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075947 restraints weight = 11235.956| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13789 Z= 0.124 Angle : 0.667 13.892 18619 Z= 0.318 Chirality : 0.042 0.157 2127 Planarity : 0.004 0.050 2349 Dihedral : 12.813 123.860 2124 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 8.36 % Allowed : 26.56 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1662 helix: 0.31 (0.18), residues: 858 sheet: -1.28 (0.41), residues: 172 loop : -1.05 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 90 HIS 0.003 0.000 HIS F 79 PHE 0.018 0.001 PHE D 154 TYR 0.007 0.001 TYR E 72 ARG 0.007 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 581) hydrogen bonds : angle 4.72893 ( 1665) covalent geometry : bond 0.00281 (13788) covalent geometry : angle 0.66705 (18619) Misc. bond : bond 0.00273 ( 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 286 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 163 time to evaluate : 1.722 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: 0.8031 (m-70) cc_final: 0.7799 (m170) REVERT: A 139 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.7040 (ttmm) REVERT: A 213 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7400 (mttp) REVERT: A 224 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: A 258 ASN cc_start: 0.7677 (t0) cc_final: 0.7071 (p0) REVERT: B 71 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7872 (tp30) REVERT: B 72 TYR cc_start: 0.8077 (m-10) cc_final: 0.7482 (m-10) REVERT: B 96 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7846 (pp) REVERT: B 121 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8241 (ttp-170) REVERT: B 153 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7899 (mmt90) REVERT: B 185 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8676 (tt0) REVERT: B 248 MET cc_start: 0.8760 (tpp) cc_final: 0.8053 (tpp) REVERT: B 275 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.7759 (t0) REVERT: C 112 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8520 (mmtm) REVERT: C 248 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7719 (tpt) REVERT: D 47 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6242 (pp30) REVERT: D 96 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7546 (pp) REVERT: D 197 PHE cc_start: 0.8662 (t80) cc_final: 0.8461 (t80) REVERT: E 86 MET cc_start: 0.8215 (ptt) cc_final: 0.7918 (pmm) REVERT: E 190 PHE cc_start: 0.8915 (t80) cc_final: 0.8704 (t80) REVERT: F 85 ASN cc_start: 0.9508 (m110) cc_final: 0.9261 (m-40) REVERT: F 86 MET cc_start: 0.9141 (ptp) cc_final: 0.8625 (ptp) REVERT: F 87 HIS cc_start: 0.7713 (m90) cc_final: 0.6603 (t-170) REVERT: F 281 HIS cc_start: 0.8367 (m170) cc_final: 0.7448 (t70) REVERT: F 342 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7854 (tttp) REVERT: F 343 MET cc_start: 0.7867 (tpt) cc_final: 0.7615 (tpp) outliers start: 123 outliers final: 90 residues processed: 270 average time/residue: 0.2482 time to fit residues: 99.3406 Evaluate side-chains 258 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 156 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET 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 302 MET 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 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 185 GLN Chi-restraints excluded: chain B residue 232 ILE 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 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 112 LYS 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 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 C residue 340 ILE 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 155 ILE 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 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 142 ILE Chi-restraints excluded: chain E residue 155 ILE 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 310 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 80 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN E 256 HIS 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 = 0.3718 r_free = 0.3718 target = 0.098017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.071044 restraints weight = 39381.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.073801 restraints weight = 17907.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075684 restraints weight = 11175.210| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13789 Z= 0.133 Angle : 0.660 12.837 18619 Z= 0.316 Chirality : 0.042 0.175 2127 Planarity : 0.004 0.051 2349 Dihedral : 12.410 125.051 2108 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 7.81 % Allowed : 27.58 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1662 helix: 0.40 (0.18), residues: 859 sheet: -1.20 (0.42), residues: 172 loop : -1.03 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 90 HIS 0.006 0.001 HIS F 79 PHE 0.026 0.001 PHE C 197 TYR 0.010 0.001 TYR F 72 ARG 0.007 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 581) hydrogen bonds : angle 4.68714 ( 1665) covalent geometry : bond 0.00303 (13788) covalent geometry : angle 0.66024 (18619) Misc. bond : bond 0.00262 ( 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 273 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 158 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6973 (ttmm) REVERT: A 213 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7494 (mttp) REVERT: A 224 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: A 258 ASN cc_start: 0.7724 (t0) cc_final: 0.7127 (p0) REVERT: B 71 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7880 (tp30) REVERT: B 72 TYR cc_start: 0.8055 (m-10) cc_final: 0.7505 (m-10) REVERT: B 96 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7936 (pp) REVERT: B 153 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7868 (mmt90) REVERT: B 185 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8663 (tt0) REVERT: B 248 MET cc_start: 0.8752 (tpp) cc_final: 0.8025 (tpp) REVERT: B 275 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.7707 (t0) REVERT: C 112 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8504 (mmtm) REVERT: C 248 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7773 (tpt) REVERT: D 47 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6360 (pp30) REVERT: D 96 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7678 (pp) REVERT: E 86 MET cc_start: 0.8185 (ptt) cc_final: 0.7916 (pmm) REVERT: E 217 MET cc_start: 0.8615 (mmp) cc_final: 0.8312 (mmm) REVERT: F 72 TYR cc_start: 0.8804 (m-10) cc_final: 0.8550 (m-10) REVERT: F 85 ASN cc_start: 0.9506 (m110) cc_final: 0.9227 (m-40) REVERT: F 86 MET cc_start: 0.9136 (ptp) cc_final: 0.8679 (ptp) REVERT: F 87 HIS cc_start: 0.7693 (m90) cc_final: 0.6821 (t70) REVERT: F 281 HIS cc_start: 0.8363 (m170) cc_final: 0.7452 (t70) REVERT: F 342 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7875 (tttp) REVERT: F 343 MET cc_start: 0.7903 (tpt) cc_final: 0.7653 (tpp) outliers start: 115 outliers final: 91 residues processed: 256 average time/residue: 0.2991 time to fit residues: 114.6484 Evaluate side-chains 257 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 155 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET 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 48 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 120 SER Chi-restraints excluded: chain B residue 130 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 185 GLN Chi-restraints excluded: chain B residue 232 ILE 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 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 112 LYS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 142 ILE 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 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 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 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 155 ILE 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 73 GLU 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 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 310 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 114 optimal weight: 0.1980 chunk 118 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 264 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 = 0.3716 r_free = 0.3716 target = 0.097761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.070801 restraints weight = 39268.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073587 restraints weight = 17803.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075449 restraints weight = 11081.736| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3966 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= 0.143 Angle : 0.667 12.699 18619 Z= 0.318 Chirality : 0.042 0.145 2127 Planarity : 0.004 0.050 2349 Dihedral : 12.334 125.980 2099 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 7.88 % Allowed : 27.58 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1662 helix: 0.44 (0.18), residues: 861 sheet: -1.18 (0.42), residues: 173 loop : -0.98 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 220 HIS 0.002 0.000 HIS B 79 PHE 0.020 0.001 PHE D 154 TYR 0.008 0.001 TYR F 72 ARG 0.009 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 581) hydrogen bonds : angle 4.68686 ( 1665) covalent geometry : bond 0.00331 (13788) covalent geometry : angle 0.66659 (18619) Misc. bond : bond 0.00264 ( 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 276 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 160 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6922 (ttmm) REVERT: A 213 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7482 (mttp) REVERT: A 224 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: A 258 ASN cc_start: 0.7735 (t0) cc_final: 0.7148 (p0) REVERT: B 71 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7873 (tp30) REVERT: B 72 TYR cc_start: 0.8056 (m-10) cc_final: 0.7506 (m-10) REVERT: B 96 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7915 (pp) REVERT: B 153 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7827 (mmt90) REVERT: B 185 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: B 248 MET cc_start: 0.8779 (tpp) cc_final: 0.8006 (tpp) REVERT: B 275 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7720 (t0) REVERT: C 112 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8511 (mmtm) REVERT: C 248 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7771 (tpt) REVERT: D 47 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6289 (pp30) REVERT: D 96 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7771 (pp) REVERT: D 117 PHE cc_start: 0.8214 (m-80) cc_final: 0.7632 (m-80) REVERT: E 86 MET cc_start: 0.8194 (ptt) cc_final: 0.7929 (pmm) REVERT: E 217 MET cc_start: 0.8640 (mmp) cc_final: 0.8295 (mmm) REVERT: E 250 ARG cc_start: 0.6414 (OUTLIER) cc_final: 0.5936 (mpt90) REVERT: E 341 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8671 (mm-30) REVERT: F 85 ASN cc_start: 0.9504 (m110) cc_final: 0.9142 (m-40) REVERT: F 86 MET cc_start: 0.9109 (ptp) cc_final: 0.8344 (ptp) REVERT: F 87 HIS cc_start: 0.7690 (m90) cc_final: 0.6772 (t-170) REVERT: F 281 HIS cc_start: 0.8378 (m170) cc_final: 0.7440 (t70) REVERT: F 342 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7872 (tttp) REVERT: F 343 MET cc_start: 0.7901 (tpt) cc_final: 0.7654 (tpp) outliers start: 116 outliers final: 96 residues processed: 259 average time/residue: 0.2252 time to fit residues: 86.6773 Evaluate side-chains 263 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 154 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET 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 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 48 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 120 SER Chi-restraints excluded: chain B residue 130 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 185 GLN Chi-restraints excluded: chain B residue 232 ILE 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 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 112 LYS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 142 ILE 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 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 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 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 155 ILE Chi-restraints excluded: chain D residue 207 GLU 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 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 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 250 ARG 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 F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 25 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.098890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071754 restraints weight = 39110.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074584 restraints weight = 17780.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076465 restraints weight = 11079.668| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13789 Z= 0.126 Angle : 0.669 12.911 18619 Z= 0.318 Chirality : 0.042 0.172 2127 Planarity : 0.004 0.047 2349 Dihedral : 12.133 125.579 2099 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 8.15 % Allowed : 27.31 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1662 helix: 0.56 (0.18), residues: 860 sheet: -1.01 (0.42), residues: 172 loop : -0.90 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 166 HIS 0.003 0.000 HIS B 79 PHE 0.019 0.001 PHE C 197 TYR 0.017 0.001 TYR F 72 ARG 0.008 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 581) hydrogen bonds : angle 4.64740 ( 1665) covalent geometry : bond 0.00286 (13788) covalent geometry : angle 0.66898 (18619) Misc. bond : bond 0.00286 ( 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 286 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 166 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7954 (m-70) cc_final: 0.7743 (m-70) REVERT: A 224 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: A 258 ASN cc_start: 0.7771 (t0) cc_final: 0.7242 (p0) REVERT: B 71 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7839 (tp30) REVERT: B 72 TYR cc_start: 0.8007 (m-10) cc_final: 0.7411 (m-10) REVERT: B 96 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7876 (pp) REVERT: B 153 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7915 (mmt90) REVERT: B 185 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: B 248 MET cc_start: 0.8766 (tpp) cc_final: 0.7947 (tpp) REVERT: B 275 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7732 (t0) REVERT: C 53 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8793 (mmmt) REVERT: C 112 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8510 (mmtm) REVERT: C 248 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7743 (tpt) REVERT: D 96 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7610 (pp) REVERT: D 117 PHE cc_start: 0.8252 (m-80) cc_final: 0.7681 (m-80) REVERT: D 248 MET cc_start: 0.8586 (tpp) cc_final: 0.8370 (ttp) REVERT: E 73 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: E 86 MET cc_start: 0.8194 (ptt) cc_final: 0.7881 (pmm) REVERT: E 266 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8415 (tm-30) REVERT: E 341 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8665 (mm-30) REVERT: F 75 SER cc_start: 0.9133 (m) cc_final: 0.8567 (p) REVERT: F 85 ASN cc_start: 0.9421 (m110) cc_final: 0.9090 (m110) REVERT: F 87 HIS cc_start: 0.7605 (m90) cc_final: 0.6908 (t-170) REVERT: F 281 HIS cc_start: 0.8397 (m170) cc_final: 0.7520 (t70) REVERT: F 312 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7710 (ttp80) REVERT: F 316 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7209 (p0) REVERT: F 342 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7856 (tttp) REVERT: F 343 MET cc_start: 0.7923 (tpt) cc_final: 0.7668 (tpp) outliers start: 120 outliers final: 89 residues processed: 265 average time/residue: 0.2877 time to fit residues: 114.8497 Evaluate side-chains 258 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 156 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET 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 287 VAL 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 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 106 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 130 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 185 GLN 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 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 112 LYS 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 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 291 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 340 ILE 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 155 ILE 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 300 LYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 58 LEU 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 155 ILE 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 341 GLU Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 GLU 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 Chi-restraints excluded: chain F residue 316 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 41 optimal weight: 0.0370 chunk 157 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN F 79 HIS F 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.098266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.071015 restraints weight = 39008.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.073791 restraints weight = 17909.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075655 restraints weight = 11242.518| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13789 Z= 0.134 Angle : 0.682 12.817 18619 Z= 0.324 Chirality : 0.042 0.164 2127 Planarity : 0.004 0.046 2349 Dihedral : 11.922 126.318 2081 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 6.93 % Allowed : 28.74 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1662 helix: 0.56 (0.18), residues: 859 sheet: -0.93 (0.42), residues: 172 loop : -0.84 (0.27), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 166 HIS 0.002 0.000 HIS B 79 PHE 0.034 0.001 PHE C 197 TYR 0.020 0.001 TYR F 72 ARG 0.008 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 581) hydrogen bonds : angle 4.66948 ( 1665) covalent geometry : bond 0.00309 (13788) covalent geometry : angle 0.68180 (18619) Misc. bond : bond 0.00292 ( 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 265 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 163 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: A 258 ASN cc_start: 0.7746 (t0) cc_final: 0.7183 (p0) REVERT: A 343 MET cc_start: 0.3000 (OUTLIER) cc_final: 0.2525 (mmm) REVERT: B 71 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7900 (tp30) REVERT: B 72 TYR cc_start: 0.8064 (m-10) cc_final: 0.7537 (m-10) REVERT: B 96 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7900 (pp) REVERT: B 153 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7609 (mmt90) REVERT: B 185 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: B 248 MET cc_start: 0.8764 (tpp) cc_final: 0.7958 (tpp) REVERT: B 275 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.7686 (t0) REVERT: B 302 MET cc_start: 0.7897 (ttp) cc_final: 0.7524 (tmm) REVERT: C 53 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8759 (mmmt) REVERT: C 112 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8509 (mmtm) REVERT: C 248 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7727 (tpt) REVERT: D 96 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7684 (pp) REVERT: D 117 PHE cc_start: 0.8222 (m-80) cc_final: 0.7626 (m-80) REVERT: D 248 MET cc_start: 0.8613 (tpp) cc_final: 0.8373 (ttp) REVERT: E 73 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: E 86 MET cc_start: 0.8222 (ptt) cc_final: 0.7946 (pmm) REVERT: E 341 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8645 (mm-30) REVERT: F 72 TYR cc_start: 0.8652 (m-80) cc_final: 0.8298 (m-80) REVERT: F 281 HIS cc_start: 0.8411 (m170) cc_final: 0.7484 (t70) REVERT: F 312 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7650 (ttp80) REVERT: F 316 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7158 (p0) REVERT: F 342 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7853 (tttp) REVERT: F 343 MET cc_start: 0.7932 (tpt) cc_final: 0.7678 (tpp) outliers start: 102 outliers final: 83 residues processed: 246 average time/residue: 0.2283 time to fit residues: 84.7037 Evaluate side-chains 253 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 157 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET 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 287 VAL 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 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 106 THR 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 184 LEU Chi-restraints excluded: chain B residue 185 GLN 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 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 112 LYS 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 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 291 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 340 ILE 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 155 ILE 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 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 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE 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 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 F residue 129 VAL Chi-restraints excluded: chain F residue 149 GLU 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 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 301 GLU Chi-restraints excluded: chain F residue 316 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 48 optimal weight: 0.0470 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS F 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.098715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.071358 restraints weight = 39169.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074175 restraints weight = 17897.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.076049 restraints weight = 11199.766| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4406 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= 0.130 Angle : 0.683 13.150 18619 Z= 0.325 Chirality : 0.042 0.187 2127 Planarity : 0.004 0.045 2349 Dihedral : 11.791 126.268 2075 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 6.52 % Allowed : 29.21 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1662 helix: 0.60 (0.18), residues: 866 sheet: -0.89 (0.42), residues: 172 loop : -0.80 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 166 HIS 0.007 0.001 HIS F 79 PHE 0.034 0.001 PHE C 197 TYR 0.015 0.001 TYR F 72 ARG 0.008 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 581) hydrogen bonds : angle 4.64695 ( 1665) covalent geometry : bond 0.00299 (13788) covalent geometry : angle 0.68290 (18619) Misc. bond : bond 0.00299 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6212.16 seconds wall clock time: 115 minutes 8.74 seconds (6908.74 seconds total)