Starting phenix.real_space_refine on Tue Nov 18 07:47:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dw0_8922/11_2025/6dw0_8922.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dw0_8922/11_2025/6dw0_8922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dw0_8922/11_2025/6dw0_8922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dw0_8922/11_2025/6dw0_8922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dw0_8922/11_2025/6dw0_8922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dw0_8922/11_2025/6dw0_8922.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.073 sd= 2.932 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7643 2.51 5 N 1954 2.21 5 O 2269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11929 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2221 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 11, 'TRANS': 287} Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 7, 'GLN:plan1': 3, 'HIS:plan': 1, 'TRP:plan': 3, 'TYR:plan': 5, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 159 Chain: "C" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2260 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 12, 'TRANS': 283} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4, 'PHE:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 2, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2229 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 12, 'TRANS': 283} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 7, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 129 Chain: "E" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2459 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 6, 'PHE:plan': 6, 'GLN:plan1': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2472 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 4, 'TYR:plan': 3, 'TRP:plan': 3, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 110 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'ABU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.43, per 1000 atoms: 0.29 Number of scatterers: 11929 At special positions: 0 Unit cell: (131.098, 97.35, 92.158, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2269 8.00 N 1954 7.00 C 7643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG F 1 " - " ASN C 110 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN E 149 " " NAG I 1 " - " ASN E 80 " " NAG J 1 " - " ASN B 149 " " NAG K 1 " - " ASN B 80 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 594.5 milliseconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2908 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 19 sheets defined 34.9% alpha, 39.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 233 through 257 removed outlier: 4.092A pdb=" N ILE D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN D 239 " --> pdb=" O TYR D 235 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Proline residue: D 243 - end of helix removed outlier: 3.586A pdb=" N LEU D 246 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 248 " --> pdb=" O CYS D 244 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL D 249 " --> pdb=" O THR D 245 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 284 removed outlier: 3.932A pdb=" N ARG D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR D 266 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER D 267 " --> pdb=" O PRO D 263 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR D 278 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER D 280 " --> pdb=" O MET D 276 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 320 removed outlier: 3.548A pdb=" N VAL D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYS D 303 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 319 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE D 320 " --> pdb=" O THR D 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.528A pdb=" N LEU C 74 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 75' Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.504A pdb=" N ALA C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 176 Processing helix chain 'C' and resid 222 through 244 removed outlier: 4.470A pdb=" N THR C 229 " --> pdb=" O PHE C 225 " (cutoff:3.500A) Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 251 through 274 removed outlier: 3.845A pdb=" N THR C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 256 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR C 260 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 307 removed outlier: 3.652A pdb=" N TRP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 296 " --> pdb=" O CYS C 292 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 297 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.808A pdb=" N ARG A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.811A pdb=" N LYS A 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.572A pdb=" N ALA A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.924A pdb=" N VAL A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 240 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 250 through 276 removed outlier: 3.827A pdb=" N ARG A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 307 removed outlier: 3.724A pdb=" N VAL A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 21 removed outlier: 3.650A pdb=" N THR E 15 " --> pdb=" O TYR E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 73 removed outlier: 3.907A pdb=" N SER E 73 " --> pdb=" O LYS E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.623A pdb=" N VAL E 87 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA E 88 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 217 through 242 removed outlier: 4.339A pdb=" N PHE E 221 " --> pdb=" O ASN E 217 " (cutoff:3.500A) Proline residue: E 228 - end of helix removed outlier: 4.405A pdb=" N LEU E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.594A pdb=" N ARG E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 258 " --> pdb=" O GLY E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 302 removed outlier: 4.357A pdb=" N TYR E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 302 " --> pdb=" O GLU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 345 removed outlier: 3.766A pdb=" N PHE E 328 " --> pdb=" O SER E 324 " (cutoff:3.500A) Proline residue: E 329 - end of helix removed outlier: 3.580A pdb=" N HIS E 345 " --> pdb=" O LEU E 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 21 removed outlier: 3.528A pdb=" N THR B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 242 removed outlier: 3.556A pdb=" N TYR B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix removed outlier: 3.687A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.603A pdb=" N ARG B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 272 removed outlier: 3.780A pdb=" N THR B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.762A pdb=" N PHE B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 345 Proline residue: B 329 - end of helix Processing sheet with id=AA1, first strand: chain 'D' and resid 95 through 98 removed outlier: 3.529A pdb=" N ILE D 133 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 131 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU D 71 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL D 65 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR D 73 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE D 77 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL D 59 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA D 79 " --> pdb=" O MET D 57 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N MET D 57 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR D 81 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR D 55 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 95 through 98 removed outlier: 3.529A pdb=" N ILE D 133 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 131 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU D 71 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL D 65 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR D 73 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE D 77 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL D 59 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA D 79 " --> pdb=" O MET D 57 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N MET D 57 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR D 81 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR D 55 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AA4, first strand: chain 'D' and resid 202 through 214 removed outlier: 5.199A pdb=" N PHE D 203 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER D 230 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG D 207 " --> pdb=" O TYR D 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 107 through 108 removed outlier: 7.192A pdb=" N GLU C 58 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C 60 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N PHE C 49 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP C 62 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 108 removed outlier: 7.192A pdb=" N GLU C 58 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C 60 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N PHE C 49 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP C 62 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N VAL C 179 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE C 44 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 85 removed outlier: 4.121A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.781A pdb=" N GLY C 194 " --> pdb=" O HIS C 217 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS C 219 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU C 192 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AB1, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.804A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 129 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 105 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.804A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 129 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP A 62 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS A 70 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 39 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.191A pdb=" N SER A 158 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 210 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.191A pdb=" N SER A 158 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 210 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 209 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 194 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS A 219 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 192 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.719A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS E 68 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP E 37 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 106 removed outlier: 5.877A pdb=" N ASP E 101 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ALA E 135 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS E 103 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS E 68 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP E 37 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 176 " --> pdb=" O ILE E 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.980A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS E 192 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG E 213 " --> pdb=" O ASP E 190 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.293A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS B 68 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP B 37 " --> pdb=" O LYS B 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.447A pdb=" N ASP B 101 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA B 135 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 103 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS B 68 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP B 37 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR B 176 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 42 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 98 removed outlier: 4.971A pdb=" N ASP B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1755 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: 2.12 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3599 1.34 - 1.46: 2329 1.46 - 1.58: 6138 1.58 - 1.69: 1 1.69 - 1.81: 109 Bond restraints: 12176 Sorted by residual: bond pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " ideal model delta sigma weight residual 1.524 1.576 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C TYR B 143 " pdb=" N PRO B 144 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.49e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 bond pdb=" C5 MAN G 6 " pdb=" O5 MAN G 6 " ideal model delta sigma weight residual 1.418 1.460 -0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.88e+00 ... (remaining 12171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 16212 2.56 - 5.12: 326 5.12 - 7.68: 59 7.68 - 10.24: 16 10.24 - 12.80: 1 Bond angle restraints: 16614 Sorted by residual: angle pdb=" C MET A 111 " pdb=" N THR A 112 " pdb=" CA THR A 112 " ideal model delta sigma weight residual 121.54 131.44 -9.90 1.91e+00 2.74e-01 2.69e+01 angle pdb=" C ALA D 261 " pdb=" N VAL D 262 " pdb=" CA VAL D 262 " ideal model delta sigma weight residual 120.24 123.33 -3.09 6.30e-01 2.52e+00 2.40e+01 angle pdb=" N VAL A 251 " pdb=" CA VAL A 251 " pdb=" C VAL A 251 " ideal model delta sigma weight residual 108.88 118.87 -9.99 2.16e+00 2.14e-01 2.14e+01 angle pdb=" N GLY A 34 " pdb=" CA GLY A 34 " pdb=" C GLY A 34 " ideal model delta sigma weight residual 115.72 108.83 6.89 1.51e+00 4.39e-01 2.08e+01 angle pdb=" N GLY C 223 " pdb=" CA GLY C 223 " pdb=" C GLY C 223 " ideal model delta sigma weight residual 113.18 122.41 -9.23 2.37e+00 1.78e-01 1.52e+01 ... (remaining 16609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 7180 23.94 - 47.88: 200 47.88 - 71.81: 31 71.81 - 95.75: 39 95.75 - 119.69: 44 Dihedral angle restraints: 7494 sinusoidal: 3000 harmonic: 4494 Sorted by residual: dihedral pdb=" CA THR D 126 " pdb=" C THR D 126 " pdb=" N PRO D 127 " pdb=" CA PRO D 127 " ideal model delta harmonic sigma weight residual -180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 48.69 44.31 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 136.97 -43.97 1 1.00e+01 1.00e-02 2.69e+01 ... (remaining 7491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1718 0.070 - 0.141: 297 0.141 - 0.211: 35 0.211 - 0.281: 3 0.281 - 0.351: 5 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CB ILE C 222 " pdb=" CA ILE C 222 " pdb=" CG1 ILE C 222 " pdb=" CG2 ILE C 222 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 110 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 2055 not shown) Planarity restraints: 2052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 227 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO E 228 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 228 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 228 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 142 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C ARG B 142 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG B 142 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR B 143 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 145 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO C 146 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.029 5.00e-02 4.00e+02 ... (remaining 2049 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3275 2.81 - 3.33: 10706 3.33 - 3.85: 19816 3.85 - 4.38: 21669 4.38 - 4.90: 37554 Nonbonded interactions: 93020 Sorted by model distance: nonbonded pdb=" OG SER E 73 " pdb=" O PRO E 120 " model vdw 2.282 3.040 nonbonded pdb=" O GLY C 258 " pdb=" OG1 THR C 261 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR E 151 " pdb=" OE2 GLU E 153 " model vdw 2.304 3.040 nonbonded pdb=" O GLY E 254 " pdb=" OG1 THR E 257 " model vdw 2.306 3.040 nonbonded pdb=" OG SER C 68 " pdb=" O LEU C 126 " model vdw 2.308 3.040 ... (remaining 93015 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 12 through 70 or (resid 71 through 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 through 76 or (resid 77 and (na \ me N or name CA or name C or name O or name CB )) or resid 78 through 79 or (res \ id 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 through 227 or (resid 228 and (name N or name CA or name C or name O \ or name CB )) or resid 229 through 233 or (resid 234 through 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 through 237 or (resid 238 \ and (name N or name CA or name C or name O or name CB )) or resid 239 through 2 \ 40 or (resid 241 through 242 and (name N or name CA or name C or name O or name \ CB )) or resid 243 or (resid 244 through 249 and (name N or name CA or name C or \ name O or name CB )) or resid 250 or (resid 251 and (name N or name CA or name \ C or name O or name CB )) or resid 252 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 307)) selection = (chain 'C' and (resid 12 through 34 or (resid 35 through 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 86 or (res \ id 87 and (name N or name CA or name C or name O or name CB )) or resid 88 throu \ gh 164 or (resid 165 and (name N or name CA or name C or name O or name CB )) or \ resid 166 through 175 or (resid 176 and (name N or name CA or name C or name O \ or name CB )) or resid 177 or (resid 178 and (name N or name CA or name C or nam \ e O or name CB )) or resid 179 through 260 or (resid 261 and (name N or name CA \ or name C or name O or name CB )) or resid 262 through 272 or (resid 273 through \ 274 and (name N or name CA or name C or name O or name CB )) or resid 275 throu \ gh 277 or (resid 278 and (name N or name CA or name C or name O or name CB )) or \ resid 279 through 280 or (resid 281 through 282 and (name N or name CA or name \ C or name O or name CB )) or resid 283 through 285 or (resid 286 and (name N or \ name CA or name C or name O or name CB )) or resid 287 or (resid 288 and (name N \ or name CA or name C or name O or name CB )) or resid 289 through 291 or (resid \ 292 through 295 and (name N or name CA or name C or name O or name CB )) or res \ id 296 or (resid 297 and (name N or name CA or name C or name O or name CB )) or \ resid 298 through 302 or (resid 303 through 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 307)) } ncs_group { reference = (chain 'B' and (resid 10 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 191 or (resid 192 and (name N or n \ ame CA or name C or name O or name CB )) or resid 193 through 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 21 \ 9 or (resid 220 through 221 and (name N or name CA or name C or name O or name C \ B )) or resid 222 through 223 or (resid 224 and (name N or name CA or name C or \ name O or name CB )) or resid 225 through 229 or (resid 230 and (name N or name \ CA or name C or name O or name CB )) or resid 231 through 234 or (resid 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 240 or \ (resid 241 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 2 through 243 or (resid 244 and (name N or name CA or name C or name O or name C \ B )) or resid 245 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 276 or (resid 277 and (name N or name \ CA or name C or name O or name CB )) or resid 278 through 290 or (resid 291 and \ (name N or name CA or name C or name O or name CB )) or resid 292 or (resid 293 \ and (name N or name CA or name C or name O or name CB )) or resid 294 through 34 \ 5)) selection = (chain 'E' and (resid 10 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 29 or (resid 30 and (name N or nam \ e CA or name C or name O or name CB )) or resid 31 through 138 or (resid 139 and \ (name N or name CA or name C or name O or name CB )) or resid 140 or (resid 141 \ and (name N or name CA or name C or name O or name CB )) or resid 142 through 2 \ 26 or (resid 227 and (name N or name CA or name C or name O or name CB )) or res \ id 228 through 252 or (resid 253 and (name N or name CA or name C or name O or n \ ame CB )) or resid 254 through 285 or (resid 286 and (name N or name CA or name \ C or name O or name CB )) or resid 287 through 320 or (resid 321 and (name N or \ name CA or name C or name O or name CB )) or resid 322 or (resid 323 and (name N \ or name CA or name C or name O or name CB )) or resid 324 or (resid 325 through \ 329 and (name N or name CA or name C or name O or name CB )) or resid 330 throu \ gh 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) or \ resid 333 through 345)) } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.950 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 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 : 0.005 0.055 12202 Z= 0.243 Angle : 0.984 12.802 16687 Z= 0.506 Chirality : 0.055 0.351 2058 Planarity : 0.006 0.058 2046 Dihedral : 16.587 119.691 4571 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.18), residues: 1515 helix: -2.78 (0.16), residues: 455 sheet: -2.19 (0.23), residues: 428 loop : -2.68 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 186 TYR 0.026 0.002 TYR E 342 PHE 0.023 0.002 PHE D 113 TRP 0.031 0.003 TRP C 94 HIS 0.012 0.002 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00497 (12176) covalent geometry : angle 0.97378 (16614) SS BOND : bond 0.00182 ( 5) SS BOND : angle 2.10957 ( 10) hydrogen bonds : bond 0.18347 ( 517) hydrogen bonds : angle 7.57764 ( 1755) link_ALPHA1-2 : bond 0.00428 ( 1) link_ALPHA1-2 : angle 2.38432 ( 3) link_ALPHA1-3 : bond 0.00409 ( 3) link_ALPHA1-3 : angle 2.06838 ( 9) link_ALPHA1-6 : bond 0.00032 ( 1) link_ALPHA1-6 : angle 1.59175 ( 3) link_BETA1-4 : bond 0.00647 ( 10) link_BETA1-4 : angle 2.26957 ( 30) link_NAG-ASN : bond 0.00376 ( 6) link_NAG-ASN : angle 2.86193 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 788 time to evaluate : 0.471 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 ASN cc_start: 0.9371 (m-40) cc_final: 0.9157 (t0) REVERT: D 36 GLU cc_start: 0.8550 (pm20) cc_final: 0.8293 (pm20) REVERT: D 39 ASP cc_start: 0.9072 (t0) cc_final: 0.8666 (t70) REVERT: D 40 ASN cc_start: 0.8362 (m-40) cc_final: 0.7013 (m-40) REVERT: D 51 THR cc_start: 0.9476 (m) cc_final: 0.8992 (p) REVERT: D 54 HIS cc_start: 0.8977 (m-70) cc_final: 0.8518 (m-70) REVERT: D 57 MET cc_start: 0.9152 (ptp) cc_final: 0.8949 (ptp) REVERT: D 58 TYR cc_start: 0.8678 (t80) cc_final: 0.8285 (t80) REVERT: D 60 ASN cc_start: 0.9258 (t0) cc_final: 0.8807 (m110) REVERT: D 90 ASN cc_start: 0.7174 (t0) cc_final: 0.6472 (p0) REVERT: D 101 ASN cc_start: 0.8345 (m110) cc_final: 0.7703 (t0) REVERT: D 105 LYS cc_start: 0.9133 (mttt) cc_final: 0.8748 (mttp) REVERT: D 107 TRP cc_start: 0.8892 (t60) cc_final: 0.8563 (t60) REVERT: D 110 ASP cc_start: 0.8483 (t70) cc_final: 0.7523 (t70) REVERT: D 112 PHE cc_start: 0.8003 (p90) cc_final: 0.7086 (p90) REVERT: D 122 HIS cc_start: 0.8561 (m-70) cc_final: 0.7595 (m90) REVERT: D 138 ARG cc_start: 0.8926 (ttp-170) cc_final: 0.8095 (ttp80) REVERT: D 144 ARG cc_start: 0.8550 (tmm-80) cc_final: 0.7358 (tmm-80) REVERT: D 161 ASP cc_start: 0.8389 (m-30) cc_final: 0.8159 (m-30) REVERT: D 172 TYR cc_start: 0.7225 (t80) cc_final: 0.6852 (t80) REVERT: D 182 GLN cc_start: 0.8483 (tp40) cc_final: 0.8100 (tp-100) REVERT: D 222 VAL cc_start: 0.9486 (t) cc_final: 0.9067 (m) REVERT: C 13 VAL cc_start: 0.9429 (t) cc_final: 0.9053 (m) REVERT: C 58 GLU cc_start: 0.8104 (pp20) cc_final: 0.7851 (pp20) REVERT: C 113 MET cc_start: 0.8524 (mmm) cc_final: 0.8075 (mmm) REVERT: C 119 ARG cc_start: 0.9221 (mtt180) cc_final: 0.8854 (mtt90) REVERT: C 122 GLU cc_start: 0.8822 (pt0) cc_final: 0.8561 (pt0) REVERT: C 128 TYR cc_start: 0.8145 (t80) cc_final: 0.7888 (t80) REVERT: C 144 ASP cc_start: 0.8315 (t0) cc_final: 0.8052 (t70) REVERT: C 165 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7923 (mp0) REVERT: C 170 TRP cc_start: 0.8579 (m100) cc_final: 0.8065 (m100) REVERT: C 173 GLU cc_start: 0.8355 (mp0) cc_final: 0.8143 (mp0) REVERT: C 191 ASP cc_start: 0.8722 (m-30) cc_final: 0.8458 (m-30) REVERT: C 196 THR cc_start: 0.8396 (m) cc_final: 0.8067 (p) REVERT: C 217 HIS cc_start: 0.9040 (m-70) cc_final: 0.8837 (m90) REVERT: A 20 ARG cc_start: 0.8961 (mtt90) cc_final: 0.8651 (ttm110) REVERT: A 30 ARG cc_start: 0.8161 (ptt90) cc_final: 0.7546 (ptt90) REVERT: A 52 VAL cc_start: 0.8841 (m) cc_final: 0.8540 (p) REVERT: A 54 ASP cc_start: 0.8429 (m-30) cc_final: 0.7814 (m-30) REVERT: A 57 MET cc_start: 0.8998 (ttm) cc_final: 0.8199 (ttm) REVERT: A 89 MET cc_start: 0.8875 (tpp) cc_final: 0.8646 (tpp) REVERT: A 105 LYS cc_start: 0.8631 (tptt) cc_final: 0.8395 (pttp) REVERT: A 109 HIS cc_start: 0.8695 (m-70) cc_final: 0.8369 (m170) REVERT: A 113 MET cc_start: 0.8794 (mmm) cc_final: 0.8349 (mmm) REVERT: A 114 PRO cc_start: 0.9223 (Cg_exo) cc_final: 0.8995 (Cg_endo) REVERT: A 140 MET cc_start: 0.9184 (mpp) cc_final: 0.8408 (mpp) REVERT: A 144 ASP cc_start: 0.8510 (p0) cc_final: 0.8045 (p0) REVERT: A 150 HIS cc_start: 0.8091 (m-70) cc_final: 0.7752 (m90) REVERT: A 245 TRP cc_start: 0.7599 (m100) cc_final: 0.7000 (m100) REVERT: E 21 LYS cc_start: 0.9136 (tmtm) cc_final: 0.8906 (tmtt) REVERT: E 44 VAL cc_start: 0.9583 (t) cc_final: 0.9378 (p) REVERT: E 54 ASN cc_start: 0.9417 (m110) cc_final: 0.9200 (m-40) REVERT: E 55 MET cc_start: 0.9186 (mtt) cc_final: 0.8810 (mtt) REVERT: E 64 GLN cc_start: 0.9082 (tt0) cc_final: 0.8662 (tp40) REVERT: E 69 ASP cc_start: 0.8911 (t0) cc_final: 0.8645 (t0) REVERT: E 81 LEU cc_start: 0.9322 (mt) cc_final: 0.9042 (mt) REVERT: E 90 GLN cc_start: 0.8945 (mt0) cc_final: 0.8408 (mt0) REVERT: E 93 VAL cc_start: 0.9627 (m) cc_final: 0.9093 (m) REVERT: E 101 ASP cc_start: 0.8287 (p0) cc_final: 0.7824 (p0) REVERT: E 126 TYR cc_start: 0.8787 (t80) cc_final: 0.8184 (t80) REVERT: E 167 TYR cc_start: 0.8570 (p90) cc_final: 0.8352 (p90) REVERT: E 169 ASN cc_start: 0.9028 (t0) cc_final: 0.8461 (t0) REVERT: E 175 VAL cc_start: 0.9280 (t) cc_final: 0.9062 (t) REVERT: E 181 ILE cc_start: 0.9252 (mm) cc_final: 0.8969 (mm) REVERT: E 191 TYR cc_start: 0.8987 (p90) cc_final: 0.8465 (p90) REVERT: E 210 LEU cc_start: 0.9321 (tp) cc_final: 0.8678 (tp) REVERT: E 213 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.7710 (ptp-110) REVERT: E 264 ILE cc_start: 0.9287 (mm) cc_final: 0.9038 (mm) REVERT: E 342 TYR cc_start: 0.8231 (m-80) cc_final: 0.7856 (m-80) REVERT: B 13 LYS cc_start: 0.8949 (tttm) cc_final: 0.8537 (ttmt) REVERT: B 15 THR cc_start: 0.9605 (p) cc_final: 0.9393 (p) REVERT: B 17 ASP cc_start: 0.9369 (m-30) cc_final: 0.9024 (m-30) REVERT: B 37 ASP cc_start: 0.8712 (p0) cc_final: 0.8389 (p0) REVERT: B 55 MET cc_start: 0.9091 (mmp) cc_final: 0.8625 (mmm) REVERT: B 63 PHE cc_start: 0.9055 (t80) cc_final: 0.8463 (t80) REVERT: B 65 GLN cc_start: 0.9077 (pt0) cc_final: 0.8697 (pt0) REVERT: B 66 SER cc_start: 0.9553 (p) cc_final: 0.9293 (t) REVERT: B 96 THR cc_start: 0.9609 (m) cc_final: 0.9354 (p) REVERT: B 114 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7815 (mtm180) REVERT: B 125 LEU cc_start: 0.9120 (tp) cc_final: 0.8862 (tp) REVERT: B 133 THR cc_start: 0.8963 (m) cc_final: 0.8583 (p) REVERT: B 147 GLU cc_start: 0.8820 (tt0) cc_final: 0.8446 (tp30) REVERT: B 151 THR cc_start: 0.8347 (p) cc_final: 0.7992 (p) REVERT: B 167 TYR cc_start: 0.8509 (p90) cc_final: 0.8115 (p90) REVERT: B 169 ASN cc_start: 0.8912 (t0) cc_final: 0.8037 (t0) REVERT: B 198 VAL cc_start: 0.9599 (t) cc_final: 0.9302 (m) REVERT: B 209 SER cc_start: 0.9186 (t) cc_final: 0.8878 (t) REVERT: B 213 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7537 (mtm180) REVERT: B 216 ARG cc_start: 0.8903 (ttm-80) cc_final: 0.8589 (mtm180) outliers start: 1 outliers final: 0 residues processed: 788 average time/residue: 0.1245 time to fit residues: 136.0278 Evaluate side-chains 649 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 649 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0040 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 GLN D 122 HIS D 258 ASN C 115 ASN C 307 ASN A 27 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.158956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118902 restraints weight = 21772.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123835 restraints weight = 12036.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127174 restraints weight = 7901.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129485 restraints weight = 5805.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131061 restraints weight = 4631.872| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12202 Z= 0.143 Angle : 0.802 12.691 16687 Z= 0.389 Chirality : 0.048 0.249 2058 Planarity : 0.005 0.055 2046 Dihedral : 15.015 101.622 2087 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.42 % Allowed : 20.39 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.20), residues: 1515 helix: -1.37 (0.21), residues: 453 sheet: -1.75 (0.24), residues: 427 loop : -2.20 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 186 TYR 0.020 0.002 TYR A 59 PHE 0.036 0.002 PHE B 221 TRP 0.014 0.002 TRP B 168 HIS 0.007 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00305 (12176) covalent geometry : angle 0.79052 (16614) SS BOND : bond 0.00546 ( 5) SS BOND : angle 1.86185 ( 10) hydrogen bonds : bond 0.04589 ( 517) hydrogen bonds : angle 5.64998 ( 1755) link_ALPHA1-2 : bond 0.00533 ( 1) link_ALPHA1-2 : angle 1.87758 ( 3) link_ALPHA1-3 : bond 0.00635 ( 3) link_ALPHA1-3 : angle 1.76776 ( 9) link_ALPHA1-6 : bond 0.00476 ( 1) link_ALPHA1-6 : angle 2.82885 ( 3) link_BETA1-4 : bond 0.00526 ( 10) link_BETA1-4 : angle 2.54958 ( 30) link_NAG-ASN : bond 0.00418 ( 6) link_NAG-ASN : angle 1.95622 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 687 time to evaluate : 0.453 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 ASN cc_start: 0.9516 (m-40) cc_final: 0.9109 (m110) REVERT: D 39 ASP cc_start: 0.9157 (t0) cc_final: 0.8667 (t70) REVERT: D 40 ASN cc_start: 0.8739 (m-40) cc_final: 0.8487 (m-40) REVERT: D 51 THR cc_start: 0.9275 (m) cc_final: 0.9030 (p) REVERT: D 54 HIS cc_start: 0.8934 (m-70) cc_final: 0.8614 (m-70) REVERT: D 82 TRP cc_start: 0.9223 (p90) cc_final: 0.8996 (p90) REVERT: D 88 LYS cc_start: 0.9105 (mttt) cc_final: 0.8896 (mtmm) REVERT: D 90 ASN cc_start: 0.7401 (t0) cc_final: 0.6631 (p0) REVERT: D 101 ASN cc_start: 0.8465 (m110) cc_final: 0.7787 (t0) REVERT: D 107 TRP cc_start: 0.8971 (t60) cc_final: 0.8714 (t60) REVERT: D 110 ASP cc_start: 0.8761 (t70) cc_final: 0.8433 (t70) REVERT: D 113 PHE cc_start: 0.9062 (m-80) cc_final: 0.8781 (m-10) REVERT: D 115 ASN cc_start: 0.8130 (p0) cc_final: 0.7454 (p0) REVERT: D 122 HIS cc_start: 0.8345 (m90) cc_final: 0.7590 (m90) REVERT: D 138 ARG cc_start: 0.8841 (ttp-170) cc_final: 0.8250 (ttp80) REVERT: D 144 ARG cc_start: 0.8337 (tmm-80) cc_final: 0.7189 (tmm-80) REVERT: D 172 TYR cc_start: 0.7274 (t80) cc_final: 0.6513 (t80) REVERT: D 239 GLN cc_start: 0.8838 (mt0) cc_final: 0.8434 (pt0) REVERT: C 25 TYR cc_start: 0.8315 (t80) cc_final: 0.8066 (t80) REVERT: C 58 GLU cc_start: 0.8011 (pp20) cc_final: 0.7749 (pp20) REVERT: C 70 LYS cc_start: 0.8060 (tmtm) cc_final: 0.7848 (tmtm) REVERT: C 97 ASP cc_start: 0.8574 (p0) cc_final: 0.8213 (p0) REVERT: C 113 MET cc_start: 0.8631 (mmm) cc_final: 0.8144 (mmm) REVERT: C 144 ASP cc_start: 0.8305 (t0) cc_final: 0.7955 (t70) REVERT: C 219 LYS cc_start: 0.8809 (tmtm) cc_final: 0.8480 (tptt) REVERT: A 70 LYS cc_start: 0.8568 (tmmt) cc_final: 0.8352 (tmmt) REVERT: A 105 LYS cc_start: 0.8500 (tptt) cc_final: 0.8224 (pttp) REVERT: A 107 VAL cc_start: 0.7870 (m) cc_final: 0.7658 (p) REVERT: A 109 HIS cc_start: 0.8524 (m-70) cc_final: 0.8306 (m90) REVERT: A 113 MET cc_start: 0.8716 (mmm) cc_final: 0.8286 (mmm) REVERT: A 130 MET cc_start: 0.8439 (ptp) cc_final: 0.8235 (ptp) REVERT: A 144 ASP cc_start: 0.8214 (p0) cc_final: 0.7636 (p0) REVERT: A 150 HIS cc_start: 0.7757 (m-70) cc_final: 0.7480 (m90) REVERT: A 189 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: A 190 TYR cc_start: 0.8753 (m-10) cc_final: 0.8436 (m-10) REVERT: A 216 PHE cc_start: 0.8842 (m-10) cc_final: 0.8476 (m-10) REVERT: A 245 TRP cc_start: 0.7467 (m100) cc_final: 0.6880 (m100) REVERT: E 21 LYS cc_start: 0.9075 (tmtm) cc_final: 0.8706 (pptt) REVERT: E 44 VAL cc_start: 0.9433 (t) cc_final: 0.9121 (p) REVERT: E 53 VAL cc_start: 0.9673 (t) cc_final: 0.9366 (p) REVERT: E 57 TYR cc_start: 0.8738 (p90) cc_final: 0.8531 (p90) REVERT: E 64 GLN cc_start: 0.9081 (tt0) cc_final: 0.8629 (tt0) REVERT: E 68 LYS cc_start: 0.9310 (mmmm) cc_final: 0.9036 (mmmm) REVERT: E 69 ASP cc_start: 0.8727 (t0) cc_final: 0.8432 (t0) REVERT: E 81 LEU cc_start: 0.9126 (mt) cc_final: 0.8729 (mt) REVERT: E 112 LYS cc_start: 0.9142 (ttmm) cc_final: 0.8788 (ttmm) REVERT: E 133 THR cc_start: 0.9079 (m) cc_final: 0.8690 (p) REVERT: E 169 ASN cc_start: 0.8930 (t0) cc_final: 0.8554 (t0) REVERT: E 180 LYS cc_start: 0.9545 (mtpp) cc_final: 0.9151 (mppt) REVERT: E 191 TYR cc_start: 0.8768 (p90) cc_final: 0.8466 (p90) REVERT: B 13 LYS cc_start: 0.9075 (tttm) cc_final: 0.8772 (ttmt) REVERT: B 17 ASP cc_start: 0.9268 (m-30) cc_final: 0.9010 (m-30) REVERT: B 41 ARG cc_start: 0.8637 (mtt90) cc_final: 0.7777 (mtt90) REVERT: B 55 MET cc_start: 0.9083 (mmp) cc_final: 0.8826 (tpp) REVERT: B 61 MET cc_start: 0.8056 (ppp) cc_final: 0.7450 (ppp) REVERT: B 63 PHE cc_start: 0.8977 (t80) cc_final: 0.8759 (t80) REVERT: B 89 ASP cc_start: 0.8772 (m-30) cc_final: 0.8507 (m-30) REVERT: B 133 THR cc_start: 0.9020 (m) cc_final: 0.8698 (p) REVERT: B 147 GLU cc_start: 0.8664 (tt0) cc_final: 0.8375 (tp30) REVERT: B 148 GLN cc_start: 0.8056 (mm110) cc_final: 0.7607 (mm110) REVERT: B 151 THR cc_start: 0.8481 (p) cc_final: 0.8093 (p) REVERT: B 153 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8652 (mm-30) REVERT: B 168 TRP cc_start: 0.8144 (m-90) cc_final: 0.7905 (m-10) REVERT: B 192 LYS cc_start: 0.8625 (mmmt) cc_final: 0.7968 (mmmm) REVERT: B 209 SER cc_start: 0.8938 (t) cc_final: 0.8313 (t) REVERT: B 213 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7638 (mtm180) REVERT: B 247 SER cc_start: 0.9022 (p) cc_final: 0.8804 (t) outliers start: 54 outliers final: 35 residues processed: 700 average time/residue: 0.1129 time to fit residues: 111.7087 Evaluate side-chains 683 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 647 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 134 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116184 restraints weight = 22348.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121010 restraints weight = 12436.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.124281 restraints weight = 8171.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126517 restraints weight = 5990.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127981 restraints weight = 4788.307| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12202 Z= 0.174 Angle : 0.805 10.580 16687 Z= 0.392 Chirality : 0.048 0.223 2058 Planarity : 0.005 0.068 2046 Dihedral : 11.586 86.627 2087 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.65 % Allowed : 24.24 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.20), residues: 1515 helix: -0.76 (0.22), residues: 459 sheet: -1.44 (0.24), residues: 429 loop : -2.05 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 132 TYR 0.024 0.002 TYR E 126 PHE 0.018 0.002 PHE C 297 TRP 0.015 0.001 TRP B 92 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00377 (12176) covalent geometry : angle 0.79110 (16614) SS BOND : bond 0.00519 ( 5) SS BOND : angle 3.00443 ( 10) hydrogen bonds : bond 0.04111 ( 517) hydrogen bonds : angle 5.38304 ( 1755) link_ALPHA1-2 : bond 0.00577 ( 1) link_ALPHA1-2 : angle 2.66426 ( 3) link_ALPHA1-3 : bond 0.00662 ( 3) link_ALPHA1-3 : angle 1.63918 ( 9) link_ALPHA1-6 : bond 0.00790 ( 1) link_ALPHA1-6 : angle 3.40173 ( 3) link_BETA1-4 : bond 0.00445 ( 10) link_BETA1-4 : angle 2.48882 ( 30) link_NAG-ASN : bond 0.00284 ( 6) link_NAG-ASN : angle 1.94498 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 660 time to evaluate : 0.466 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9175 (t0) cc_final: 0.8728 (t70) REVERT: D 40 ASN cc_start: 0.8576 (m-40) cc_final: 0.8315 (m-40) REVERT: D 51 THR cc_start: 0.9349 (m) cc_final: 0.9099 (p) REVERT: D 54 HIS cc_start: 0.8933 (m-70) cc_final: 0.8655 (m-70) REVERT: D 88 LYS cc_start: 0.9078 (mttt) cc_final: 0.8848 (mtmm) REVERT: D 90 ASN cc_start: 0.7358 (t0) cc_final: 0.6665 (p0) REVERT: D 97 ARG cc_start: 0.9104 (mmt90) cc_final: 0.7955 (mtm-85) REVERT: D 101 ASN cc_start: 0.8459 (m110) cc_final: 0.7831 (t0) REVERT: D 110 ASP cc_start: 0.8957 (t70) cc_final: 0.8703 (t70) REVERT: D 115 ASN cc_start: 0.8043 (p0) cc_final: 0.7476 (p0) REVERT: D 138 ARG cc_start: 0.8728 (ttp-170) cc_final: 0.8073 (ttp80) REVERT: D 148 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7859 (p0) REVERT: D 164 SER cc_start: 0.8653 (p) cc_final: 0.8430 (t) REVERT: D 172 TYR cc_start: 0.7370 (t80) cc_final: 0.6644 (t80) REVERT: D 182 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8117 (mm-40) REVERT: D 207 ARG cc_start: 0.8623 (ptt90) cc_final: 0.8334 (ptt90) REVERT: D 214 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8621 (tppt) REVERT: D 239 GLN cc_start: 0.8681 (mt0) cc_final: 0.8214 (pt0) REVERT: C 25 TYR cc_start: 0.8456 (t80) cc_final: 0.7942 (t80) REVERT: C 58 GLU cc_start: 0.8176 (pp20) cc_final: 0.7837 (pp20) REVERT: C 70 LYS cc_start: 0.8130 (tmtm) cc_final: 0.7788 (tmtm) REVERT: C 97 ASP cc_start: 0.8606 (p0) cc_final: 0.8197 (p0) REVERT: C 144 ASP cc_start: 0.8396 (t0) cc_final: 0.8108 (t70) REVERT: C 165 GLU cc_start: 0.8820 (mm-30) cc_final: 0.7670 (mp0) REVERT: C 289 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8770 (pp) REVERT: A 47 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9080 (p) REVERT: A 70 LYS cc_start: 0.8620 (tmmt) cc_final: 0.8330 (tmmt) REVERT: A 94 TRP cc_start: 0.9320 (t60) cc_final: 0.8741 (t60) REVERT: A 102 ASN cc_start: 0.7836 (t0) cc_final: 0.7535 (t0) REVERT: A 105 LYS cc_start: 0.8646 (tptt) cc_final: 0.8371 (pttm) REVERT: A 107 VAL cc_start: 0.7955 (m) cc_final: 0.7732 (p) REVERT: A 109 HIS cc_start: 0.8638 (m-70) cc_final: 0.8398 (m90) REVERT: A 113 MET cc_start: 0.8741 (mmm) cc_final: 0.8409 (mmm) REVERT: A 130 MET cc_start: 0.8512 (ptp) cc_final: 0.8230 (ptp) REVERT: A 137 GLU cc_start: 0.8833 (pp20) cc_final: 0.8596 (tm-30) REVERT: A 144 ASP cc_start: 0.8143 (p0) cc_final: 0.7586 (p0) REVERT: A 150 HIS cc_start: 0.7250 (m-70) cc_final: 0.7040 (m90) REVERT: A 167 VAL cc_start: 0.8903 (t) cc_final: 0.8338 (p) REVERT: A 189 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8019 (pm20) REVERT: A 190 TYR cc_start: 0.8666 (m-10) cc_final: 0.8348 (m-10) REVERT: A 241 GLN cc_start: 0.9110 (tp-100) cc_final: 0.7702 (tp-100) REVERT: A 245 TRP cc_start: 0.7611 (m100) cc_final: 0.6350 (m100) REVERT: E 21 LYS cc_start: 0.9151 (tmtm) cc_final: 0.8765 (pptt) REVERT: E 28 ARG cc_start: 0.8778 (ptt180) cc_final: 0.8472 (ptt90) REVERT: E 30 ASP cc_start: 0.8843 (t0) cc_final: 0.8450 (t0) REVERT: E 40 MET cc_start: 0.8701 (mtt) cc_final: 0.8428 (mmt) REVERT: E 44 VAL cc_start: 0.9482 (t) cc_final: 0.9230 (p) REVERT: E 55 MET cc_start: 0.8619 (mtt) cc_final: 0.8298 (tpt) REVERT: E 61 MET cc_start: 0.8886 (ptm) cc_final: 0.8528 (ppp) REVERT: E 64 GLN cc_start: 0.9099 (tt0) cc_final: 0.8613 (tt0) REVERT: E 67 TRP cc_start: 0.9377 (p90) cc_final: 0.9164 (p90) REVERT: E 68 LYS cc_start: 0.9322 (mmmm) cc_final: 0.8957 (mmmm) REVERT: E 69 ASP cc_start: 0.8751 (t0) cc_final: 0.8536 (t70) REVERT: E 90 GLN cc_start: 0.8745 (mt0) cc_final: 0.8407 (pt0) REVERT: E 112 LYS cc_start: 0.9170 (ttmm) cc_final: 0.8842 (ttmm) REVERT: E 129 ARG cc_start: 0.8783 (ttp80) cc_final: 0.7321 (ttp80) REVERT: E 133 THR cc_start: 0.9067 (m) cc_final: 0.8694 (p) REVERT: E 138 MET cc_start: 0.7367 (mtt) cc_final: 0.6543 (mtt) REVERT: E 141 ARG cc_start: 0.8816 (mtt90) cc_final: 0.8547 (mtt90) REVERT: E 142 ARG cc_start: 0.7917 (ttm170) cc_final: 0.7674 (ttm110) REVERT: E 169 ASN cc_start: 0.9107 (t0) cc_final: 0.8598 (t0) REVERT: E 213 ARG cc_start: 0.8487 (mtm-85) cc_final: 0.7678 (ptp-110) REVERT: B 13 LYS cc_start: 0.9096 (tttm) cc_final: 0.8704 (ttmt) REVERT: B 17 ASP cc_start: 0.9236 (m-30) cc_final: 0.8897 (m-30) REVERT: B 41 ARG cc_start: 0.8731 (mtt90) cc_final: 0.7929 (mtt90) REVERT: B 61 MET cc_start: 0.8290 (ppp) cc_final: 0.7341 (ppp) REVERT: B 63 PHE cc_start: 0.9073 (t80) cc_final: 0.8729 (t80) REVERT: B 68 LYS cc_start: 0.8269 (tppt) cc_final: 0.7851 (tppp) REVERT: B 89 ASP cc_start: 0.8865 (m-30) cc_final: 0.8463 (m-30) REVERT: B 90 GLN cc_start: 0.8934 (mm110) cc_final: 0.8700 (mm-40) REVERT: B 129 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7118 (ttt-90) REVERT: B 133 THR cc_start: 0.9063 (m) cc_final: 0.8743 (p) REVERT: B 148 GLN cc_start: 0.7985 (mm110) cc_final: 0.7401 (mm110) REVERT: B 150 CYS cc_start: 0.7280 (m) cc_final: 0.6988 (m) REVERT: B 151 THR cc_start: 0.8432 (p) cc_final: 0.8015 (p) REVERT: B 153 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8441 (mm-30) REVERT: B 169 ASN cc_start: 0.8618 (t0) cc_final: 0.7747 (t0) REVERT: B 192 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8514 (mmmt) REVERT: B 247 SER cc_start: 0.9043 (p) cc_final: 0.8817 (t) outliers start: 69 outliers final: 51 residues processed: 679 average time/residue: 0.1189 time to fit residues: 113.0569 Evaluate side-chains 685 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 630 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 345 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.152113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113302 restraints weight = 22670.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117881 restraints weight = 12340.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121011 restraints weight = 8086.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123103 restraints weight = 5941.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124555 restraints weight = 4770.444| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 12202 Z= 0.234 Angle : 0.842 12.206 16687 Z= 0.411 Chirality : 0.049 0.488 2058 Planarity : 0.005 0.058 2046 Dihedral : 9.666 81.206 2087 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 6.96 % Allowed : 24.24 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.21), residues: 1515 helix: -0.29 (0.22), residues: 459 sheet: -1.42 (0.25), residues: 410 loop : -1.94 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 20 TYR 0.020 0.002 TYR A 159 PHE 0.021 0.002 PHE C 297 TRP 0.036 0.002 TRP B 168 HIS 0.008 0.002 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00511 (12176) covalent geometry : angle 0.82667 (16614) SS BOND : bond 0.00672 ( 5) SS BOND : angle 4.02553 ( 10) hydrogen bonds : bond 0.03988 ( 517) hydrogen bonds : angle 5.43111 ( 1755) link_ALPHA1-2 : bond 0.00718 ( 1) link_ALPHA1-2 : angle 2.48004 ( 3) link_ALPHA1-3 : bond 0.00581 ( 3) link_ALPHA1-3 : angle 1.58998 ( 9) link_ALPHA1-6 : bond 0.01667 ( 1) link_ALPHA1-6 : angle 2.34636 ( 3) link_BETA1-4 : bond 0.00452 ( 10) link_BETA1-4 : angle 2.51265 ( 30) link_NAG-ASN : bond 0.00315 ( 6) link_NAG-ASN : angle 2.07743 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 633 time to evaluate : 0.457 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9130 (t0) cc_final: 0.8763 (t70) REVERT: D 40 ASN cc_start: 0.8634 (m-40) cc_final: 0.8354 (m-40) REVERT: D 54 HIS cc_start: 0.8943 (m-70) cc_final: 0.8636 (m90) REVERT: D 90 ASN cc_start: 0.7456 (t0) cc_final: 0.6671 (p0) REVERT: D 97 ARG cc_start: 0.9143 (mmt90) cc_final: 0.8162 (mtm-85) REVERT: D 99 ASN cc_start: 0.8854 (t0) cc_final: 0.8351 (t0) REVERT: D 101 ASN cc_start: 0.8688 (m110) cc_final: 0.7968 (m110) REVERT: D 114 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.7969 (mmm160) REVERT: D 115 ASN cc_start: 0.8305 (p0) cc_final: 0.7422 (p0) REVERT: D 138 ARG cc_start: 0.8812 (ttp-170) cc_final: 0.8132 (ttp80) REVERT: D 148 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7900 (p0) REVERT: D 172 TYR cc_start: 0.7497 (t80) cc_final: 0.6751 (t80) REVERT: D 176 ARG cc_start: 0.8867 (ptm-80) cc_final: 0.8619 (ptm-80) REVERT: D 207 ARG cc_start: 0.8605 (ptt90) cc_final: 0.8101 (ptt90) REVERT: D 214 LYS cc_start: 0.9236 (ttpt) cc_final: 0.8669 (tppt) REVERT: D 219 ASP cc_start: 0.9060 (t0) cc_final: 0.8783 (t0) REVERT: D 222 VAL cc_start: 0.9507 (t) cc_final: 0.9121 (m) REVERT: D 223 MET cc_start: 0.8577 (mmm) cc_final: 0.7786 (mmm) REVERT: C 25 TYR cc_start: 0.8596 (t80) cc_final: 0.8083 (t80) REVERT: C 58 GLU cc_start: 0.8262 (pp20) cc_final: 0.7928 (pp20) REVERT: C 70 LYS cc_start: 0.8193 (tmtm) cc_final: 0.7975 (tmtm) REVERT: C 97 ASP cc_start: 0.8577 (p0) cc_final: 0.8178 (p0) REVERT: C 102 ASN cc_start: 0.8541 (p0) cc_final: 0.7029 (t0) REVERT: C 165 GLU cc_start: 0.8804 (mm-30) cc_final: 0.7595 (mp0) REVERT: C 289 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8939 (pp) REVERT: A 44 ILE cc_start: 0.8689 (pp) cc_final: 0.8412 (pp) REVERT: A 47 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9087 (p) REVERT: A 57 MET cc_start: 0.8343 (tpp) cc_final: 0.7539 (tpp) REVERT: A 70 LYS cc_start: 0.8613 (tmmt) cc_final: 0.8307 (tmmt) REVERT: A 102 ASN cc_start: 0.8000 (t0) cc_final: 0.7663 (t0) REVERT: A 105 LYS cc_start: 0.8662 (tptt) cc_final: 0.8268 (pttp) REVERT: A 107 VAL cc_start: 0.7958 (m) cc_final: 0.7662 (p) REVERT: A 137 GLU cc_start: 0.8878 (pp20) cc_final: 0.8594 (tm-30) REVERT: A 144 ASP cc_start: 0.8121 (p0) cc_final: 0.7607 (p0) REVERT: A 167 VAL cc_start: 0.9123 (t) cc_final: 0.8726 (p) REVERT: A 189 GLN cc_start: 0.8205 (pm20) cc_final: 0.7987 (pm20) REVERT: A 190 TYR cc_start: 0.8552 (m-10) cc_final: 0.8262 (m-10) REVERT: A 213 THR cc_start: 0.8306 (m) cc_final: 0.7686 (p) REVERT: A 215 HIS cc_start: 0.8141 (m-70) cc_final: 0.7938 (m90) REVERT: A 221 LYS cc_start: 0.8554 (mmmm) cc_final: 0.8345 (mmmm) REVERT: A 241 GLN cc_start: 0.9060 (tp-100) cc_final: 0.7669 (tp-100) REVERT: A 245 TRP cc_start: 0.7494 (m100) cc_final: 0.6344 (m100) REVERT: E 17 ASP cc_start: 0.9037 (m-30) cc_final: 0.8741 (m-30) REVERT: E 18 ARG cc_start: 0.8632 (ptp-110) cc_final: 0.8416 (ptp90) REVERT: E 21 LYS cc_start: 0.9156 (tmtm) cc_final: 0.8801 (pptt) REVERT: E 30 ASP cc_start: 0.8817 (t0) cc_final: 0.8600 (t0) REVERT: E 40 MET cc_start: 0.8588 (mtt) cc_final: 0.8284 (mmt) REVERT: E 44 VAL cc_start: 0.9507 (t) cc_final: 0.9286 (p) REVERT: E 61 MET cc_start: 0.8892 (ptm) cc_final: 0.8640 (ppp) REVERT: E 64 GLN cc_start: 0.9009 (tt0) cc_final: 0.8510 (tt0) REVERT: E 68 LYS cc_start: 0.9374 (mmmm) cc_final: 0.8950 (mmmm) REVERT: E 69 ASP cc_start: 0.8825 (t0) cc_final: 0.8553 (t70) REVERT: E 90 GLN cc_start: 0.8783 (mt0) cc_final: 0.8455 (pt0) REVERT: E 98 PHE cc_start: 0.9201 (m-80) cc_final: 0.8798 (m-80) REVERT: E 112 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8780 (ttmm) REVERT: E 133 THR cc_start: 0.9111 (m) cc_final: 0.8719 (p) REVERT: E 165 GLU cc_start: 0.7143 (mp0) cc_final: 0.6816 (mp0) REVERT: E 213 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8059 (ttm110) REVERT: B 13 LYS cc_start: 0.9138 (tttm) cc_final: 0.8671 (ttmt) REVERT: B 17 ASP cc_start: 0.9221 (m-30) cc_final: 0.8864 (m-30) REVERT: B 18 ARG cc_start: 0.9316 (ptm-80) cc_final: 0.9045 (ttp-110) REVERT: B 37 ASP cc_start: 0.8861 (t0) cc_final: 0.8419 (t0) REVERT: B 41 ARG cc_start: 0.8740 (mtt90) cc_final: 0.8021 (mtt90) REVERT: B 61 MET cc_start: 0.8394 (ppp) cc_final: 0.7527 (ppp) REVERT: B 63 PHE cc_start: 0.9077 (t80) cc_final: 0.8684 (t80) REVERT: B 89 ASP cc_start: 0.8846 (m-30) cc_final: 0.8535 (m-30) REVERT: B 90 GLN cc_start: 0.9158 (mm110) cc_final: 0.8871 (mm110) REVERT: B 112 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8404 (ttpp) REVERT: B 129 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7130 (ttt-90) REVERT: B 133 THR cc_start: 0.9125 (m) cc_final: 0.8764 (p) REVERT: B 142 ARG cc_start: 0.8662 (mtm180) cc_final: 0.8427 (mtm180) REVERT: B 148 GLN cc_start: 0.7770 (mm110) cc_final: 0.7342 (mm110) REVERT: B 151 THR cc_start: 0.8400 (p) cc_final: 0.7051 (p) REVERT: B 153 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8209 (mp0) REVERT: B 167 TYR cc_start: 0.8496 (p90) cc_final: 0.7849 (p90) REVERT: B 169 ASN cc_start: 0.8602 (t0) cc_final: 0.7858 (t0) outliers start: 85 outliers final: 71 residues processed: 660 average time/residue: 0.1129 time to fit residues: 106.3330 Evaluate side-chains 693 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 619 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 144 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 157 ASN C 115 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN B 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114612 restraints weight = 22534.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119333 restraints weight = 12227.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122493 restraints weight = 8000.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124625 restraints weight = 5899.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126111 restraints weight = 4756.748| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12202 Z= 0.152 Angle : 0.824 13.364 16687 Z= 0.392 Chirality : 0.048 0.320 2058 Planarity : 0.005 0.057 2046 Dihedral : 8.717 75.840 2087 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 6.06 % Allowed : 28.42 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.21), residues: 1515 helix: -0.05 (0.23), residues: 459 sheet: -1.39 (0.24), residues: 426 loop : -1.81 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 172 TYR 0.022 0.002 TYR E 126 PHE 0.017 0.002 PHE C 297 TRP 0.050 0.001 TRP B 168 HIS 0.011 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00330 (12176) covalent geometry : angle 0.81362 (16614) SS BOND : bond 0.01692 ( 5) SS BOND : angle 2.61908 ( 10) hydrogen bonds : bond 0.03723 ( 517) hydrogen bonds : angle 5.22931 ( 1755) link_ALPHA1-2 : bond 0.00750 ( 1) link_ALPHA1-2 : angle 1.71723 ( 3) link_ALPHA1-3 : bond 0.00874 ( 3) link_ALPHA1-3 : angle 1.54215 ( 9) link_ALPHA1-6 : bond 0.01241 ( 1) link_ALPHA1-6 : angle 1.63235 ( 3) link_BETA1-4 : bond 0.00459 ( 10) link_BETA1-4 : angle 2.34858 ( 30) link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 1.88544 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 641 time to evaluate : 0.463 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9110 (t0) cc_final: 0.8727 (t70) REVERT: D 40 ASN cc_start: 0.8647 (m-40) cc_final: 0.8351 (m-40) REVERT: D 54 HIS cc_start: 0.8914 (m-70) cc_final: 0.8501 (m90) REVERT: D 60 ASN cc_start: 0.9422 (t0) cc_final: 0.8756 (t0) REVERT: D 90 ASN cc_start: 0.7430 (t0) cc_final: 0.6629 (p0) REVERT: D 97 ARG cc_start: 0.9176 (mmt90) cc_final: 0.8486 (mtm-85) REVERT: D 99 ASN cc_start: 0.8887 (t0) cc_final: 0.8382 (t0) REVERT: D 101 ASN cc_start: 0.8731 (m110) cc_final: 0.7936 (m110) REVERT: D 112 PHE cc_start: 0.8048 (p90) cc_final: 0.7639 (p90) REVERT: D 114 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.7959 (mmm160) REVERT: D 115 ASN cc_start: 0.8272 (p0) cc_final: 0.7453 (p0) REVERT: D 138 ARG cc_start: 0.8793 (ttp-170) cc_final: 0.8107 (ttp80) REVERT: D 148 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7774 (p0) REVERT: D 157 ASN cc_start: 0.7777 (m110) cc_final: 0.7399 (m-40) REVERT: D 160 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7575 (ppp) REVERT: D 172 TYR cc_start: 0.7341 (t80) cc_final: 0.6868 (t80) REVERT: D 177 GLU cc_start: 0.9151 (mp0) cc_final: 0.8804 (mp0) REVERT: D 214 LYS cc_start: 0.9226 (ttpt) cc_final: 0.8657 (tppt) REVERT: C 25 TYR cc_start: 0.8546 (t80) cc_final: 0.8042 (t80) REVERT: C 30 ARG cc_start: 0.9313 (ptt90) cc_final: 0.8999 (ptt90) REVERT: C 55 HIS cc_start: 0.8346 (t-90) cc_final: 0.7927 (m-70) REVERT: C 58 GLU cc_start: 0.8237 (pp20) cc_final: 0.7892 (pp20) REVERT: C 70 LYS cc_start: 0.8178 (tmtm) cc_final: 0.7885 (tmtm) REVERT: C 97 ASP cc_start: 0.8587 (p0) cc_final: 0.8253 (p0) REVERT: C 102 ASN cc_start: 0.8451 (p0) cc_final: 0.7023 (t0) REVERT: C 165 GLU cc_start: 0.8757 (mm-30) cc_final: 0.7407 (mp0) REVERT: C 195 GLN cc_start: 0.8916 (pm20) cc_final: 0.8714 (pm20) REVERT: C 289 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8986 (pp) REVERT: A 44 ILE cc_start: 0.8662 (pp) cc_final: 0.8410 (pp) REVERT: A 102 ASN cc_start: 0.8114 (t0) cc_final: 0.7695 (t0) REVERT: A 105 LYS cc_start: 0.8618 (tptt) cc_final: 0.8232 (pttp) REVERT: A 107 VAL cc_start: 0.7978 (m) cc_final: 0.7769 (p) REVERT: A 144 ASP cc_start: 0.7558 (p0) cc_final: 0.7045 (p0) REVERT: A 167 VAL cc_start: 0.8792 (t) cc_final: 0.8181 (p) REVERT: A 213 THR cc_start: 0.8328 (m) cc_final: 0.7796 (p) REVERT: A 215 HIS cc_start: 0.8080 (m-70) cc_final: 0.7855 (m90) REVERT: A 241 GLN cc_start: 0.9074 (tp-100) cc_final: 0.7722 (tp-100) REVERT: A 245 TRP cc_start: 0.7459 (m100) cc_final: 0.6266 (m100) REVERT: A 287 TRP cc_start: 0.8865 (m100) cc_final: 0.8385 (m-10) REVERT: E 17 ASP cc_start: 0.9021 (m-30) cc_final: 0.8735 (m-30) REVERT: E 18 ARG cc_start: 0.8568 (ptp-110) cc_final: 0.8312 (ptp90) REVERT: E 21 LYS cc_start: 0.9125 (tmtm) cc_final: 0.8790 (pptt) REVERT: E 30 ASP cc_start: 0.8821 (t0) cc_final: 0.8555 (t0) REVERT: E 40 MET cc_start: 0.8618 (mtt) cc_final: 0.8292 (mmt) REVERT: E 41 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7692 (ttm170) REVERT: E 44 VAL cc_start: 0.9451 (t) cc_final: 0.9217 (p) REVERT: E 68 LYS cc_start: 0.9383 (mmmm) cc_final: 0.9110 (mmmm) REVERT: E 69 ASP cc_start: 0.8738 (t0) cc_final: 0.8466 (t70) REVERT: E 90 GLN cc_start: 0.8799 (mt0) cc_final: 0.8463 (pt0) REVERT: E 112 LYS cc_start: 0.9033 (ttmm) cc_final: 0.8796 (ttmm) REVERT: E 133 THR cc_start: 0.9091 (m) cc_final: 0.8740 (p) REVERT: E 155 GLU cc_start: 0.8955 (tt0) cc_final: 0.8216 (tt0) REVERT: E 165 GLU cc_start: 0.7189 (mp0) cc_final: 0.6911 (mp0) REVERT: E 194 VAL cc_start: 0.8933 (t) cc_final: 0.8718 (p) REVERT: E 213 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.7977 (ttm110) REVERT: E 216 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.8147 (ttp-170) REVERT: B 13 LYS cc_start: 0.9062 (tttm) cc_final: 0.8487 (ttmt) REVERT: B 17 ASP cc_start: 0.9234 (m-30) cc_final: 0.8862 (m-30) REVERT: B 18 ARG cc_start: 0.9296 (ptm-80) cc_final: 0.8996 (ttp-110) REVERT: B 37 ASP cc_start: 0.8774 (t0) cc_final: 0.8317 (t0) REVERT: B 41 ARG cc_start: 0.8831 (mtt90) cc_final: 0.8096 (mtt90) REVERT: B 61 MET cc_start: 0.8391 (ppp) cc_final: 0.7386 (ppp) REVERT: B 63 PHE cc_start: 0.9083 (t80) cc_final: 0.8681 (t80) REVERT: B 89 ASP cc_start: 0.8792 (m-30) cc_final: 0.8488 (m-30) REVERT: B 126 TYR cc_start: 0.8653 (t80) cc_final: 0.8360 (t80) REVERT: B 129 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7161 (ttt-90) REVERT: B 133 THR cc_start: 0.9107 (m) cc_final: 0.8791 (p) REVERT: B 142 ARG cc_start: 0.8408 (mtm180) cc_final: 0.8130 (mtm180) REVERT: B 148 GLN cc_start: 0.7925 (mm110) cc_final: 0.7589 (mm110) REVERT: B 151 THR cc_start: 0.8544 (p) cc_final: 0.7174 (p) REVERT: B 153 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8236 (mp0) REVERT: B 167 TYR cc_start: 0.8380 (p90) cc_final: 0.7734 (p90) REVERT: B 169 ASN cc_start: 0.8559 (t0) cc_final: 0.7451 (t0) REVERT: B 213 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7655 (ttm170) REVERT: B 216 ARG cc_start: 0.8465 (mtm180) cc_final: 0.7676 (mtm180) outliers start: 74 outliers final: 66 residues processed: 662 average time/residue: 0.1145 time to fit residues: 107.0393 Evaluate side-chains 698 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 629 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 112 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113489 restraints weight = 22581.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118142 restraints weight = 12222.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121259 restraints weight = 7997.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123391 restraints weight = 5911.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124733 restraints weight = 4762.610| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12202 Z= 0.177 Angle : 0.876 22.758 16687 Z= 0.413 Chirality : 0.049 0.535 2058 Planarity : 0.005 0.065 2046 Dihedral : 8.159 71.707 2087 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 7.37 % Allowed : 27.68 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.21), residues: 1515 helix: 0.11 (0.23), residues: 458 sheet: -1.32 (0.25), residues: 423 loop : -1.70 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 220 TYR 0.034 0.002 TYR C 293 PHE 0.016 0.002 PHE E 31 TRP 0.058 0.002 TRP B 168 HIS 0.010 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00393 (12176) covalent geometry : angle 0.86619 (16614) SS BOND : bond 0.01307 ( 5) SS BOND : angle 3.07395 ( 10) hydrogen bonds : bond 0.03703 ( 517) hydrogen bonds : angle 5.23693 ( 1755) link_ALPHA1-2 : bond 0.00580 ( 1) link_ALPHA1-2 : angle 1.64280 ( 3) link_ALPHA1-3 : bond 0.00710 ( 3) link_ALPHA1-3 : angle 1.58909 ( 9) link_ALPHA1-6 : bond 0.00702 ( 1) link_ALPHA1-6 : angle 1.83405 ( 3) link_BETA1-4 : bond 0.00480 ( 10) link_BETA1-4 : angle 2.25092 ( 30) link_NAG-ASN : bond 0.00211 ( 6) link_NAG-ASN : angle 1.81294 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 638 time to evaluate : 0.377 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9109 (t0) cc_final: 0.8725 (t70) REVERT: D 40 ASN cc_start: 0.8647 (m-40) cc_final: 0.8341 (m-40) REVERT: D 54 HIS cc_start: 0.8967 (m-70) cc_final: 0.8463 (m-70) REVERT: D 60 ASN cc_start: 0.9414 (t0) cc_final: 0.8824 (t0) REVERT: D 88 LYS cc_start: 0.8911 (mtmm) cc_final: 0.8698 (mppt) REVERT: D 90 ASN cc_start: 0.7375 (t0) cc_final: 0.6643 (p0) REVERT: D 97 ARG cc_start: 0.9250 (mmt90) cc_final: 0.8497 (mtm-85) REVERT: D 99 ASN cc_start: 0.8996 (t0) cc_final: 0.8399 (t0) REVERT: D 101 ASN cc_start: 0.8820 (m110) cc_final: 0.8054 (m110) REVERT: D 114 ARG cc_start: 0.8532 (mmm-85) cc_final: 0.8019 (mmm160) REVERT: D 115 ASN cc_start: 0.8332 (p0) cc_final: 0.7577 (p0) REVERT: D 172 TYR cc_start: 0.7347 (t80) cc_final: 0.6768 (t80) REVERT: D 182 GLN cc_start: 0.7340 (tp-100) cc_final: 0.6555 (tp-100) REVERT: D 183 TRP cc_start: 0.8065 (m100) cc_final: 0.7665 (m-10) REVERT: D 207 ARG cc_start: 0.8775 (ptt90) cc_final: 0.7872 (ptt90) REVERT: D 211 GLU cc_start: 0.7204 (mp0) cc_final: 0.6893 (mp0) REVERT: D 214 LYS cc_start: 0.9103 (ttpt) cc_final: 0.8517 (tppt) REVERT: D 219 ASP cc_start: 0.8912 (t0) cc_final: 0.8452 (t70) REVERT: D 222 VAL cc_start: 0.9461 (t) cc_final: 0.8988 (m) REVERT: D 223 MET cc_start: 0.8445 (mmp) cc_final: 0.7973 (mmp) REVERT: C 55 HIS cc_start: 0.8435 (t-90) cc_final: 0.8016 (m-70) REVERT: C 58 GLU cc_start: 0.8308 (pp20) cc_final: 0.7929 (pp20) REVERT: C 70 LYS cc_start: 0.8182 (tmtm) cc_final: 0.7861 (tmtm) REVERT: C 97 ASP cc_start: 0.8611 (p0) cc_final: 0.8236 (p0) REVERT: C 102 ASN cc_start: 0.8468 (p0) cc_final: 0.7112 (t0) REVERT: C 165 GLU cc_start: 0.8785 (mm-30) cc_final: 0.7614 (mp0) REVERT: C 220 ARG cc_start: 0.8080 (mtm110) cc_final: 0.7676 (mtm-85) REVERT: C 289 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9014 (pp) REVERT: A 44 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8488 (pp) REVERT: A 70 LYS cc_start: 0.8545 (tmmt) cc_final: 0.8327 (tmmt) REVERT: A 82 VAL cc_start: 0.9265 (p) cc_final: 0.8969 (p) REVERT: A 89 MET cc_start: 0.9109 (tpp) cc_final: 0.8906 (tpp) REVERT: A 102 ASN cc_start: 0.8197 (t0) cc_final: 0.7809 (t0) REVERT: A 105 LYS cc_start: 0.8692 (tptt) cc_final: 0.8217 (pttp) REVERT: A 107 VAL cc_start: 0.8051 (m) cc_final: 0.7811 (p) REVERT: A 113 MET cc_start: 0.8715 (mmm) cc_final: 0.8200 (mmm) REVERT: A 137 GLU cc_start: 0.8898 (pp20) cc_final: 0.8455 (pp20) REVERT: A 144 ASP cc_start: 0.7531 (p0) cc_final: 0.7144 (p0) REVERT: A 167 VAL cc_start: 0.8811 (t) cc_final: 0.8177 (p) REVERT: A 212 MET cc_start: 0.8757 (mmm) cc_final: 0.8473 (mmm) REVERT: A 213 THR cc_start: 0.8307 (m) cc_final: 0.7719 (p) REVERT: A 215 HIS cc_start: 0.8087 (m-70) cc_final: 0.7853 (m90) REVERT: A 221 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8382 (mmmm) REVERT: A 241 GLN cc_start: 0.9087 (tp-100) cc_final: 0.7749 (tp-100) REVERT: A 245 TRP cc_start: 0.7427 (m100) cc_final: 0.6402 (m100) REVERT: A 287 TRP cc_start: 0.8863 (m100) cc_final: 0.8408 (m-10) REVERT: E 17 ASP cc_start: 0.9071 (m-30) cc_final: 0.8779 (m-30) REVERT: E 18 ARG cc_start: 0.8661 (ptp-110) cc_final: 0.8336 (ptp90) REVERT: E 21 LYS cc_start: 0.9153 (tmtm) cc_final: 0.8802 (pptt) REVERT: E 30 ASP cc_start: 0.8913 (t0) cc_final: 0.8639 (t0) REVERT: E 40 MET cc_start: 0.8616 (mtt) cc_final: 0.8217 (mmt) REVERT: E 64 GLN cc_start: 0.8963 (tt0) cc_final: 0.8489 (tt0) REVERT: E 68 LYS cc_start: 0.9386 (mmmm) cc_final: 0.8998 (mmmm) REVERT: E 69 ASP cc_start: 0.8709 (t0) cc_final: 0.8419 (t70) REVERT: E 90 GLN cc_start: 0.8805 (mt0) cc_final: 0.8480 (pt0) REVERT: E 92 TRP cc_start: 0.9523 (t60) cc_final: 0.8874 (t60) REVERT: E 112 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8788 (ttmm) REVERT: E 133 THR cc_start: 0.9107 (m) cc_final: 0.8799 (p) REVERT: E 155 GLU cc_start: 0.8971 (tt0) cc_final: 0.8237 (tt0) REVERT: E 169 ASN cc_start: 0.9030 (t0) cc_final: 0.8522 (t0) REVERT: E 213 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8057 (ttm110) REVERT: B 13 LYS cc_start: 0.9059 (tttm) cc_final: 0.8516 (ttmt) REVERT: B 17 ASP cc_start: 0.9229 (m-30) cc_final: 0.8863 (m-30) REVERT: B 18 ARG cc_start: 0.9335 (ptm-80) cc_final: 0.9031 (ttp-110) REVERT: B 37 ASP cc_start: 0.8763 (t0) cc_final: 0.8487 (t0) REVERT: B 41 ARG cc_start: 0.8751 (mtt90) cc_final: 0.8296 (mtt90) REVERT: B 61 MET cc_start: 0.8408 (ppp) cc_final: 0.7411 (ppp) REVERT: B 63 PHE cc_start: 0.9061 (t80) cc_final: 0.8650 (t80) REVERT: B 89 ASP cc_start: 0.8925 (m-30) cc_final: 0.8546 (m-30) REVERT: B 90 GLN cc_start: 0.9026 (mm110) cc_final: 0.8740 (mm-40) REVERT: B 100 ASN cc_start: 0.8543 (p0) cc_final: 0.7672 (p0) REVERT: B 126 TYR cc_start: 0.8627 (t80) cc_final: 0.8316 (t80) REVERT: B 129 ARG cc_start: 0.8424 (ttp80) cc_final: 0.7140 (ttt-90) REVERT: B 133 THR cc_start: 0.9120 (m) cc_final: 0.8837 (p) REVERT: B 142 ARG cc_start: 0.8373 (mtm180) cc_final: 0.8013 (mtm180) REVERT: B 148 GLN cc_start: 0.7808 (mm110) cc_final: 0.7418 (mm110) REVERT: B 151 THR cc_start: 0.8572 (p) cc_final: 0.7198 (p) REVERT: B 153 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8015 (mp0) REVERT: B 167 TYR cc_start: 0.8480 (p90) cc_final: 0.7858 (p90) REVERT: B 169 ASN cc_start: 0.8551 (t0) cc_final: 0.7716 (t0) REVERT: B 179 ASN cc_start: 0.9144 (p0) cc_final: 0.8923 (p0) REVERT: B 216 ARG cc_start: 0.8534 (mtm180) cc_final: 0.7760 (mtm180) outliers start: 90 outliers final: 79 residues processed: 666 average time/residue: 0.1120 time to fit residues: 105.5013 Evaluate side-chains 709 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 628 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 129 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114881 restraints weight = 22076.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119652 restraints weight = 11971.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122857 restraints weight = 7830.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125026 restraints weight = 5774.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126380 restraints weight = 4650.018| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12202 Z= 0.147 Angle : 0.893 21.110 16687 Z= 0.416 Chirality : 0.049 0.393 2058 Planarity : 0.005 0.060 2046 Dihedral : 7.677 65.844 2087 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.39 % Allowed : 30.47 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.21), residues: 1515 helix: 0.16 (0.23), residues: 458 sheet: -1.21 (0.25), residues: 419 loop : -1.62 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 220 TYR 0.059 0.002 TYR C 293 PHE 0.017 0.002 PHE C 65 TRP 0.070 0.002 TRP B 168 HIS 0.010 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00328 (12176) covalent geometry : angle 0.88441 (16614) SS BOND : bond 0.00908 ( 5) SS BOND : angle 2.96842 ( 10) hydrogen bonds : bond 0.03644 ( 517) hydrogen bonds : angle 5.19498 ( 1755) link_ALPHA1-2 : bond 0.00644 ( 1) link_ALPHA1-2 : angle 1.38311 ( 3) link_ALPHA1-3 : bond 0.00751 ( 3) link_ALPHA1-3 : angle 1.46046 ( 9) link_ALPHA1-6 : bond 0.00808 ( 1) link_ALPHA1-6 : angle 1.67713 ( 3) link_BETA1-4 : bond 0.00580 ( 10) link_BETA1-4 : angle 2.11186 ( 30) link_NAG-ASN : bond 0.00223 ( 6) link_NAG-ASN : angle 1.66661 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 640 time to evaluate : 0.532 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9128 (t0) cc_final: 0.8722 (t70) REVERT: D 40 ASN cc_start: 0.8638 (m-40) cc_final: 0.8316 (m-40) REVERT: D 54 HIS cc_start: 0.8968 (m-70) cc_final: 0.8444 (m-70) REVERT: D 82 TRP cc_start: 0.9204 (p90) cc_final: 0.8957 (p90) REVERT: D 90 ASN cc_start: 0.7334 (t0) cc_final: 0.6594 (p0) REVERT: D 97 ARG cc_start: 0.9268 (mmt90) cc_final: 0.8529 (mtm-85) REVERT: D 101 ASN cc_start: 0.8729 (m110) cc_final: 0.7985 (t0) REVERT: D 114 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.7963 (mmm160) REVERT: D 115 ASN cc_start: 0.8340 (p0) cc_final: 0.7620 (p0) REVERT: D 172 TYR cc_start: 0.7296 (t80) cc_final: 0.6788 (t80) REVERT: D 182 GLN cc_start: 0.7549 (tp-100) cc_final: 0.6690 (tp-100) REVERT: D 183 TRP cc_start: 0.8107 (m100) cc_final: 0.7610 (m-10) REVERT: D 207 ARG cc_start: 0.8800 (ptt90) cc_final: 0.8515 (ptt90) REVERT: D 214 LYS cc_start: 0.9095 (ttpt) cc_final: 0.8527 (tppt) REVERT: D 219 ASP cc_start: 0.8927 (t0) cc_final: 0.8502 (t70) REVERT: D 222 VAL cc_start: 0.9446 (t) cc_final: 0.9029 (m) REVERT: D 223 MET cc_start: 0.8374 (mmp) cc_final: 0.8024 (mmp) REVERT: C 26 ASP cc_start: 0.8949 (t0) cc_final: 0.8728 (t0) REVERT: C 30 ARG cc_start: 0.9319 (ptt90) cc_final: 0.8951 (ptt90) REVERT: C 55 HIS cc_start: 0.8492 (t-90) cc_final: 0.8132 (m-70) REVERT: C 58 GLU cc_start: 0.8326 (pp20) cc_final: 0.7948 (pp20) REVERT: C 70 LYS cc_start: 0.8015 (tmtm) cc_final: 0.7695 (tmtm) REVERT: C 97 ASP cc_start: 0.8621 (p0) cc_final: 0.8318 (p0) REVERT: C 102 ASN cc_start: 0.8473 (p0) cc_final: 0.7122 (t0) REVERT: C 118 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8939 (mp) REVERT: C 165 GLU cc_start: 0.8733 (mm-30) cc_final: 0.7398 (mp0) REVERT: A 44 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8544 (pp) REVERT: A 57 MET cc_start: 0.6944 (tpp) cc_final: 0.6608 (tpt) REVERT: A 58 GLU cc_start: 0.7243 (pt0) cc_final: 0.6579 (pt0) REVERT: A 89 MET cc_start: 0.9103 (tpp) cc_final: 0.8873 (tpp) REVERT: A 102 ASN cc_start: 0.8249 (t0) cc_final: 0.7867 (t0) REVERT: A 105 LYS cc_start: 0.8676 (tptt) cc_final: 0.8191 (pttp) REVERT: A 107 VAL cc_start: 0.8035 (m) cc_final: 0.7780 (p) REVERT: A 113 MET cc_start: 0.8717 (mmm) cc_final: 0.8165 (mmm) REVERT: A 128 TYR cc_start: 0.9245 (t80) cc_final: 0.9024 (t80) REVERT: A 130 MET cc_start: 0.8439 (ptp) cc_final: 0.7757 (ptp) REVERT: A 138 CYS cc_start: 0.6646 (t) cc_final: 0.6242 (t) REVERT: A 144 ASP cc_start: 0.7483 (p0) cc_final: 0.7131 (p0) REVERT: A 167 VAL cc_start: 0.8764 (t) cc_final: 0.8178 (p) REVERT: A 213 THR cc_start: 0.8246 (m) cc_final: 0.7764 (p) REVERT: A 215 HIS cc_start: 0.8044 (m-70) cc_final: 0.7773 (m90) REVERT: A 221 LYS cc_start: 0.8699 (mmmm) cc_final: 0.8461 (mmmm) REVERT: A 245 TRP cc_start: 0.7422 (m100) cc_final: 0.6897 (m100) REVERT: A 287 TRP cc_start: 0.8842 (m100) cc_final: 0.8372 (m-10) REVERT: E 17 ASP cc_start: 0.9089 (m-30) cc_final: 0.8784 (m-30) REVERT: E 18 ARG cc_start: 0.8592 (ptp-110) cc_final: 0.8283 (ptp90) REVERT: E 21 LYS cc_start: 0.9137 (tmtm) cc_final: 0.8783 (pptt) REVERT: E 30 ASP cc_start: 0.8916 (t0) cc_final: 0.8630 (t0) REVERT: E 40 MET cc_start: 0.8626 (mtt) cc_final: 0.8187 (mmt) REVERT: E 64 GLN cc_start: 0.8929 (tt0) cc_final: 0.8508 (tt0) REVERT: E 68 LYS cc_start: 0.9379 (mmmm) cc_final: 0.8997 (mmmm) REVERT: E 69 ASP cc_start: 0.8673 (t0) cc_final: 0.8405 (t70) REVERT: E 90 GLN cc_start: 0.8778 (mt0) cc_final: 0.8459 (pt0) REVERT: E 92 TRP cc_start: 0.9575 (t60) cc_final: 0.9022 (t60) REVERT: E 133 THR cc_start: 0.9089 (m) cc_final: 0.8801 (p) REVERT: E 143 TYR cc_start: 0.8070 (t80) cc_final: 0.7807 (t80) REVERT: E 155 GLU cc_start: 0.8981 (tt0) cc_final: 0.8235 (tt0) REVERT: E 169 ASN cc_start: 0.9010 (t0) cc_final: 0.8489 (t0) REVERT: E 213 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.8007 (ttm110) REVERT: B 13 LYS cc_start: 0.9035 (tttm) cc_final: 0.8490 (ttmt) REVERT: B 17 ASP cc_start: 0.9236 (m-30) cc_final: 0.8873 (m-30) REVERT: B 18 ARG cc_start: 0.9352 (ptm-80) cc_final: 0.9048 (ttp-110) REVERT: B 41 ARG cc_start: 0.8790 (mtt90) cc_final: 0.8405 (mtt90) REVERT: B 61 MET cc_start: 0.8383 (ppp) cc_final: 0.7346 (ppp) REVERT: B 63 PHE cc_start: 0.9041 (t80) cc_final: 0.8596 (t80) REVERT: B 89 ASP cc_start: 0.8957 (m-30) cc_final: 0.8615 (m-30) REVERT: B 90 GLN cc_start: 0.8989 (mm110) cc_final: 0.8707 (mm-40) REVERT: B 100 ASN cc_start: 0.8470 (p0) cc_final: 0.7543 (p0) REVERT: B 126 TYR cc_start: 0.8669 (t80) cc_final: 0.8331 (t80) REVERT: B 133 THR cc_start: 0.9145 (m) cc_final: 0.8874 (p) REVERT: B 142 ARG cc_start: 0.8355 (mtm180) cc_final: 0.7953 (mtm180) REVERT: B 151 THR cc_start: 0.8629 (p) cc_final: 0.7858 (p) REVERT: B 153 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8020 (mp0) REVERT: B 216 ARG cc_start: 0.8568 (mtm180) cc_final: 0.7866 (mtm180) REVERT: B 247 SER cc_start: 0.9028 (p) cc_final: 0.8815 (t) outliers start: 78 outliers final: 71 residues processed: 664 average time/residue: 0.1130 time to fit residues: 106.9283 Evaluate side-chains 705 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 632 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 80 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN B 64 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111642 restraints weight = 22751.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116153 restraints weight = 12350.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119180 restraints weight = 8073.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121211 restraints weight = 5976.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122534 restraints weight = 4829.294| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 12202 Z= 0.274 Angle : 0.917 14.139 16687 Z= 0.446 Chirality : 0.049 0.293 2058 Planarity : 0.005 0.062 2046 Dihedral : 7.471 59.893 2087 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 7.45 % Allowed : 30.14 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.22), residues: 1515 helix: 0.15 (0.23), residues: 459 sheet: -1.20 (0.25), residues: 428 loop : -1.66 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 26 TYR 0.031 0.002 TYR B 167 PHE 0.017 0.002 PHE E 31 TRP 0.083 0.003 TRP B 168 HIS 0.009 0.002 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00596 (12176) covalent geometry : angle 0.90629 (16614) SS BOND : bond 0.00713 ( 5) SS BOND : angle 3.27507 ( 10) hydrogen bonds : bond 0.03856 ( 517) hydrogen bonds : angle 5.44294 ( 1755) link_ALPHA1-2 : bond 0.00482 ( 1) link_ALPHA1-2 : angle 1.71505 ( 3) link_ALPHA1-3 : bond 0.00527 ( 3) link_ALPHA1-3 : angle 1.62138 ( 9) link_ALPHA1-6 : bond 0.00200 ( 1) link_ALPHA1-6 : angle 2.32951 ( 3) link_BETA1-4 : bond 0.00569 ( 10) link_BETA1-4 : angle 2.22516 ( 30) link_NAG-ASN : bond 0.00199 ( 6) link_NAG-ASN : angle 1.94533 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 629 time to evaluate : 0.427 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9113 (t0) cc_final: 0.8752 (t70) REVERT: D 40 ASN cc_start: 0.8526 (m-40) cc_final: 0.8217 (m-40) REVERT: D 54 HIS cc_start: 0.8990 (m-70) cc_final: 0.8463 (m-70) REVERT: D 60 ASN cc_start: 0.9388 (t0) cc_final: 0.8754 (t0) REVERT: D 82 TRP cc_start: 0.9413 (p90) cc_final: 0.8953 (p90) REVERT: D 90 ASN cc_start: 0.7306 (t0) cc_final: 0.6502 (p0) REVERT: D 97 ARG cc_start: 0.9253 (mmt90) cc_final: 0.8516 (mtm-85) REVERT: D 101 ASN cc_start: 0.8697 (m110) cc_final: 0.8449 (t0) REVERT: D 112 PHE cc_start: 0.8128 (p90) cc_final: 0.7092 (p90) REVERT: D 114 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8016 (mmm160) REVERT: D 115 ASN cc_start: 0.8498 (p0) cc_final: 0.7855 (p0) REVERT: D 172 TYR cc_start: 0.7499 (t80) cc_final: 0.7238 (t80) REVERT: D 182 GLN cc_start: 0.7789 (tp-100) cc_final: 0.6904 (tp-100) REVERT: D 207 ARG cc_start: 0.8819 (ptt90) cc_final: 0.8047 (ptt90) REVERT: D 214 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8574 (tppt) REVERT: D 223 MET cc_start: 0.8371 (mmp) cc_final: 0.8137 (mmp) REVERT: D 224 SER cc_start: 0.9147 (t) cc_final: 0.8373 (p) REVERT: C 25 TYR cc_start: 0.8572 (t80) cc_final: 0.8296 (t80) REVERT: C 55 HIS cc_start: 0.8484 (t-90) cc_final: 0.8123 (m-70) REVERT: C 58 GLU cc_start: 0.8466 (pp20) cc_final: 0.8071 (pp20) REVERT: C 70 LYS cc_start: 0.8187 (tmtm) cc_final: 0.7899 (tmtm) REVERT: C 97 ASP cc_start: 0.8604 (p0) cc_final: 0.8281 (p0) REVERT: C 102 ASN cc_start: 0.8427 (p0) cc_final: 0.7113 (t0) REVERT: C 118 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8926 (mp) REVERT: C 165 GLU cc_start: 0.8825 (mm-30) cc_final: 0.7599 (mp0) REVERT: A 70 LYS cc_start: 0.8491 (tmmt) cc_final: 0.8274 (tmmt) REVERT: A 89 MET cc_start: 0.9170 (tpp) cc_final: 0.8879 (tpp) REVERT: A 102 ASN cc_start: 0.8337 (t0) cc_final: 0.7928 (t0) REVERT: A 105 LYS cc_start: 0.8700 (tptt) cc_final: 0.8141 (pttp) REVERT: A 107 VAL cc_start: 0.8074 (m) cc_final: 0.7797 (p) REVERT: A 113 MET cc_start: 0.8878 (mmm) cc_final: 0.8521 (mmm) REVERT: A 137 GLU cc_start: 0.8889 (pp20) cc_final: 0.8468 (pp20) REVERT: A 144 ASP cc_start: 0.7568 (p0) cc_final: 0.7219 (p0) REVERT: A 167 VAL cc_start: 0.9143 (t) cc_final: 0.8695 (p) REVERT: A 212 MET cc_start: 0.8743 (mmm) cc_final: 0.8329 (mmm) REVERT: A 241 GLN cc_start: 0.9100 (tp-100) cc_final: 0.7902 (tp-100) REVERT: A 245 TRP cc_start: 0.7321 (m100) cc_final: 0.6362 (m100) REVERT: A 287 TRP cc_start: 0.8877 (m100) cc_final: 0.8443 (m-10) REVERT: E 17 ASP cc_start: 0.9080 (m-30) cc_final: 0.8835 (m-30) REVERT: E 21 LYS cc_start: 0.9132 (tmtm) cc_final: 0.8761 (pptt) REVERT: E 30 ASP cc_start: 0.8932 (t0) cc_final: 0.8646 (t0) REVERT: E 40 MET cc_start: 0.8718 (mtt) cc_final: 0.8234 (mmt) REVERT: E 64 GLN cc_start: 0.8984 (tt0) cc_final: 0.8475 (tt0) REVERT: E 68 LYS cc_start: 0.9369 (mmmm) cc_final: 0.9047 (mmmm) REVERT: E 69 ASP cc_start: 0.8757 (t0) cc_final: 0.8466 (t70) REVERT: E 90 GLN cc_start: 0.8880 (mt0) cc_final: 0.8545 (pt0) REVERT: E 98 PHE cc_start: 0.9285 (m-80) cc_final: 0.8945 (m-80) REVERT: E 121 ASP cc_start: 0.9291 (p0) cc_final: 0.8956 (p0) REVERT: E 133 THR cc_start: 0.9111 (m) cc_final: 0.8794 (p) REVERT: E 169 ASN cc_start: 0.8972 (t0) cc_final: 0.8518 (t0) REVERT: E 213 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7925 (ttm110) REVERT: B 13 LYS cc_start: 0.9120 (tttm) cc_final: 0.8640 (ttmm) REVERT: B 17 ASP cc_start: 0.9224 (m-30) cc_final: 0.8882 (m-30) REVERT: B 18 ARG cc_start: 0.9363 (ptm-80) cc_final: 0.9070 (ttp-110) REVERT: B 41 ARG cc_start: 0.8782 (mtt90) cc_final: 0.8358 (mtt90) REVERT: B 61 MET cc_start: 0.8419 (ppp) cc_final: 0.7354 (ppp) REVERT: B 63 PHE cc_start: 0.9102 (t80) cc_final: 0.8652 (t80) REVERT: B 89 ASP cc_start: 0.9006 (m-30) cc_final: 0.8710 (m-30) REVERT: B 90 GLN cc_start: 0.9141 (mm110) cc_final: 0.8880 (mm110) REVERT: B 100 ASN cc_start: 0.8451 (p0) cc_final: 0.7564 (p0) REVERT: B 126 TYR cc_start: 0.8611 (t80) cc_final: 0.8192 (t80) REVERT: B 142 ARG cc_start: 0.8467 (mtm180) cc_final: 0.8064 (mtm180) REVERT: B 148 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7370 (mm110) REVERT: B 151 THR cc_start: 0.8685 (p) cc_final: 0.7632 (p) REVERT: B 153 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8104 (mp0) REVERT: B 216 ARG cc_start: 0.8698 (mtm180) cc_final: 0.7831 (mtm180) REVERT: B 243 ASN cc_start: 0.6081 (t0) cc_final: 0.5685 (t0) outliers start: 91 outliers final: 82 residues processed: 663 average time/residue: 0.1104 time to fit residues: 104.5451 Evaluate side-chains 708 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 625 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 141 optimal weight: 0.0670 chunk 96 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.153210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113958 restraints weight = 22102.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118614 restraints weight = 11952.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121782 restraints weight = 7815.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123881 restraints weight = 5753.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125228 restraints weight = 4635.055| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12202 Z= 0.164 Angle : 0.932 14.664 16687 Z= 0.441 Chirality : 0.049 0.258 2058 Planarity : 0.005 0.059 2046 Dihedral : 7.150 56.328 2087 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.96 % Allowed : 32.10 % Favored : 60.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.22), residues: 1515 helix: 0.30 (0.24), residues: 456 sheet: -1.22 (0.25), residues: 442 loop : -1.46 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 220 TYR 0.026 0.002 TYR B 167 PHE 0.017 0.002 PHE E 31 TRP 0.091 0.002 TRP B 168 HIS 0.010 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00371 (12176) covalent geometry : angle 0.92415 (16614) SS BOND : bond 0.00735 ( 5) SS BOND : angle 3.03404 ( 10) hydrogen bonds : bond 0.03717 ( 517) hydrogen bonds : angle 5.30379 ( 1755) link_ALPHA1-2 : bond 0.00608 ( 1) link_ALPHA1-2 : angle 1.35988 ( 3) link_ALPHA1-3 : bond 0.00709 ( 3) link_ALPHA1-3 : angle 1.43367 ( 9) link_ALPHA1-6 : bond 0.00571 ( 1) link_ALPHA1-6 : angle 1.77665 ( 3) link_BETA1-4 : bond 0.00484 ( 10) link_BETA1-4 : angle 2.01168 ( 30) link_NAG-ASN : bond 0.00189 ( 6) link_NAG-ASN : angle 1.75970 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 635 time to evaluate : 0.465 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9151 (t0) cc_final: 0.8828 (t70) REVERT: D 40 ASN cc_start: 0.8549 (m-40) cc_final: 0.8180 (m-40) REVERT: D 54 HIS cc_start: 0.8986 (m-70) cc_final: 0.8479 (m-70) REVERT: D 82 TRP cc_start: 0.9314 (p90) cc_final: 0.9002 (p90) REVERT: D 90 ASN cc_start: 0.7262 (t0) cc_final: 0.6438 (p0) REVERT: D 97 ARG cc_start: 0.9248 (mmt90) cc_final: 0.8543 (mtm-85) REVERT: D 101 ASN cc_start: 0.8702 (m110) cc_final: 0.8377 (t0) REVERT: D 112 PHE cc_start: 0.8129 (p90) cc_final: 0.7160 (p90) REVERT: D 114 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8014 (mmm160) REVERT: D 115 ASN cc_start: 0.8452 (p0) cc_final: 0.7784 (p0) REVERT: D 148 ASP cc_start: 0.7938 (p0) cc_final: 0.7671 (p0) REVERT: D 182 GLN cc_start: 0.7776 (tp-100) cc_final: 0.6928 (tp-100) REVERT: D 183 TRP cc_start: 0.8051 (m100) cc_final: 0.7747 (m-10) REVERT: D 207 ARG cc_start: 0.8779 (ptt90) cc_final: 0.8265 (ptt90) REVERT: D 214 LYS cc_start: 0.9073 (ttpt) cc_final: 0.8494 (tppt) REVERT: D 223 MET cc_start: 0.8289 (mmp) cc_final: 0.7997 (mmp) REVERT: D 224 SER cc_start: 0.9187 (t) cc_final: 0.8348 (p) REVERT: C 25 TYR cc_start: 0.8521 (t80) cc_final: 0.8249 (t80) REVERT: C 55 HIS cc_start: 0.8561 (t-90) cc_final: 0.8236 (m-70) REVERT: C 58 GLU cc_start: 0.8445 (pp20) cc_final: 0.8035 (pp20) REVERT: C 70 LYS cc_start: 0.8106 (tmtm) cc_final: 0.7793 (tmtm) REVERT: C 102 ASN cc_start: 0.8412 (p0) cc_final: 0.7120 (t0) REVERT: C 118 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8893 (mp) REVERT: C 165 GLU cc_start: 0.8738 (mm-30) cc_final: 0.7433 (mp0) REVERT: A 75 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8107 (ptpp) REVERT: A 89 MET cc_start: 0.9141 (tpp) cc_final: 0.8900 (tpp) REVERT: A 102 ASN cc_start: 0.8415 (t0) cc_final: 0.8043 (t0) REVERT: A 105 LYS cc_start: 0.8704 (tptt) cc_final: 0.8165 (pttp) REVERT: A 107 VAL cc_start: 0.7910 (m) cc_final: 0.7645 (p) REVERT: A 113 MET cc_start: 0.8871 (mmm) cc_final: 0.8475 (mmm) REVERT: A 128 TYR cc_start: 0.9292 (t80) cc_final: 0.8875 (t80) REVERT: A 130 MET cc_start: 0.8458 (ptp) cc_final: 0.7693 (ptp) REVERT: A 144 ASP cc_start: 0.7524 (p0) cc_final: 0.7248 (p0) REVERT: A 167 VAL cc_start: 0.8850 (t) cc_final: 0.8231 (p) REVERT: A 212 MET cc_start: 0.8560 (mmm) cc_final: 0.8317 (mmm) REVERT: A 221 LYS cc_start: 0.8328 (mmmm) cc_final: 0.8073 (mmmm) REVERT: A 241 GLN cc_start: 0.9094 (tp-100) cc_final: 0.8708 (tm-30) REVERT: A 287 TRP cc_start: 0.8850 (m100) cc_final: 0.8128 (m-10) REVERT: E 17 ASP cc_start: 0.9038 (m-30) cc_final: 0.8706 (m-30) REVERT: E 18 ARG cc_start: 0.8703 (ptp90) cc_final: 0.8458 (ptp-110) REVERT: E 21 LYS cc_start: 0.9150 (tmtm) cc_final: 0.8744 (pptt) REVERT: E 30 ASP cc_start: 0.8952 (t0) cc_final: 0.8680 (t0) REVERT: E 40 MET cc_start: 0.8764 (mtt) cc_final: 0.8245 (mmt) REVERT: E 64 GLN cc_start: 0.8973 (tt0) cc_final: 0.8533 (tt0) REVERT: E 68 LYS cc_start: 0.9379 (mmmm) cc_final: 0.9097 (mmmm) REVERT: E 69 ASP cc_start: 0.8650 (t0) cc_final: 0.8350 (t70) REVERT: E 90 GLN cc_start: 0.8836 (mt0) cc_final: 0.8490 (pt0) REVERT: E 114 ARG cc_start: 0.9053 (mtm-85) cc_final: 0.8836 (mtm180) REVERT: E 133 THR cc_start: 0.9138 (m) cc_final: 0.8837 (p) REVERT: E 155 GLU cc_start: 0.8937 (tt0) cc_final: 0.8198 (tt0) REVERT: E 169 ASN cc_start: 0.8858 (t0) cc_final: 0.8406 (t0) REVERT: E 213 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7873 (ttm110) REVERT: E 299 TYR cc_start: 0.7483 (t80) cc_final: 0.7160 (t80) REVERT: B 13 LYS cc_start: 0.9055 (tttm) cc_final: 0.8533 (tttt) REVERT: B 17 ASP cc_start: 0.9215 (m-30) cc_final: 0.8875 (m-30) REVERT: B 18 ARG cc_start: 0.9362 (ptm-80) cc_final: 0.9055 (ttp-110) REVERT: B 41 ARG cc_start: 0.8686 (mtt90) cc_final: 0.8343 (mtt90) REVERT: B 55 MET cc_start: 0.8754 (tpt) cc_final: 0.8372 (tpt) REVERT: B 61 MET cc_start: 0.8433 (ppp) cc_final: 0.7365 (ppp) REVERT: B 63 PHE cc_start: 0.9073 (t80) cc_final: 0.8604 (t80) REVERT: B 89 ASP cc_start: 0.9030 (m-30) cc_final: 0.8766 (m-30) REVERT: B 90 GLN cc_start: 0.9067 (mm110) cc_final: 0.8818 (mm110) REVERT: B 100 ASN cc_start: 0.8443 (p0) cc_final: 0.7503 (p0) REVERT: B 126 TYR cc_start: 0.8605 (t80) cc_final: 0.8185 (t80) REVERT: B 133 THR cc_start: 0.9099 (m) cc_final: 0.8643 (p) REVERT: B 142 ARG cc_start: 0.8354 (mtm180) cc_final: 0.8057 (mtm180) REVERT: B 148 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7349 (mm110) REVERT: B 151 THR cc_start: 0.8634 (p) cc_final: 0.7871 (p) REVERT: B 153 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8059 (mp0) REVERT: B 205 TYR cc_start: 0.8594 (m-10) cc_final: 0.8148 (m-10) REVERT: B 216 ARG cc_start: 0.8685 (mtm180) cc_final: 0.7853 (mtm180) REVERT: B 275 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7509 (mp) outliers start: 85 outliers final: 76 residues processed: 664 average time/residue: 0.1176 time to fit residues: 110.2440 Evaluate side-chains 707 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 629 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 108 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.154300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114231 restraints weight = 22224.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118973 restraints weight = 12131.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122158 restraints weight = 7967.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124260 restraints weight = 5893.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125743 restraints weight = 4771.359| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12202 Z= 0.163 Angle : 0.949 15.725 16687 Z= 0.449 Chirality : 0.049 0.239 2058 Planarity : 0.005 0.060 2046 Dihedral : 6.850 52.754 2087 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.90 % Allowed : 33.99 % Favored : 60.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.22), residues: 1515 helix: 0.24 (0.24), residues: 463 sheet: -1.17 (0.25), residues: 426 loop : -1.47 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 132 TYR 0.028 0.002 TYR D 141 PHE 0.024 0.002 PHE C 303 TRP 0.077 0.002 TRP B 168 HIS 0.008 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00372 (12176) covalent geometry : angle 0.94078 (16614) SS BOND : bond 0.00740 ( 5) SS BOND : angle 3.45985 ( 10) hydrogen bonds : bond 0.03707 ( 517) hydrogen bonds : angle 5.34640 ( 1755) link_ALPHA1-2 : bond 0.00587 ( 1) link_ALPHA1-2 : angle 1.42061 ( 3) link_ALPHA1-3 : bond 0.00788 ( 3) link_ALPHA1-3 : angle 1.49478 ( 9) link_ALPHA1-6 : bond 0.00611 ( 1) link_ALPHA1-6 : angle 1.73108 ( 3) link_BETA1-4 : bond 0.00435 ( 10) link_BETA1-4 : angle 1.92848 ( 30) link_NAG-ASN : bond 0.00186 ( 6) link_NAG-ASN : angle 1.81507 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 641 time to evaluate : 0.521 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9206 (t0) cc_final: 0.8735 (t0) REVERT: D 40 ASN cc_start: 0.8551 (m-40) cc_final: 0.8273 (m-40) REVERT: D 54 HIS cc_start: 0.8981 (m-70) cc_final: 0.8482 (m-70) REVERT: D 60 ASN cc_start: 0.9370 (t0) cc_final: 0.8677 (t0) REVERT: D 88 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8727 (mmtm) REVERT: D 97 ARG cc_start: 0.9270 (mmt90) cc_final: 0.8489 (mtm-85) REVERT: D 101 ASN cc_start: 0.8749 (m110) cc_final: 0.8475 (t0) REVERT: D 114 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.7910 (mmm160) REVERT: D 115 ASN cc_start: 0.8459 (p0) cc_final: 0.7785 (p0) REVERT: D 148 ASP cc_start: 0.7916 (p0) cc_final: 0.7646 (p0) REVERT: D 172 TYR cc_start: 0.7972 (t80) cc_final: 0.7649 (t80) REVERT: D 182 GLN cc_start: 0.7775 (tp-100) cc_final: 0.6937 (tp-100) REVERT: D 183 TRP cc_start: 0.8019 (m100) cc_final: 0.7806 (m-10) REVERT: D 207 ARG cc_start: 0.8773 (ptt90) cc_final: 0.8418 (ptt90) REVERT: D 214 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8539 (tppt) REVERT: D 219 ASP cc_start: 0.8805 (t70) cc_final: 0.8580 (t70) REVERT: D 223 MET cc_start: 0.8316 (mmp) cc_final: 0.8012 (mmp) REVERT: D 224 SER cc_start: 0.9151 (t) cc_final: 0.8199 (p) REVERT: D 226 TYR cc_start: 0.9025 (m-10) cc_final: 0.8362 (m-10) REVERT: D 239 GLN cc_start: 0.8687 (mt0) cc_final: 0.8271 (pt0) REVERT: C 25 TYR cc_start: 0.8470 (t80) cc_final: 0.8192 (t80) REVERT: C 35 GLU cc_start: 0.8069 (mp0) cc_final: 0.7505 (mp0) REVERT: C 55 HIS cc_start: 0.8570 (t-90) cc_final: 0.8181 (m-70) REVERT: C 58 GLU cc_start: 0.8434 (pp20) cc_final: 0.8010 (pp20) REVERT: C 70 LYS cc_start: 0.8023 (tmtm) cc_final: 0.7701 (tmtm) REVERT: C 102 ASN cc_start: 0.8415 (p0) cc_final: 0.7136 (t0) REVERT: C 131 ARG cc_start: 0.8830 (ttt90) cc_final: 0.8624 (ttt90) REVERT: C 165 GLU cc_start: 0.8757 (mm-30) cc_final: 0.7443 (mp0) REVERT: C 198 ASP cc_start: 0.8893 (p0) cc_final: 0.8609 (p0) REVERT: C 220 ARG cc_start: 0.6930 (mtm-85) cc_final: 0.6693 (mtm-85) REVERT: A 54 ASP cc_start: 0.8489 (m-30) cc_final: 0.8261 (m-30) REVERT: A 58 GLU cc_start: 0.7012 (pt0) cc_final: 0.6722 (pt0) REVERT: A 89 MET cc_start: 0.9163 (tpp) cc_final: 0.8838 (tpp) REVERT: A 102 ASN cc_start: 0.8172 (t0) cc_final: 0.7770 (t0) REVERT: A 105 LYS cc_start: 0.8682 (tptt) cc_final: 0.8151 (pttp) REVERT: A 107 VAL cc_start: 0.7951 (m) cc_final: 0.7686 (p) REVERT: A 113 MET cc_start: 0.8861 (mmm) cc_final: 0.8411 (mmm) REVERT: A 137 GLU cc_start: 0.8564 (pp20) cc_final: 0.8128 (tm-30) REVERT: A 144 ASP cc_start: 0.7525 (p0) cc_final: 0.7212 (p0) REVERT: A 167 VAL cc_start: 0.8818 (t) cc_final: 0.8233 (p) REVERT: A 212 MET cc_start: 0.8516 (mmm) cc_final: 0.8301 (mmm) REVERT: A 221 LYS cc_start: 0.8336 (mmmm) cc_final: 0.8103 (mmmm) REVERT: A 241 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8018 (tp-100) REVERT: A 245 TRP cc_start: 0.7251 (m100) cc_final: 0.6229 (m100) REVERT: A 287 TRP cc_start: 0.8875 (m100) cc_final: 0.8426 (m-10) REVERT: E 17 ASP cc_start: 0.9032 (m-30) cc_final: 0.8679 (m-30) REVERT: E 21 LYS cc_start: 0.9132 (tmtm) cc_final: 0.8721 (pptt) REVERT: E 30 ASP cc_start: 0.8967 (t0) cc_final: 0.8693 (t0) REVERT: E 40 MET cc_start: 0.8742 (mtt) cc_final: 0.8169 (mmt) REVERT: E 64 GLN cc_start: 0.9033 (tt0) cc_final: 0.8604 (tt0) REVERT: E 68 LYS cc_start: 0.9372 (mmmm) cc_final: 0.9092 (mmmm) REVERT: E 69 ASP cc_start: 0.8653 (t0) cc_final: 0.8375 (t70) REVERT: E 90 GLN cc_start: 0.8831 (mt0) cc_final: 0.8254 (tt0) REVERT: E 92 TRP cc_start: 0.9579 (t60) cc_final: 0.9184 (t60) REVERT: E 133 THR cc_start: 0.9136 (m) cc_final: 0.8839 (p) REVERT: E 155 GLU cc_start: 0.8856 (tt0) cc_final: 0.8169 (tt0) REVERT: E 169 ASN cc_start: 0.8756 (t0) cc_final: 0.8335 (t0) REVERT: E 216 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8242 (ttp80) REVERT: E 299 TYR cc_start: 0.7497 (t80) cc_final: 0.7202 (t80) REVERT: B 13 LYS cc_start: 0.9058 (tttm) cc_final: 0.8590 (ttmm) REVERT: B 17 ASP cc_start: 0.9217 (m-30) cc_final: 0.8886 (m-30) REVERT: B 18 ARG cc_start: 0.9347 (ptm-80) cc_final: 0.9037 (ttp-110) REVERT: B 41 ARG cc_start: 0.8761 (mtt90) cc_final: 0.8402 (mtt90) REVERT: B 61 MET cc_start: 0.8400 (ppp) cc_final: 0.7337 (ppp) REVERT: B 63 PHE cc_start: 0.9071 (t80) cc_final: 0.8625 (t80) REVERT: B 89 ASP cc_start: 0.9048 (m-30) cc_final: 0.8782 (m-30) REVERT: B 90 GLN cc_start: 0.9088 (mm110) cc_final: 0.8835 (mm110) REVERT: B 100 ASN cc_start: 0.8410 (p0) cc_final: 0.7527 (p0) REVERT: B 126 TYR cc_start: 0.8613 (t80) cc_final: 0.8177 (t80) REVERT: B 133 THR cc_start: 0.9117 (m) cc_final: 0.8711 (p) REVERT: B 142 ARG cc_start: 0.8326 (mtm180) cc_final: 0.8045 (mtm180) REVERT: B 148 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7254 (mm110) REVERT: B 151 THR cc_start: 0.8628 (p) cc_final: 0.7861 (p) REVERT: B 153 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8050 (mp0) REVERT: B 216 ARG cc_start: 0.8708 (mtm180) cc_final: 0.7810 (mtm180) outliers start: 72 outliers final: 68 residues processed: 667 average time/residue: 0.1134 time to fit residues: 107.0461 Evaluate side-chains 706 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 638 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 39 optimal weight: 0.0970 chunk 54 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.153037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112984 restraints weight = 22588.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117722 restraints weight = 12280.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120922 restraints weight = 8067.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123070 restraints weight = 5961.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124510 restraints weight = 4811.935| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12202 Z= 0.184 Angle : 0.931 14.609 16687 Z= 0.449 Chirality : 0.049 0.249 2058 Planarity : 0.005 0.060 2046 Dihedral : 6.545 51.030 2087 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 6.39 % Allowed : 33.09 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.22), residues: 1515 helix: 0.27 (0.24), residues: 463 sheet: -1.21 (0.25), residues: 426 loop : -1.42 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 132 TYR 0.029 0.002 TYR A 128 PHE 0.021 0.002 PHE E 31 TRP 0.073 0.002 TRP B 168 HIS 0.007 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00415 (12176) covalent geometry : angle 0.92263 (16614) SS BOND : bond 0.00616 ( 5) SS BOND : angle 3.33408 ( 10) hydrogen bonds : bond 0.03699 ( 517) hydrogen bonds : angle 5.34630 ( 1755) link_ALPHA1-2 : bond 0.00327 ( 1) link_ALPHA1-2 : angle 1.37241 ( 3) link_ALPHA1-3 : bond 0.00597 ( 3) link_ALPHA1-3 : angle 1.49249 ( 9) link_ALPHA1-6 : bond 0.00440 ( 1) link_ALPHA1-6 : angle 1.91357 ( 3) link_BETA1-4 : bond 0.00473 ( 10) link_BETA1-4 : angle 1.92199 ( 30) link_NAG-ASN : bond 0.00174 ( 6) link_NAG-ASN : angle 1.84000 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3096.81 seconds wall clock time: 53 minutes 52.92 seconds (3232.92 seconds total)