Starting phenix.real_space_refine on Wed Jul 30 10:43:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dw0_8922/07_2025/6dw0_8922.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dw0_8922/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6dw0_8922/07_2025/6dw0_8922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dw0_8922/07_2025/6dw0_8922.map" model { file = "/net/cci-nas-00/data/ceres_data/6dw0_8922/07_2025/6dw0_8922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dw0_8922/07_2025/6dw0_8922.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.073 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 7} 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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, '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: {'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 3, 'PHE:plan': 6, 'ARG: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: {'TYR:plan': 3, 'PHE:plan': 5, 'ARG:plan': 4, 'TRP:plan': 3, 'ASP:plan': 4} 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: 8.04, per 1000 atoms: 0.67 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: 4.18 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 1.94 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: 7.65 Time building geometry restraints manager: 5.13 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: 1.190 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.600 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (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 TRP 0.031 0.003 TRP C 94 HIS 0.012 0.002 HIS D 122 PHE 0.023 0.002 PHE D 113 TYR 0.026 0.002 TYR E 342 ARG 0.006 0.001 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 6) link_NAG-ASN : angle 2.86193 ( 18) 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_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) hydrogen bonds : bond 0.18347 ( 517) hydrogen bonds : angle 7.57764 ( 1755) SS BOND : bond 0.00182 ( 5) SS BOND : angle 2.10957 ( 10) covalent geometry : bond 0.00497 (12176) covalent geometry : angle 0.97378 (16614) *********************** 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 : 1.228 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: 0.8292 (pm20) REVERT: D 39 ASP cc_start: 0.9072 (t0) cc_final: 0.8665 (t70) REVERT: D 40 ASN cc_start: 0.8362 (m-40) cc_final: 0.7012 (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: 0.8950 (ptp) REVERT: D 58 TYR cc_start: 0.8678 (t80) cc_final: 0.8284 (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: 0.6471 (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: 0.8749 (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: 0.7520 (t70) REVERT: D 112 PHE cc_start: 0.8003 (p90) cc_final: 0.7089 (p90) REVERT: D 122 HIS cc_start: 0.8561 (m-70) cc_final: 0.7594 (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: 0.6851 (t80) REVERT: D 182 GLN cc_start: 0.8483 (tp40) cc_final: 0.8101 (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: 0.7850 (pp20) REVERT: C 113 MET cc_start: 0.8524 (mmm) cc_final: 0.8074 (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: 0.8457 (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: 0.7548 (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: 0.7813 (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: 0.8348 (mmm) REVERT: A 114 PRO cc_start: 0.9223 (Cg_exo) cc_final: 0.8996 (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: 0.9377 (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: 0.8660 (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: 0.9043 (mt) REVERT: E 90 GLN cc_start: 0.8945 (mt0) cc_final: 0.8409 (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: 0.7825 (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: 0.8353 (p90) REVERT: E 169 ASN cc_start: 0.9028 (t0) cc_final: 0.8460 (t0) REVERT: E 175 VAL cc_start: 0.9280 (t) cc_final: 0.9061 (t) REVERT: E 181 ILE cc_start: 0.9252 (mm) cc_final: 0.8970 (mm) REVERT: E 191 TYR cc_start: 0.8987 (p90) cc_final: 0.8466 (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: 0.7857 (m-80) REVERT: B 13 LYS cc_start: 0.8949 (tttm) cc_final: 0.8517 (ttmt) REVERT: B 17 ASP cc_start: 0.9369 (m-30) cc_final: 0.9020 (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: 0.8624 (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: 0.7814 (mtm180) REVERT: B 125 LEU cc_start: 0.9120 (tp) cc_final: 0.8863 (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: 0.2780 time to fit residues: 300.3271 Evaluate side-chains 648 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.154652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115656 restraints weight = 22173.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120378 restraints weight = 12340.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123574 restraints weight = 8125.837| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12202 Z= 0.199 Angle : 0.814 12.132 16687 Z= 0.401 Chirality : 0.049 0.263 2058 Planarity : 0.005 0.057 2046 Dihedral : 14.830 101.022 2087 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.08 % Allowed : 20.07 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.20), residues: 1515 helix: -1.18 (0.21), residues: 453 sheet: -1.78 (0.24), residues: 429 loop : -2.13 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 92 HIS 0.007 0.002 HIS E 119 PHE 0.039 0.002 PHE B 221 TYR 0.021 0.002 TYR A 59 ARG 0.007 0.001 ARG C 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 6) link_NAG-ASN : angle 2.06967 ( 18) link_ALPHA1-6 : bond 0.00123 ( 1) link_ALPHA1-6 : angle 3.01517 ( 3) link_BETA1-4 : bond 0.00470 ( 10) link_BETA1-4 : angle 2.56476 ( 30) link_ALPHA1-2 : bond 0.00428 ( 1) link_ALPHA1-2 : angle 2.24137 ( 3) link_ALPHA1-3 : bond 0.00832 ( 3) link_ALPHA1-3 : angle 1.92049 ( 9) hydrogen bonds : bond 0.04480 ( 517) hydrogen bonds : angle 5.71049 ( 1755) SS BOND : bond 0.01086 ( 5) SS BOND : angle 1.89510 ( 10) covalent geometry : bond 0.00425 (12176) covalent geometry : angle 0.80139 (16614) *********************** 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 731 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 669 time to evaluate : 2.069 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: D 32 ASN cc_start: 0.9530 (m-40) cc_final: 0.9173 (m110) REVERT: D 39 ASP cc_start: 0.9158 (t0) cc_final: 0.8640 (t70) REVERT: D 40 ASN cc_start: 0.8665 (m-40) cc_final: 0.8433 (m-40) REVERT: D 51 THR cc_start: 0.9271 (m) cc_final: 0.9041 (p) REVERT: D 54 HIS cc_start: 0.8982 (m-70) cc_final: 0.8666 (m-70) REVERT: D 57 MET cc_start: 0.9127 (ptp) cc_final: 0.8924 (ptp) REVERT: D 58 TYR cc_start: 0.8800 (t80) cc_final: 0.8595 (t80) REVERT: D 88 LYS cc_start: 0.9168 (mttt) cc_final: 0.8945 (mtmm) REVERT: D 90 ASN cc_start: 0.7376 (t0) cc_final: 0.6663 (p0) REVERT: D 101 ASN cc_start: 0.8547 (m110) cc_final: 0.7801 (t0) REVERT: D 110 ASP cc_start: 0.8920 (t70) cc_final: 0.8637 (t70) REVERT: D 115 ASN cc_start: 0.8162 (p0) cc_final: 0.7541 (p0) REVERT: D 131 LEU cc_start: 0.8750 (tp) cc_final: 0.8518 (tp) REVERT: D 138 ARG cc_start: 0.8882 (ttp-170) cc_final: 0.8200 (ttp80) REVERT: D 172 TYR cc_start: 0.7410 (t80) cc_final: 0.6820 (t80) REVERT: D 176 ARG cc_start: 0.8768 (ptm-80) cc_final: 0.8517 (ptm-80) REVERT: C 25 TYR cc_start: 0.8447 (t80) cc_final: 0.8196 (t80) REVERT: C 58 GLU cc_start: 0.8113 (pp20) cc_final: 0.7850 (pp20) REVERT: C 65 PHE cc_start: 0.8629 (t80) cc_final: 0.8035 (t80) REVERT: C 67 GLN cc_start: 0.8489 (pt0) cc_final: 0.7904 (pt0) REVERT: C 97 ASP cc_start: 0.8665 (p0) cc_final: 0.8262 (p0) REVERT: C 113 MET cc_start: 0.8897 (mmm) cc_final: 0.8420 (mmm) REVERT: C 144 ASP cc_start: 0.8367 (t0) cc_final: 0.8085 (t70) REVERT: C 196 THR cc_start: 0.8297 (m) cc_final: 0.8073 (p) REVERT: C 212 MET cc_start: 0.8228 (mmm) cc_final: 0.7900 (mtm) REVERT: C 217 HIS cc_start: 0.8850 (m-70) cc_final: 0.8576 (m-70) REVERT: A 16 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8468 (ttp-110) REVERT: A 47 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9049 (p) REVERT: A 70 LYS cc_start: 0.8582 (tmmt) cc_final: 0.8372 (tmmt) REVERT: A 105 LYS cc_start: 0.8610 (tptt) cc_final: 0.8266 (pttp) REVERT: A 107 VAL cc_start: 0.7895 (m) cc_final: 0.7675 (p) REVERT: A 109 HIS cc_start: 0.8597 (m-70) cc_final: 0.8386 (m90) REVERT: A 113 MET cc_start: 0.8818 (mmm) cc_final: 0.8428 (mmm) REVERT: A 130 MET cc_start: 0.8521 (ptp) cc_final: 0.8197 (ptp) REVERT: A 144 ASP cc_start: 0.8267 (p0) cc_final: 0.7728 (p0) REVERT: A 150 HIS cc_start: 0.7880 (m-70) cc_final: 0.7612 (m90) REVERT: A 167 VAL cc_start: 0.9071 (t) cc_final: 0.8584 (p) REVERT: A 189 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8195 (pm20) REVERT: A 190 TYR cc_start: 0.8837 (m-10) cc_final: 0.8492 (m-10) REVERT: A 216 PHE cc_start: 0.8895 (m-10) cc_final: 0.8470 (m-10) REVERT: A 220 ARG cc_start: 0.8885 (ttm-80) cc_final: 0.8671 (tpp80) REVERT: A 241 GLN cc_start: 0.9079 (tp-100) cc_final: 0.7672 (tp-100) REVERT: A 245 TRP cc_start: 0.7531 (m100) cc_final: 0.6373 (m100) REVERT: E 20 LEU cc_start: 0.9295 (mm) cc_final: 0.8521 (mm) REVERT: E 21 LYS cc_start: 0.9141 (tmtm) cc_final: 0.8763 (pptt) REVERT: E 37 ASP cc_start: 0.8098 (t0) cc_final: 0.7811 (t0) REVERT: E 44 VAL cc_start: 0.9474 (t) cc_final: 0.9148 (p) REVERT: E 64 GLN cc_start: 0.9131 (tt0) cc_final: 0.8728 (tt0) REVERT: E 68 LYS cc_start: 0.9316 (mmmm) cc_final: 0.8999 (mmmm) REVERT: E 69 ASP cc_start: 0.8905 (t0) cc_final: 0.8654 (t70) REVERT: E 81 LEU cc_start: 0.9124 (mt) cc_final: 0.8691 (mt) REVERT: E 90 GLN cc_start: 0.8872 (mt0) cc_final: 0.8145 (tt0) REVERT: E 92 TRP cc_start: 0.9566 (t60) cc_final: 0.9205 (t60) REVERT: E 112 LYS cc_start: 0.9134 (ttmm) cc_final: 0.8780 (ttmm) REVERT: E 117 ARG cc_start: 0.8599 (ttm170) cc_final: 0.8320 (ttm170) REVERT: E 129 ARG cc_start: 0.8648 (ttt-90) cc_final: 0.7491 (ttp80) REVERT: E 131 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9048 (m) REVERT: E 133 THR cc_start: 0.9086 (m) cc_final: 0.8687 (p) REVERT: E 169 ASN cc_start: 0.9018 (t0) cc_final: 0.8535 (t0) REVERT: E 180 LYS cc_start: 0.9553 (mtpp) cc_final: 0.9136 (mppt) REVERT: E 191 TYR cc_start: 0.8830 (p90) cc_final: 0.8561 (p90) REVERT: B 13 LYS cc_start: 0.9088 (tttm) cc_final: 0.8620 (ttmt) REVERT: B 17 ASP cc_start: 0.9330 (m-30) cc_final: 0.9085 (m-30) REVERT: B 41 ARG cc_start: 0.8695 (mtt90) cc_final: 0.7775 (mtt90) REVERT: B 55 MET cc_start: 0.9077 (mmp) cc_final: 0.8753 (tpp) REVERT: B 61 MET cc_start: 0.8150 (ppp) cc_final: 0.7431 (ppp) REVERT: B 63 PHE cc_start: 0.8991 (t80) cc_final: 0.8751 (t80) REVERT: B 96 THR cc_start: 0.9581 (m) cc_final: 0.9362 (p) REVERT: B 129 ARG cc_start: 0.8417 (ttp80) cc_final: 0.7219 (ttt-90) REVERT: B 133 THR cc_start: 0.9040 (m) cc_final: 0.8714 (p) REVERT: B 142 ARG cc_start: 0.8325 (pmm-80) cc_final: 0.7951 (ptp-170) REVERT: B 147 GLU cc_start: 0.8785 (tt0) cc_final: 0.8468 (tp30) REVERT: B 148 GLN cc_start: 0.8050 (mm110) cc_final: 0.7579 (mm110) REVERT: B 151 THR cc_start: 0.8507 (p) cc_final: 0.8125 (p) REVERT: B 153 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8681 (mm-30) REVERT: B 168 TRP cc_start: 0.8258 (m-90) cc_final: 0.7942 (m-10) REVERT: B 169 ASN cc_start: 0.8683 (t0) cc_final: 0.8444 (t0) REVERT: B 192 LYS cc_start: 0.8641 (mmmt) cc_final: 0.7968 (mmmm) REVERT: B 209 SER cc_start: 0.8996 (t) cc_final: 0.8321 (t) REVERT: B 213 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7541 (mtm180) REVERT: B 217 ASN cc_start: 0.7750 (p0) cc_final: 0.7513 (p0) outliers start: 62 outliers final: 43 residues processed: 687 average time/residue: 0.3249 time to fit residues: 316.6182 Evaluate side-chains 692 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 645 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 16 ARG 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 68 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 162 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 42 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 15 THR 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 46 SER Chi-restraints excluded: chain B residue 53 VAL 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 59 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** A 115 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** B 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.152709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114348 restraints weight = 22780.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119018 restraints weight = 12428.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122193 restraints weight = 8085.461| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12202 Z= 0.198 Angle : 0.810 9.551 16687 Z= 0.396 Chirality : 0.048 0.227 2058 Planarity : 0.005 0.052 2046 Dihedral : 11.575 87.002 2087 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.90 % Allowed : 23.83 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.21), residues: 1515 helix: -0.59 (0.22), residues: 459 sheet: -1.52 (0.24), residues: 431 loop : -2.04 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 92 HIS 0.006 0.002 HIS C 150 PHE 0.021 0.002 PHE A 216 TYR 0.023 0.002 TYR E 126 ARG 0.007 0.001 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 6) link_NAG-ASN : angle 2.11359 ( 18) link_ALPHA1-6 : bond 0.00861 ( 1) link_ALPHA1-6 : angle 3.44922 ( 3) link_BETA1-4 : bond 0.00417 ( 10) link_BETA1-4 : angle 2.52550 ( 30) link_ALPHA1-2 : bond 0.00653 ( 1) link_ALPHA1-2 : angle 2.65441 ( 3) link_ALPHA1-3 : bond 0.00647 ( 3) link_ALPHA1-3 : angle 1.62301 ( 9) hydrogen bonds : bond 0.04107 ( 517) hydrogen bonds : angle 5.52024 ( 1755) SS BOND : bond 0.00485 ( 5) SS BOND : angle 2.25409 ( 10) covalent geometry : bond 0.00430 (12176) covalent geometry : angle 0.79677 (16614) *********************** 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 722 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 650 time to evaluate : 1.245 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: D 39 ASP cc_start: 0.9142 (t0) cc_final: 0.8647 (t70) REVERT: D 40 ASN cc_start: 0.8616 (m-40) cc_final: 0.8383 (m-40) REVERT: D 51 THR cc_start: 0.9355 (m) cc_final: 0.9110 (p) REVERT: D 54 HIS cc_start: 0.8988 (m-70) cc_final: 0.8712 (m90) REVERT: D 57 MET cc_start: 0.9118 (ptp) cc_final: 0.8893 (ptp) REVERT: D 58 TYR cc_start: 0.8877 (t80) cc_final: 0.8653 (t80) REVERT: D 90 ASN cc_start: 0.7440 (t0) cc_final: 0.6662 (p0) REVERT: D 101 ASN cc_start: 0.8526 (m110) cc_final: 0.7862 (t0) REVERT: D 110 ASP cc_start: 0.9081 (t70) cc_final: 0.8867 (t70) REVERT: D 115 ASN cc_start: 0.8065 (p0) cc_final: 0.7094 (p0) REVERT: D 138 ARG cc_start: 0.8730 (ttp-170) cc_final: 0.8002 (ttp80) REVERT: D 148 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7828 (p0) REVERT: D 172 TYR cc_start: 0.7412 (t80) cc_final: 0.6579 (t80) REVERT: D 182 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8131 (mm-40) REVERT: D 207 ARG cc_start: 0.8650 (ptt90) cc_final: 0.8289 (ptt90) REVERT: D 214 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8588 (tppt) REVERT: D 215 THR cc_start: 0.9398 (t) cc_final: 0.9196 (t) REVERT: D 222 VAL cc_start: 0.9537 (t) cc_final: 0.9274 (m) REVERT: D 223 MET cc_start: 0.8650 (mmm) cc_final: 0.8408 (mmm) REVERT: C 25 TYR cc_start: 0.8620 (t80) cc_final: 0.8150 (t80) REVERT: C 58 GLU cc_start: 0.8242 (pp20) cc_final: 0.7919 (pp20) REVERT: C 65 PHE cc_start: 0.8675 (t80) cc_final: 0.8140 (t80) REVERT: C 67 GLN cc_start: 0.8582 (pt0) cc_final: 0.8030 (pt0) REVERT: C 70 LYS cc_start: 0.8200 (tmtm) cc_final: 0.7988 (tmtm) REVERT: C 97 ASP cc_start: 0.8663 (p0) cc_final: 0.8228 (p0) REVERT: C 126 LEU cc_start: 0.9127 (mt) cc_final: 0.8920 (mm) REVERT: C 144 ASP cc_start: 0.8464 (t0) cc_final: 0.8114 (t70) REVERT: C 165 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8650 (mm-30) REVERT: C 188 ASN cc_start: 0.8095 (p0) cc_final: 0.7749 (p0) REVERT: C 189 GLN cc_start: 0.9067 (mt0) cc_final: 0.8803 (mt0) REVERT: C 195 GLN cc_start: 0.9093 (pm20) cc_final: 0.8841 (pm20) REVERT: C 212 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7920 (mtm) REVERT: C 221 LYS cc_start: 0.8959 (mttm) cc_final: 0.8468 (mtmt) REVERT: C 289 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8789 (pp) REVERT: A 16 ARG cc_start: 0.8692 (mtt90) cc_final: 0.8391 (ttp-110) REVERT: A 47 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9060 (p) REVERT: A 57 MET cc_start: 0.8425 (tpp) cc_final: 0.8215 (tpp) REVERT: A 70 LYS cc_start: 0.8648 (tmmt) cc_final: 0.8356 (tmmt) REVERT: A 77 LYS cc_start: 0.9258 (mppt) cc_final: 0.9049 (mppt) REVERT: A 94 TRP cc_start: 0.9418 (t60) cc_final: 0.8964 (t60) REVERT: A 102 ASN cc_start: 0.7754 (t0) cc_final: 0.7472 (t0) REVERT: A 105 LYS cc_start: 0.8698 (tptt) cc_final: 0.8313 (pttp) REVERT: A 107 VAL cc_start: 0.7812 (m) cc_final: 0.7565 (p) REVERT: A 109 HIS cc_start: 0.8598 (m-70) cc_final: 0.8367 (m90) REVERT: A 113 MET cc_start: 0.8818 (mmm) cc_final: 0.8498 (mmm) REVERT: A 130 MET cc_start: 0.8578 (ptp) cc_final: 0.8235 (ptp) REVERT: A 137 GLU cc_start: 0.8841 (pp20) cc_final: 0.8595 (tm-30) REVERT: A 144 ASP cc_start: 0.8179 (p0) cc_final: 0.7631 (p0) REVERT: A 150 HIS cc_start: 0.7441 (m-70) cc_final: 0.7216 (m90) REVERT: A 167 VAL cc_start: 0.9100 (t) cc_final: 0.8657 (p) REVERT: A 189 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: A 190 TYR cc_start: 0.8700 (m-10) cc_final: 0.8392 (m-10) REVERT: A 215 HIS cc_start: 0.8208 (m-70) cc_final: 0.7688 (m90) REVERT: A 241 GLN cc_start: 0.9093 (tp-100) cc_final: 0.7723 (tp-100) REVERT: A 245 TRP cc_start: 0.7537 (m100) cc_final: 0.6319 (m100) REVERT: E 18 ARG cc_start: 0.8781 (ptp90) cc_final: 0.8481 (ptp90) REVERT: E 21 LYS cc_start: 0.9162 (tmtm) cc_final: 0.8756 (pptt) REVERT: E 28 ARG cc_start: 0.8780 (ptt180) cc_final: 0.8535 (ptm160) REVERT: E 30 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8791 (t0) REVERT: E 37 ASP cc_start: 0.8097 (t0) cc_final: 0.7789 (t0) REVERT: E 40 MET cc_start: 0.8710 (mtt) cc_final: 0.8416 (mtt) REVERT: E 61 MET cc_start: 0.8937 (ptm) cc_final: 0.8620 (ppp) REVERT: E 64 GLN cc_start: 0.9029 (tt0) cc_final: 0.8578 (tt0) REVERT: E 68 LYS cc_start: 0.9364 (mmmm) cc_final: 0.8925 (mmmm) REVERT: E 69 ASP cc_start: 0.8878 (t0) cc_final: 0.8594 (t70) REVERT: E 90 GLN cc_start: 0.8852 (mt0) cc_final: 0.8462 (pt0) REVERT: E 112 LYS cc_start: 0.9164 (ttmm) cc_final: 0.8871 (ttmm) REVERT: E 133 THR cc_start: 0.9081 (m) cc_final: 0.8699 (p) REVERT: E 141 ARG cc_start: 0.8789 (mtt90) cc_final: 0.8504 (mtt90) REVERT: E 142 ARG cc_start: 0.8023 (ttm170) cc_final: 0.7798 (ttm110) REVERT: E 169 ASN cc_start: 0.9129 (t0) cc_final: 0.8561 (t0) REVERT: E 213 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.7741 (ptp-110) REVERT: B 13 LYS cc_start: 0.9048 (tttm) cc_final: 0.8616 (ttmt) REVERT: B 17 ASP cc_start: 0.9279 (m-30) cc_final: 0.8953 (m-30) REVERT: B 41 ARG cc_start: 0.8507 (mtt90) cc_final: 0.7911 (mtt90) REVERT: B 55 MET cc_start: 0.8975 (mmp) cc_final: 0.8743 (mmm) REVERT: B 61 MET cc_start: 0.8308 (ppp) cc_final: 0.7345 (ppp) REVERT: B 63 PHE cc_start: 0.9114 (t80) cc_final: 0.8797 (t80) REVERT: B 89 ASP cc_start: 0.8718 (m-30) cc_final: 0.8454 (t0) REVERT: B 90 GLN cc_start: 0.8956 (mm110) cc_final: 0.8693 (mm-40) REVERT: B 96 THR cc_start: 0.9588 (m) cc_final: 0.9328 (p) REVERT: B 112 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8492 (ttpp) REVERT: B 129 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7055 (ttt-90) REVERT: B 133 THR cc_start: 0.9087 (m) cc_final: 0.8770 (p) REVERT: B 145 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8674 (tm) REVERT: B 147 GLU cc_start: 0.8813 (tt0) cc_final: 0.8369 (tp30) REVERT: B 151 THR cc_start: 0.8369 (p) cc_final: 0.8012 (p) REVERT: B 168 TRP cc_start: 0.8326 (m-90) cc_final: 0.8099 (m-10) REVERT: B 209 SER cc_start: 0.8935 (t) cc_final: 0.8608 (t) REVERT: B 213 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7401 (mtm180) REVERT: B 342 TYR cc_start: 0.8211 (t80) cc_final: 0.7964 (t80) outliers start: 72 outliers final: 53 residues processed: 674 average time/residue: 0.2810 time to fit residues: 265.7947 Evaluate side-chains 692 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 632 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 THR 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 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 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 93 ILE 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 212 MET 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 40 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 SER 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 30 ASP Chi-restraints excluded: chain E residue 42 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 B residue 11 TYR 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 46 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 145 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 222 ILE Chi-restraints excluded: chain B residue 231 LEU 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 97 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ** 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** B 64 GLN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.154997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114690 restraints weight = 22492.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119393 restraints weight = 12318.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122617 restraints weight = 8133.366| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12202 Z= 0.163 Angle : 0.798 13.375 16687 Z= 0.383 Chirality : 0.047 0.234 2058 Planarity : 0.004 0.052 2046 Dihedral : 9.658 80.691 2087 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.39 % Allowed : 24.41 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.21), residues: 1515 helix: -0.16 (0.23), residues: 459 sheet: -1.32 (0.25), residues: 401 loop : -2.00 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 69 HIS 0.009 0.001 HIS C 150 PHE 0.019 0.002 PHE C 297 TYR 0.018 0.002 TYR D 72 ARG 0.010 0.001 ARG B 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 6) link_NAG-ASN : angle 2.00391 ( 18) link_ALPHA1-6 : bond 0.01609 ( 1) link_ALPHA1-6 : angle 2.04829 ( 3) link_BETA1-4 : bond 0.00432 ( 10) link_BETA1-4 : angle 2.49096 ( 30) link_ALPHA1-2 : bond 0.00706 ( 1) link_ALPHA1-2 : angle 2.19071 ( 3) link_ALPHA1-3 : bond 0.00795 ( 3) link_ALPHA1-3 : angle 1.59144 ( 9) hydrogen bonds : bond 0.03828 ( 517) hydrogen bonds : angle 5.33128 ( 1755) SS BOND : bond 0.00346 ( 5) SS BOND : angle 1.52497 ( 10) covalent geometry : bond 0.00354 (12176) covalent geometry : angle 0.78671 (16614) *********************** 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 740 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 662 time to evaluate : 1.370 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: D 39 ASP cc_start: 0.9085 (t0) cc_final: 0.8645 (t70) REVERT: D 40 ASN cc_start: 0.8671 (m-40) cc_final: 0.8412 (m-40) REVERT: D 54 HIS cc_start: 0.8964 (m-70) cc_final: 0.8712 (m90) REVERT: D 58 TYR cc_start: 0.8850 (t80) cc_final: 0.8545 (t80) REVERT: D 90 ASN cc_start: 0.7236 (t0) cc_final: 0.6385 (p0) REVERT: D 97 ARG cc_start: 0.9249 (mmt90) cc_final: 0.8729 (mtm-85) REVERT: D 99 ASN cc_start: 0.8857 (t0) cc_final: 0.8371 (t0) REVERT: D 101 ASN cc_start: 0.8667 (m110) cc_final: 0.7992 (m110) REVERT: D 115 ASN cc_start: 0.8038 (p0) cc_final: 0.7129 (p0) REVERT: D 148 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7955 (p0) REVERT: D 172 TYR cc_start: 0.7426 (t80) cc_final: 0.6600 (t80) REVERT: D 214 LYS cc_start: 0.9243 (ttpt) cc_final: 0.8625 (tppt) REVERT: D 219 ASP cc_start: 0.8977 (t0) cc_final: 0.8637 (t0) REVERT: D 222 VAL cc_start: 0.9531 (t) cc_final: 0.9258 (m) REVERT: D 223 MET cc_start: 0.8574 (mmm) cc_final: 0.8343 (mmm) REVERT: C 25 TYR cc_start: 0.8581 (t80) cc_final: 0.8070 (t80) REVERT: C 58 GLU cc_start: 0.8240 (pp20) cc_final: 0.7896 (pp20) REVERT: C 65 PHE cc_start: 0.8738 (t80) cc_final: 0.8354 (t80) REVERT: C 67 GLN cc_start: 0.8577 (pt0) cc_final: 0.8346 (pt0) REVERT: C 70 LYS cc_start: 0.8231 (tmtm) cc_final: 0.7941 (tmtm) REVERT: C 81 THR cc_start: 0.8468 (p) cc_final: 0.8204 (t) REVERT: C 97 ASP cc_start: 0.8607 (p0) cc_final: 0.8256 (p0) REVERT: C 102 ASN cc_start: 0.8486 (p0) cc_final: 0.6973 (t0) REVERT: C 186 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7332 (mmm160) REVERT: C 212 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7773 (mtm) REVERT: C 289 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8938 (pp) REVERT: A 44 ILE cc_start: 0.8777 (pp) cc_final: 0.8468 (pp) REVERT: A 47 THR cc_start: 0.9408 (OUTLIER) cc_final: 0.9115 (p) REVERT: A 57 MET cc_start: 0.8269 (tpp) cc_final: 0.8035 (tpt) REVERT: A 70 LYS cc_start: 0.8652 (tmmt) cc_final: 0.8334 (tmmt) REVERT: A 94 TRP cc_start: 0.9375 (t60) cc_final: 0.9019 (t60) REVERT: A 102 ASN cc_start: 0.7850 (t0) cc_final: 0.7448 (t0) REVERT: A 105 LYS cc_start: 0.8674 (tptt) cc_final: 0.8313 (pttm) REVERT: A 107 VAL cc_start: 0.8000 (m) cc_final: 0.7719 (p) REVERT: A 144 ASP cc_start: 0.7717 (p0) cc_final: 0.7247 (p0) REVERT: A 150 HIS cc_start: 0.7250 (m-70) cc_final: 0.7013 (m90) REVERT: A 167 VAL cc_start: 0.8955 (t) cc_final: 0.8395 (p) REVERT: A 189 GLN cc_start: 0.8169 (pm20) cc_final: 0.7959 (pm20) REVERT: A 190 TYR cc_start: 0.8579 (m-10) cc_final: 0.8288 (m-10) REVERT: A 212 MET cc_start: 0.8535 (mmm) cc_final: 0.8273 (mmm) REVERT: A 215 HIS cc_start: 0.8274 (m-70) cc_final: 0.8016 (m90) REVERT: A 221 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8355 (mmmm) REVERT: A 241 GLN cc_start: 0.9091 (tp-100) cc_final: 0.7733 (tp-100) REVERT: A 245 TRP cc_start: 0.7409 (m100) cc_final: 0.6266 (m100) REVERT: E 21 LYS cc_start: 0.9165 (tmtm) cc_final: 0.8802 (pptt) REVERT: E 30 ASP cc_start: 0.9080 (t0) cc_final: 0.8831 (t0) REVERT: E 37 ASP cc_start: 0.8112 (t0) cc_final: 0.7886 (t0) REVERT: E 40 MET cc_start: 0.8599 (mtt) cc_final: 0.8264 (mmt) REVERT: E 64 GLN cc_start: 0.8992 (tt0) cc_final: 0.8494 (tt0) REVERT: E 68 LYS cc_start: 0.9391 (mmmm) cc_final: 0.8941 (mmmm) REVERT: E 69 ASP cc_start: 0.8835 (t0) cc_final: 0.8565 (t70) REVERT: E 90 GLN cc_start: 0.8822 (mt0) cc_final: 0.8476 (pt0) REVERT: E 112 LYS cc_start: 0.9188 (ttmm) cc_final: 0.8969 (ttmm) REVERT: E 133 THR cc_start: 0.9081 (m) cc_final: 0.8691 (p) REVERT: E 142 ARG cc_start: 0.8030 (ttm170) cc_final: 0.7672 (ttm170) REVERT: E 169 ASN cc_start: 0.9029 (t0) cc_final: 0.8495 (t0) REVERT: E 213 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.7767 (ptp-110) REVERT: B 13 LYS cc_start: 0.9053 (tttm) cc_final: 0.8583 (ttmt) REVERT: B 17 ASP cc_start: 0.9263 (m-30) cc_final: 0.8930 (m-30) REVERT: B 37 ASP cc_start: 0.8860 (t0) cc_final: 0.8395 (t0) REVERT: B 41 ARG cc_start: 0.8752 (mtt90) cc_final: 0.8048 (mtt90) REVERT: B 61 MET cc_start: 0.8342 (ppp) cc_final: 0.7407 (ppp) REVERT: B 63 PHE cc_start: 0.9049 (t80) cc_final: 0.8648 (t80) REVERT: B 90 GLN cc_start: 0.9105 (mm110) cc_final: 0.8810 (mm110) REVERT: B 96 THR cc_start: 0.9571 (m) cc_final: 0.9304 (p) REVERT: B 126 TYR cc_start: 0.8577 (t80) cc_final: 0.8288 (t80) REVERT: B 129 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7095 (ttt-90) REVERT: B 133 THR cc_start: 0.9082 (m) cc_final: 0.8752 (p) REVERT: B 142 ARG cc_start: 0.8246 (mtp180) cc_final: 0.7749 (mtm180) REVERT: B 148 GLN cc_start: 0.7749 (mm110) cc_final: 0.7250 (mm110) REVERT: B 167 TYR cc_start: 0.8483 (p90) cc_final: 0.7788 (p90) REVERT: B 169 ASN cc_start: 0.8620 (t0) cc_final: 0.7525 (t0) REVERT: B 209 SER cc_start: 0.8991 (t) cc_final: 0.8758 (t) REVERT: B 216 ARG cc_start: 0.8600 (mtm180) cc_final: 0.7748 (mtm180) outliers start: 78 outliers final: 62 residues processed: 682 average time/residue: 0.2498 time to fit residues: 240.5864 Evaluate side-chains 703 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 637 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 76 ILE Chi-restraints excluded: chain D residue 81 THR 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 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 212 MET 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 127 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 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 E residue 42 ILE Chi-restraints excluded: chain E residue 44 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 332 PHE Chi-restraints excluded: chain B residue 11 TYR 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 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 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 285 LEU 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 21 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 113 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 = 0.3994 r_free = 0.3994 target = 0.155693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115684 restraints weight = 22120.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120363 restraints weight = 12109.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123555 restraints weight = 7981.750| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12202 Z= 0.145 Angle : 0.821 13.588 16687 Z= 0.391 Chirality : 0.047 0.240 2058 Planarity : 0.005 0.051 2046 Dihedral : 8.685 76.087 2087 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.90 % Allowed : 27.35 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.21), residues: 1515 helix: 0.04 (0.23), residues: 459 sheet: -1.33 (0.25), residues: 419 loop : -1.78 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 168 HIS 0.007 0.001 HIS E 267 PHE 0.019 0.001 PHE C 64 TYR 0.034 0.002 TYR C 293 ARG 0.009 0.001 ARG E 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 6) link_NAG-ASN : angle 1.92219 ( 18) link_ALPHA1-6 : bond 0.01133 ( 1) link_ALPHA1-6 : angle 1.59813 ( 3) link_BETA1-4 : bond 0.00457 ( 10) link_BETA1-4 : angle 2.41492 ( 30) link_ALPHA1-2 : bond 0.00721 ( 1) link_ALPHA1-2 : angle 1.65988 ( 3) link_ALPHA1-3 : bond 0.00912 ( 3) link_ALPHA1-3 : angle 1.60938 ( 9) hydrogen bonds : bond 0.03681 ( 517) hydrogen bonds : angle 5.22548 ( 1755) SS BOND : bond 0.00358 ( 5) SS BOND : angle 1.55667 ( 10) covalent geometry : bond 0.00318 (12176) covalent geometry : angle 0.81140 (16614) *********************** 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 739 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 667 time to evaluate : 1.380 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: 0.9107 (t0) cc_final: 0.8613 (t70) REVERT: D 40 ASN cc_start: 0.8671 (m-40) cc_final: 0.8372 (m-40) REVERT: D 54 HIS cc_start: 0.8952 (m-70) cc_final: 0.8671 (m90) REVERT: D 58 TYR cc_start: 0.8799 (t80) cc_final: 0.8593 (t80) REVERT: D 60 ASN cc_start: 0.9408 (t0) cc_final: 0.8717 (t0) REVERT: D 82 TRP cc_start: 0.9300 (p90) cc_final: 0.9005 (p90) REVERT: D 90 ASN cc_start: 0.7264 (t0) cc_final: 0.6423 (p0) REVERT: D 99 ASN cc_start: 0.8936 (t0) cc_final: 0.8431 (t0) REVERT: D 101 ASN cc_start: 0.8748 (m110) cc_final: 0.7988 (m110) REVERT: D 115 ASN cc_start: 0.8147 (p0) cc_final: 0.7337 (p0) REVERT: D 148 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7847 (p0) REVERT: D 157 ASN cc_start: 0.7896 (m-40) cc_final: 0.7678 (m-40) REVERT: D 172 TYR cc_start: 0.7149 (t80) cc_final: 0.6597 (t80) REVERT: D 176 ARG cc_start: 0.8671 (ptm160) cc_final: 0.8402 (ptm-80) REVERT: D 207 ARG cc_start: 0.8631 (ptt90) cc_final: 0.8160 (ptt90) REVERT: D 214 LYS cc_start: 0.9133 (ttpt) cc_final: 0.8610 (tppt) REVERT: D 219 ASP cc_start: 0.9035 (t0) cc_final: 0.8673 (t0) REVERT: C 25 TYR cc_start: 0.8514 (t80) cc_final: 0.7954 (t80) REVERT: C 55 HIS cc_start: 0.8384 (t-90) cc_final: 0.7999 (m-70) REVERT: C 58 GLU cc_start: 0.8294 (pp20) cc_final: 0.7965 (pp20) REVERT: C 65 PHE cc_start: 0.8744 (t80) cc_final: 0.8499 (t80) REVERT: C 70 LYS cc_start: 0.8160 (tmtm) cc_final: 0.7863 (tmtm) REVERT: C 81 THR cc_start: 0.8534 (p) cc_final: 0.8263 (t) REVERT: C 97 ASP cc_start: 0.8564 (p0) cc_final: 0.8172 (p0) REVERT: C 102 ASN cc_start: 0.8419 (p0) cc_final: 0.6964 (t0) REVERT: C 165 GLU cc_start: 0.8832 (mm-30) cc_final: 0.7663 (mp0) REVERT: C 186 ARG cc_start: 0.8297 (mmm160) cc_final: 0.8036 (mmp80) REVERT: C 189 GLN cc_start: 0.9106 (pm20) cc_final: 0.8786 (pm20) REVERT: C 212 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7715 (mtm) REVERT: C 289 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.9000 (pp) REVERT: A 44 ILE cc_start: 0.8729 (pp) cc_final: 0.8453 (pp) REVERT: A 92 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8396 (mtmm) REVERT: A 94 TRP cc_start: 0.9377 (t60) cc_final: 0.9055 (t60) REVERT: A 102 ASN cc_start: 0.8037 (t0) cc_final: 0.7660 (t0) REVERT: A 105 LYS cc_start: 0.8630 (tptt) cc_final: 0.8223 (pttp) REVERT: A 107 VAL cc_start: 0.7973 (m) cc_final: 0.7696 (p) REVERT: A 144 ASP cc_start: 0.7438 (p0) cc_final: 0.6997 (p0) REVERT: A 150 HIS cc_start: 0.6976 (m-70) cc_final: 0.6670 (m90) REVERT: A 167 VAL cc_start: 0.8842 (t) cc_final: 0.8266 (p) REVERT: A 215 HIS cc_start: 0.8228 (m-70) cc_final: 0.7963 (m90) REVERT: A 241 GLN cc_start: 0.9080 (tp-100) cc_final: 0.7921 (tp-100) REVERT: A 245 TRP cc_start: 0.7445 (m100) cc_final: 0.6183 (m100) REVERT: A 287 TRP cc_start: 0.8881 (m100) cc_final: 0.8386 (m-10) REVERT: E 21 LYS cc_start: 0.9154 (tmtm) cc_final: 0.8802 (pptt) REVERT: E 28 ARG cc_start: 0.8794 (ptm160) cc_final: 0.8545 (ptm160) REVERT: E 30 ASP cc_start: 0.9140 (t0) cc_final: 0.8907 (t0) REVERT: E 40 MET cc_start: 0.8651 (mtt) cc_final: 0.8230 (mmt) REVERT: E 64 GLN cc_start: 0.8924 (tt0) cc_final: 0.8416 (tt0) REVERT: E 68 LYS cc_start: 0.9392 (mmmm) cc_final: 0.8939 (mmmm) REVERT: E 69 ASP cc_start: 0.8815 (t0) cc_final: 0.8537 (t70) REVERT: E 90 GLN cc_start: 0.8800 (mt0) cc_final: 0.8484 (pt0) REVERT: E 112 LYS cc_start: 0.9186 (ttmm) cc_final: 0.8925 (ttmm) REVERT: E 133 THR cc_start: 0.9051 (m) cc_final: 0.8685 (p) REVERT: E 169 ASN cc_start: 0.8978 (t0) cc_final: 0.8224 (t0) REVERT: E 213 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.7743 (ptp-110) REVERT: E 215 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8690 (pttp) REVERT: E 216 ARG cc_start: 0.8691 (ttp-170) cc_final: 0.8268 (ttp-170) REVERT: B 13 LYS cc_start: 0.9060 (tttm) cc_final: 0.8597 (ttmt) REVERT: B 17 ASP cc_start: 0.9237 (m-30) cc_final: 0.8878 (m-30) REVERT: B 37 ASP cc_start: 0.8787 (t0) cc_final: 0.8429 (t0) REVERT: B 41 ARG cc_start: 0.8636 (mtt90) cc_final: 0.7942 (mtt90) REVERT: B 61 MET cc_start: 0.8383 (ppp) cc_final: 0.7390 (ppp) REVERT: B 62 TYR cc_start: 0.8836 (m-10) cc_final: 0.8611 (m-10) REVERT: B 63 PHE cc_start: 0.9066 (t80) cc_final: 0.8672 (t80) REVERT: B 89 ASP cc_start: 0.8860 (m-30) cc_final: 0.8545 (t70) REVERT: B 90 GLN cc_start: 0.9077 (mm110) cc_final: 0.8710 (mm110) REVERT: B 126 TYR cc_start: 0.8601 (t80) cc_final: 0.8348 (t80) REVERT: B 133 THR cc_start: 0.9079 (m) cc_final: 0.8829 (p) REVERT: B 142 ARG cc_start: 0.8426 (mtp180) cc_final: 0.8072 (mtm180) REVERT: B 167 TYR cc_start: 0.8564 (p90) cc_final: 0.8018 (p90) REVERT: B 169 ASN cc_start: 0.8624 (t0) cc_final: 0.7487 (t0) REVERT: B 192 LYS cc_start: 0.8687 (mmmt) cc_final: 0.8449 (mmmm) REVERT: B 216 ARG cc_start: 0.8609 (mtm180) cc_final: 0.7795 (mtm180) outliers start: 72 outliers final: 64 residues processed: 685 average time/residue: 0.2409 time to fit residues: 231.5229 Evaluate side-chains 723 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 656 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 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 228 ASP 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 212 MET 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 185 SER Chi-restraints excluded: chain A residue 206 THR 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 42 ILE Chi-restraints excluded: chain E residue 44 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 332 PHE Chi-restraints excluded: chain B residue 11 TYR 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 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 222 ILE Chi-restraints excluded: chain B residue 224 GLN 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 285 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 52 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 117 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 64 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 = 0.4003 r_free = 0.4003 target = 0.156339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116185 restraints weight = 22308.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120987 restraints weight = 12165.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124239 restraints weight = 7983.347| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12202 Z= 0.142 Angle : 0.868 16.177 16687 Z= 0.411 Chirality : 0.048 0.252 2058 Planarity : 0.005 0.049 2046 Dihedral : 8.083 71.750 2087 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.98 % Allowed : 29.81 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.21), residues: 1515 helix: 0.13 (0.23), residues: 458 sheet: -1.27 (0.25), residues: 424 loop : -1.62 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 168 HIS 0.009 0.001 HIS C 150 PHE 0.016 0.001 PHE C 64 TYR 0.059 0.002 TYR C 293 ARG 0.011 0.001 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 6) link_NAG-ASN : angle 1.70116 ( 18) link_ALPHA1-6 : bond 0.01078 ( 1) link_ALPHA1-6 : angle 1.68312 ( 3) link_BETA1-4 : bond 0.00481 ( 10) link_BETA1-4 : angle 2.24413 ( 30) link_ALPHA1-2 : bond 0.00610 ( 1) link_ALPHA1-2 : angle 1.42543 ( 3) link_ALPHA1-3 : bond 0.00865 ( 3) link_ALPHA1-3 : angle 1.55046 ( 9) hydrogen bonds : bond 0.03653 ( 517) hydrogen bonds : angle 5.17726 ( 1755) SS BOND : bond 0.01264 ( 5) SS BOND : angle 3.06097 ( 10) covalent geometry : bond 0.00309 (12176) covalent geometry : angle 0.85843 (16614) *********************** 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 730 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 657 time to evaluate : 1.421 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: 0.9130 (t0) cc_final: 0.8638 (t70) REVERT: D 40 ASN cc_start: 0.8668 (m-40) cc_final: 0.8359 (m-40) REVERT: D 54 HIS cc_start: 0.8946 (m-70) cc_final: 0.8636 (m-70) REVERT: D 58 TYR cc_start: 0.8753 (t80) cc_final: 0.8552 (t80) REVERT: D 82 TRP cc_start: 0.9217 (p90) cc_final: 0.8975 (p90) REVERT: D 90 ASN cc_start: 0.7227 (t0) cc_final: 0.6386 (p0) REVERT: D 99 ASN cc_start: 0.8956 (t0) cc_final: 0.8355 (t0) REVERT: D 101 ASN cc_start: 0.8768 (m110) cc_final: 0.8004 (m110) REVERT: D 115 ASN cc_start: 0.8411 (p0) cc_final: 0.7669 (p0) REVERT: D 172 TYR cc_start: 0.7166 (t80) cc_final: 0.6679 (t80) REVERT: D 207 ARG cc_start: 0.8623 (ptt90) cc_final: 0.8243 (ptt90) REVERT: D 214 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8569 (tppt) REVERT: D 219 ASP cc_start: 0.8993 (t0) cc_final: 0.8599 (t0) REVERT: D 223 MET cc_start: 0.8645 (mmm) cc_final: 0.8017 (mmm) REVERT: C 55 HIS cc_start: 0.8492 (t-90) cc_final: 0.8130 (m-70) REVERT: C 58 GLU cc_start: 0.8313 (pp20) cc_final: 0.8007 (pp20) REVERT: C 70 LYS cc_start: 0.7999 (tmtm) cc_final: 0.7689 (tmtm) REVERT: C 97 ASP cc_start: 0.8573 (p0) cc_final: 0.8358 (p0) REVERT: C 100 PHE cc_start: 0.9315 (m-80) cc_final: 0.9061 (m-80) REVERT: C 102 ASN cc_start: 0.8376 (p0) cc_final: 0.6952 (t0) REVERT: C 165 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8578 (mm-30) REVERT: C 189 GLN cc_start: 0.9209 (pm20) cc_final: 0.8950 (pm20) REVERT: A 44 ILE cc_start: 0.8772 (pp) cc_final: 0.8511 (pp) REVERT: A 57 MET cc_start: 0.8273 (tpp) cc_final: 0.7783 (tpt) REVERT: A 77 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8929 (mmmt) REVERT: A 94 TRP cc_start: 0.9389 (t60) cc_final: 0.9061 (t60) REVERT: A 102 ASN cc_start: 0.8028 (t0) cc_final: 0.7701 (t0) REVERT: A 105 LYS cc_start: 0.8615 (tptt) cc_final: 0.8205 (pttp) REVERT: A 107 VAL cc_start: 0.7994 (m) cc_final: 0.7758 (p) REVERT: A 113 MET cc_start: 0.8725 (mmm) cc_final: 0.8179 (mmm) REVERT: A 144 ASP cc_start: 0.7235 (p0) cc_final: 0.6823 (p0) REVERT: A 167 VAL cc_start: 0.8808 (t) cc_final: 0.8267 (p) REVERT: A 215 HIS cc_start: 0.8138 (m-70) cc_final: 0.7849 (m90) REVERT: A 221 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8435 (mmmm) REVERT: A 241 GLN cc_start: 0.9062 (tp-100) cc_final: 0.7883 (tp-100) REVERT: A 245 TRP cc_start: 0.7366 (m100) cc_final: 0.6236 (m100) REVERT: A 287 TRP cc_start: 0.8895 (m100) cc_final: 0.8362 (m-10) REVERT: E 18 ARG cc_start: 0.8617 (ptp90) cc_final: 0.8164 (tmm-80) REVERT: E 21 LYS cc_start: 0.9163 (tmtm) cc_final: 0.8800 (pptt) REVERT: E 40 MET cc_start: 0.8637 (mtt) cc_final: 0.8180 (mmt) REVERT: E 64 GLN cc_start: 0.8931 (tt0) cc_final: 0.8414 (tt0) REVERT: E 68 LYS cc_start: 0.9392 (mmmm) cc_final: 0.9104 (mmmm) REVERT: E 90 GLN cc_start: 0.8768 (mt0) cc_final: 0.8469 (pt0) REVERT: E 92 TRP cc_start: 0.9428 (t60) cc_final: 0.9202 (t60) REVERT: E 112 LYS cc_start: 0.9170 (ttmm) cc_final: 0.8910 (ttmm) REVERT: E 133 THR cc_start: 0.9064 (m) cc_final: 0.8722 (p) REVERT: E 167 TYR cc_start: 0.8015 (p90) cc_final: 0.7763 (p90) REVERT: E 169 ASN cc_start: 0.8759 (t0) cc_final: 0.8176 (t0) REVERT: E 181 ILE cc_start: 0.9022 (mm) cc_final: 0.8795 (mm) REVERT: E 212 PHE cc_start: 0.9462 (m-80) cc_final: 0.9254 (m-80) REVERT: E 213 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.7765 (ptp-110) REVERT: E 216 ARG cc_start: 0.8798 (ttp-170) cc_final: 0.8477 (ttp-170) REVERT: B 13 LYS cc_start: 0.9048 (tttm) cc_final: 0.8581 (ttmt) REVERT: B 17 ASP cc_start: 0.9238 (m-30) cc_final: 0.8886 (m-30) REVERT: B 37 ASP cc_start: 0.8717 (t0) cc_final: 0.8432 (t0) REVERT: B 41 ARG cc_start: 0.8669 (mtt90) cc_final: 0.8061 (mtt90) REVERT: B 55 MET cc_start: 0.8757 (mmm) cc_final: 0.8395 (tpt) REVERT: B 56 ASP cc_start: 0.8973 (p0) cc_final: 0.8769 (p0) REVERT: B 61 MET cc_start: 0.8352 (ppp) cc_final: 0.7338 (ppp) REVERT: B 62 TYR cc_start: 0.8814 (m-10) cc_final: 0.8610 (m-10) REVERT: B 63 PHE cc_start: 0.9042 (t80) cc_final: 0.8618 (t80) REVERT: B 89 ASP cc_start: 0.8981 (m-30) cc_final: 0.8690 (t0) REVERT: B 90 GLN cc_start: 0.9061 (mm110) cc_final: 0.8744 (mm110) REVERT: B 112 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8476 (ttpp) REVERT: B 126 TYR cc_start: 0.8740 (t80) cc_final: 0.8483 (t80) REVERT: B 133 THR cc_start: 0.9082 (m) cc_final: 0.8722 (p) REVERT: B 142 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8162 (mtm180) REVERT: B 148 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7493 (mm110) REVERT: B 153 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8136 (mp0) REVERT: B 167 TYR cc_start: 0.8489 (p90) cc_final: 0.7920 (p90) REVERT: B 169 ASN cc_start: 0.8672 (t0) cc_final: 0.7638 (t0) REVERT: B 213 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7655 (ttm170) REVERT: B 216 ARG cc_start: 0.8636 (mtm180) cc_final: 0.7791 (mtm180) REVERT: B 261 MET cc_start: 0.9106 (ttp) cc_final: 0.8664 (ttp) outliers start: 73 outliers final: 61 residues processed: 674 average time/residue: 0.2806 time to fit residues: 268.0376 Evaluate side-chains 697 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 636 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 42 LEU 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 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 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 67 GLN 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 173 GLU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL 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 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 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 66 SER 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 332 PHE Chi-restraints excluded: chain B residue 11 TYR 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 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 222 ILE 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 285 LEU 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 146 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** 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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.148692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109830 restraints weight = 23149.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114228 restraints weight = 12637.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117170 restraints weight = 8312.764| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 12202 Z= 0.324 Angle : 0.951 12.947 16687 Z= 0.465 Chirality : 0.051 0.260 2058 Planarity : 0.005 0.050 2046 Dihedral : 7.846 65.009 2087 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 8.11 % Allowed : 29.16 % Favored : 62.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.21), residues: 1515 helix: 0.10 (0.23), residues: 459 sheet: -1.49 (0.24), residues: 419 loop : -1.70 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP B 168 HIS 0.013 0.003 HIS A 141 PHE 0.024 0.002 PHE E 31 TYR 0.048 0.003 TYR C 293 ARG 0.012 0.001 ARG D 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 6) link_NAG-ASN : angle 2.01444 ( 18) link_ALPHA1-6 : bond 0.00217 ( 1) link_ALPHA1-6 : angle 2.42467 ( 3) link_BETA1-4 : bond 0.00634 ( 10) link_BETA1-4 : angle 2.43465 ( 30) link_ALPHA1-2 : bond 0.00506 ( 1) link_ALPHA1-2 : angle 1.91396 ( 3) link_ALPHA1-3 : bond 0.00530 ( 3) link_ALPHA1-3 : angle 1.74374 ( 9) hydrogen bonds : bond 0.04012 ( 517) hydrogen bonds : angle 5.54991 ( 1755) SS BOND : bond 0.00615 ( 5) SS BOND : angle 3.43087 ( 10) covalent geometry : bond 0.00702 (12176) covalent geometry : angle 0.93910 (16614) *********************** 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 728 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 629 time to evaluate : 1.365 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: D 39 ASP cc_start: 0.9100 (t0) cc_final: 0.8676 (t70) REVERT: D 40 ASN cc_start: 0.8609 (m-40) cc_final: 0.8312 (m-40) REVERT: D 54 HIS cc_start: 0.9009 (m-70) cc_final: 0.8633 (m-70) REVERT: D 58 TYR cc_start: 0.8808 (t80) cc_final: 0.8583 (t80) REVERT: D 60 ASN cc_start: 0.9417 (t0) cc_final: 0.8683 (t0) REVERT: D 82 TRP cc_start: 0.9453 (p90) cc_final: 0.9137 (p90) REVERT: D 97 ARG cc_start: 0.9245 (mmt90) cc_final: 0.8961 (mtm-85) REVERT: D 101 ASN cc_start: 0.9028 (m110) cc_final: 0.8273 (t0) REVERT: D 112 PHE cc_start: 0.8052 (p90) cc_final: 0.7026 (p90) REVERT: D 114 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.7912 (mmm160) REVERT: D 115 ASN cc_start: 0.8625 (p0) cc_final: 0.8393 (p0) REVERT: D 139 VAL cc_start: 0.9716 (t) cc_final: 0.9486 (p) REVERT: D 172 TYR cc_start: 0.7500 (t80) cc_final: 0.7115 (t80) REVERT: D 182 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7550 (tp-100) REVERT: D 207 ARG cc_start: 0.8702 (ptt90) cc_final: 0.8132 (ptt90) REVERT: D 214 LYS cc_start: 0.9147 (ttpt) cc_final: 0.8617 (tppt) REVERT: D 223 MET cc_start: 0.8663 (mmm) cc_final: 0.8413 (mmp) REVERT: C 25 TYR cc_start: 0.8697 (t80) cc_final: 0.8245 (t80) REVERT: C 30 ARG cc_start: 0.9462 (ptt90) cc_final: 0.8696 (ppt90) REVERT: C 55 HIS cc_start: 0.8526 (t-90) cc_final: 0.8131 (m-70) REVERT: C 58 GLU cc_start: 0.8496 (pp20) cc_final: 0.8107 (pp20) REVERT: C 70 LYS cc_start: 0.8245 (tmtm) cc_final: 0.7966 (tmtm) REVERT: C 97 ASP cc_start: 0.8631 (p0) cc_final: 0.8181 (p0) REVERT: C 102 ASN cc_start: 0.8384 (p0) cc_final: 0.7004 (t0) REVERT: C 165 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8442 (mm-30) REVERT: C 189 GLN cc_start: 0.9151 (pm20) cc_final: 0.8852 (pm20) REVERT: C 285 MET cc_start: 0.7385 (mtt) cc_final: 0.7053 (mpp) REVERT: A 44 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8649 (pp) REVERT: A 70 LYS cc_start: 0.8482 (tmmt) cc_final: 0.8243 (tmmt) REVERT: A 102 ASN cc_start: 0.8318 (t0) cc_final: 0.7983 (t0) REVERT: A 105 LYS cc_start: 0.8782 (tptt) cc_final: 0.8195 (pttp) REVERT: A 107 VAL cc_start: 0.8001 (m) cc_final: 0.7743 (p) REVERT: A 113 MET cc_start: 0.8879 (mmm) cc_final: 0.8364 (mmm) REVERT: A 137 GLU cc_start: 0.8971 (pp20) cc_final: 0.8396 (pp20) REVERT: A 144 ASP cc_start: 0.8153 (p0) cc_final: 0.7708 (p0) REVERT: A 167 VAL cc_start: 0.9187 (t) cc_final: 0.8732 (p) REVERT: A 241 GLN cc_start: 0.9119 (tp-100) cc_final: 0.7914 (tp-100) REVERT: A 245 TRP cc_start: 0.7413 (m100) cc_final: 0.6318 (m100) REVERT: A 287 TRP cc_start: 0.8905 (m100) cc_final: 0.8428 (m-10) REVERT: E 17 ASP cc_start: 0.9045 (m-30) cc_final: 0.8745 (m-30) REVERT: E 21 LYS cc_start: 0.9164 (tmtm) cc_final: 0.8808 (pptt) REVERT: E 28 ARG cc_start: 0.8718 (ptm160) cc_final: 0.8095 (ppt170) REVERT: E 40 MET cc_start: 0.8631 (mtt) cc_final: 0.8188 (mmt) REVERT: E 64 GLN cc_start: 0.9066 (tt0) cc_final: 0.8579 (tt0) REVERT: E 68 LYS cc_start: 0.9389 (mmmm) cc_final: 0.9074 (mmmm) REVERT: E 90 GLN cc_start: 0.8857 (mt0) cc_final: 0.8413 (pt0) REVERT: E 98 PHE cc_start: 0.9264 (m-80) cc_final: 0.8886 (m-80) REVERT: E 112 LYS cc_start: 0.9185 (ttmm) cc_final: 0.8843 (ttmm) REVERT: E 121 ASP cc_start: 0.9276 (p0) cc_final: 0.9018 (p0) REVERT: E 133 THR cc_start: 0.9152 (m) cc_final: 0.8838 (p) REVERT: E 181 ILE cc_start: 0.9163 (mm) cc_final: 0.8942 (mm) REVERT: E 193 MET cc_start: 0.7198 (mpp) cc_final: 0.6992 (mpp) REVERT: E 213 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.7721 (ptp-110) REVERT: E 216 ARG cc_start: 0.8844 (ttp-170) cc_final: 0.8468 (ttp-170) REVERT: B 13 LYS cc_start: 0.9073 (tttm) cc_final: 0.8686 (ttmm) REVERT: B 17 ASP cc_start: 0.9256 (m-30) cc_final: 0.8935 (m-30) REVERT: B 18 ARG cc_start: 0.9405 (ptm-80) cc_final: 0.9111 (ttp-110) REVERT: B 41 ARG cc_start: 0.8769 (mtt90) cc_final: 0.8213 (mtt90) REVERT: B 55 MET cc_start: 0.8543 (mmm) cc_final: 0.8079 (tpt) REVERT: B 61 MET cc_start: 0.8403 (ppp) cc_final: 0.7313 (ppp) REVERT: B 63 PHE cc_start: 0.9129 (t80) cc_final: 0.8680 (t80) REVERT: B 83 LEU cc_start: 0.9009 (tp) cc_final: 0.8785 (tp) REVERT: B 89 ASP cc_start: 0.9005 (m-30) cc_final: 0.8683 (t0) REVERT: B 90 GLN cc_start: 0.9143 (mm110) cc_final: 0.8817 (mm110) REVERT: B 112 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8720 (mtmm) REVERT: B 137 MET cc_start: 0.8616 (mmm) cc_final: 0.8209 (mmm) REVERT: B 142 ARG cc_start: 0.8581 (mtp180) cc_final: 0.7987 (mtm180) REVERT: B 148 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7733 (mm110) REVERT: B 169 ASN cc_start: 0.8608 (t0) cc_final: 0.7820 (t0) REVERT: B 213 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7635 (ttm170) REVERT: B 216 ARG cc_start: 0.8847 (mtm180) cc_final: 0.7756 (mtm180) REVERT: B 243 ASN cc_start: 0.6150 (t0) cc_final: 0.5736 (t0) outliers start: 99 outliers final: 85 residues processed: 662 average time/residue: 0.2371 time to fit residues: 221.4145 Evaluate side-chains 708 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 622 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 74 ILE 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 180 VAL Chi-restraints excluded: chain D residue 202 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 273 VAL 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 44 ILE 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 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 173 GLU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 15 THR 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 63 VAL Chi-restraints excluded: chain A residue 93 ILE 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 142 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 190 TYR 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 15 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 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 332 PHE Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 15 THR 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 104 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 151 THR 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 222 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 89 optimal weight: 3.9990 chunk 141 optimal weight: 0.0070 chunk 114 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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** A 215 HIS ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3973 r_free = 0.3973 target = 0.153668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114055 restraints weight = 22556.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118739 restraints weight = 12238.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121892 restraints weight = 8023.615| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12202 Z= 0.157 Angle : 0.922 15.993 16687 Z= 0.435 Chirality : 0.050 0.449 2058 Planarity : 0.004 0.048 2046 Dihedral : 7.356 61.473 2087 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.14 % Allowed : 31.61 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1515 helix: 0.42 (0.24), residues: 458 sheet: -1.22 (0.25), residues: 417 loop : -1.58 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP B 168 HIS 0.011 0.001 HIS C 150 PHE 0.018 0.002 PHE C 64 TYR 0.028 0.002 TYR B 167 ARG 0.008 0.001 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 1.84083 ( 18) link_ALPHA1-6 : bond 0.00624 ( 1) link_ALPHA1-6 : angle 1.56770 ( 3) link_BETA1-4 : bond 0.00400 ( 10) link_BETA1-4 : angle 2.10716 ( 30) link_ALPHA1-2 : bond 0.00655 ( 1) link_ALPHA1-2 : angle 1.30734 ( 3) link_ALPHA1-3 : bond 0.00843 ( 3) link_ALPHA1-3 : angle 1.45229 ( 9) hydrogen bonds : bond 0.03704 ( 517) hydrogen bonds : angle 5.31278 ( 1755) SS BOND : bond 0.00406 ( 5) SS BOND : angle 2.64819 ( 10) covalent geometry : bond 0.00353 (12176) covalent geometry : angle 0.91457 (16614) *********************** 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 728 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 653 time to evaluate : 1.777 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: 0.9097 (t0) cc_final: 0.8640 (t70) REVERT: D 40 ASN cc_start: 0.8666 (m-40) cc_final: 0.8333 (m-40) REVERT: D 54 HIS cc_start: 0.9009 (m-70) cc_final: 0.8762 (m-70) REVERT: D 58 TYR cc_start: 0.8841 (t80) cc_final: 0.8554 (t80) REVERT: D 77 PHE cc_start: 0.9257 (m-80) cc_final: 0.9048 (m-80) REVERT: D 97 ARG cc_start: 0.9219 (mmt90) cc_final: 0.9002 (mtm-85) REVERT: D 101 ASN cc_start: 0.8648 (m110) cc_final: 0.8329 (t0) REVERT: D 112 PHE cc_start: 0.7901 (p90) cc_final: 0.7175 (p90) REVERT: D 115 ASN cc_start: 0.8580 (p0) cc_final: 0.8301 (p0) REVERT: D 132 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7763 (mmt90) REVERT: D 172 TYR cc_start: 0.7349 (t80) cc_final: 0.7034 (t80) REVERT: D 207 ARG cc_start: 0.8753 (ptt90) cc_final: 0.8393 (ptt90) REVERT: D 214 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8603 (tppt) REVERT: D 219 ASP cc_start: 0.9035 (t0) cc_final: 0.8809 (t0) REVERT: D 223 MET cc_start: 0.8578 (mmm) cc_final: 0.7874 (mmm) REVERT: D 239 GLN cc_start: 0.8686 (mt0) cc_final: 0.8254 (pt0) REVERT: C 25 TYR cc_start: 0.8549 (t80) cc_final: 0.8034 (t80) REVERT: C 30 ARG cc_start: 0.9466 (ptt90) cc_final: 0.8690 (ppt90) REVERT: C 55 HIS cc_start: 0.8531 (t-90) cc_final: 0.8152 (m-70) REVERT: C 58 GLU cc_start: 0.8445 (pp20) cc_final: 0.8064 (pp20) REVERT: C 70 LYS cc_start: 0.8057 (tmtm) cc_final: 0.7733 (tmtm) REVERT: C 97 ASP cc_start: 0.8577 (p0) cc_final: 0.8342 (p0) REVERT: C 100 PHE cc_start: 0.9326 (m-80) cc_final: 0.8988 (m-80) REVERT: C 102 ASN cc_start: 0.8361 (p0) cc_final: 0.6989 (t0) REVERT: C 165 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8434 (mm-30) REVERT: C 189 GLN cc_start: 0.9111 (pm20) cc_final: 0.8905 (pm20) REVERT: C 213 THR cc_start: 0.8520 (m) cc_final: 0.8103 (p) REVERT: A 44 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8675 (pp) REVERT: A 75 LYS cc_start: 0.8781 (ptpp) cc_final: 0.8157 (ptpp) REVERT: A 77 LYS cc_start: 0.9309 (mtmt) cc_final: 0.8951 (mppt) REVERT: A 102 ASN cc_start: 0.8183 (t0) cc_final: 0.7852 (t0) REVERT: A 105 LYS cc_start: 0.8764 (tptt) cc_final: 0.8237 (pttp) REVERT: A 107 VAL cc_start: 0.7928 (m) cc_final: 0.7658 (p) REVERT: A 113 MET cc_start: 0.8865 (mmm) cc_final: 0.8464 (mmm) REVERT: A 137 GLU cc_start: 0.8906 (pp20) cc_final: 0.8438 (pp20) REVERT: A 144 ASP cc_start: 0.7441 (p0) cc_final: 0.6994 (p0) REVERT: A 167 VAL cc_start: 0.8793 (t) cc_final: 0.8196 (p) REVERT: A 241 GLN cc_start: 0.9091 (tp-100) cc_final: 0.8024 (tp-100) REVERT: A 245 TRP cc_start: 0.7263 (m100) cc_final: 0.6217 (m100) REVERT: A 287 TRP cc_start: 0.8864 (m100) cc_final: 0.8386 (m-10) REVERT: E 28 ARG cc_start: 0.8778 (ptm160) cc_final: 0.8359 (ppt170) REVERT: E 40 MET cc_start: 0.8695 (mtt) cc_final: 0.8276 (mmt) REVERT: E 41 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7806 (ttm170) REVERT: E 64 GLN cc_start: 0.9032 (tt0) cc_final: 0.8826 (tt0) REVERT: E 68 LYS cc_start: 0.9358 (mmmm) cc_final: 0.8785 (mmmm) REVERT: E 90 GLN cc_start: 0.8795 (mt0) cc_final: 0.8368 (pt0) REVERT: E 112 LYS cc_start: 0.9142 (ttmm) cc_final: 0.8843 (ttmm) REVERT: E 121 ASP cc_start: 0.9174 (p0) cc_final: 0.8799 (p0) REVERT: E 133 THR cc_start: 0.9131 (m) cc_final: 0.8817 (p) REVERT: E 213 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8068 (mtm110) REVERT: E 216 ARG cc_start: 0.8824 (ttp-170) cc_final: 0.8612 (ttm-80) REVERT: B 13 LYS cc_start: 0.9059 (tttm) cc_final: 0.8645 (ttmm) REVERT: B 17 ASP cc_start: 0.9221 (m-30) cc_final: 0.8896 (m-30) REVERT: B 18 ARG cc_start: 0.9368 (ptm-80) cc_final: 0.9114 (ttp-110) REVERT: B 41 ARG cc_start: 0.8667 (mtt90) cc_final: 0.8305 (mtt90) REVERT: B 55 MET cc_start: 0.8807 (mmm) cc_final: 0.8199 (tpt) REVERT: B 56 ASP cc_start: 0.8652 (p0) cc_final: 0.8350 (p0) REVERT: B 61 MET cc_start: 0.8456 (ppp) cc_final: 0.7341 (ppp) REVERT: B 63 PHE cc_start: 0.9101 (t80) cc_final: 0.8659 (t80) REVERT: B 89 ASP cc_start: 0.9074 (m-30) cc_final: 0.8737 (t0) REVERT: B 90 GLN cc_start: 0.9070 (mm110) cc_final: 0.8757 (mm110) REVERT: B 126 TYR cc_start: 0.8685 (t80) cc_final: 0.8365 (t80) REVERT: B 133 THR cc_start: 0.8992 (m) cc_final: 0.8745 (p) REVERT: B 137 MET cc_start: 0.8491 (mmm) cc_final: 0.8060 (mmm) REVERT: B 142 ARG cc_start: 0.8380 (mtp180) cc_final: 0.7995 (mtm180) REVERT: B 148 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7675 (mm-40) REVERT: B 213 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7644 (ttm170) REVERT: B 216 ARG cc_start: 0.8702 (mtm180) cc_final: 0.7695 (mtm180) outliers start: 75 outliers final: 66 residues processed: 676 average time/residue: 0.3185 time to fit residues: 307.7322 Evaluate side-chains 697 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 630 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 LEU 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 128 ASN 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 242 ILE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 67 GLN 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 173 GLU 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 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 222 ILE Chi-restraints excluded: chain A residue 239 LEU 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 58 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 66 SER 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 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 11 TYR 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 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 222 ILE 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 285 LEU Chi-restraints excluded: chain B residue 297 LEU 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 83 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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 228 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** ** 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 = 0.3961 r_free = 0.3961 target = 0.152766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113574 restraints weight = 22644.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118195 restraints weight = 12295.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121324 restraints weight = 8074.248| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12202 Z= 0.184 Angle : 0.929 14.874 16687 Z= 0.441 Chirality : 0.049 0.326 2058 Planarity : 0.005 0.049 2046 Dihedral : 6.946 56.279 2087 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.65 % Allowed : 33.66 % Favored : 60.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.22), residues: 1515 helix: 0.39 (0.24), residues: 460 sheet: -1.21 (0.25), residues: 418 loop : -1.53 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP B 168 HIS 0.009 0.002 HIS C 150 PHE 0.027 0.002 PHE B 289 TYR 0.024 0.002 TYR B 167 ARG 0.007 0.001 ARG D 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 6) link_NAG-ASN : angle 1.82209 ( 18) link_ALPHA1-6 : bond 0.00423 ( 1) link_ALPHA1-6 : angle 1.88684 ( 3) link_BETA1-4 : bond 0.00441 ( 10) link_BETA1-4 : angle 2.12507 ( 30) link_ALPHA1-2 : bond 0.00549 ( 1) link_ALPHA1-2 : angle 1.45524 ( 3) link_ALPHA1-3 : bond 0.00530 ( 3) link_ALPHA1-3 : angle 1.46828 ( 9) hydrogen bonds : bond 0.03645 ( 517) hydrogen bonds : angle 5.30970 ( 1755) SS BOND : bond 0.00342 ( 5) SS BOND : angle 2.69802 ( 10) covalent geometry : bond 0.00416 (12176) covalent geometry : angle 0.92156 (16614) *********************** 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 690 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 621 time to evaluate : 1.353 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: D 39 ASP cc_start: 0.9126 (t0) cc_final: 0.8689 (t70) REVERT: D 40 ASN cc_start: 0.8571 (m-40) cc_final: 0.8253 (m-40) REVERT: D 54 HIS cc_start: 0.8998 (m-70) cc_final: 0.8769 (m-70) REVERT: D 60 ASN cc_start: 0.9414 (t0) cc_final: 0.8812 (t0) REVERT: D 77 PHE cc_start: 0.9316 (m-80) cc_final: 0.9048 (m-80) REVERT: D 97 ARG cc_start: 0.9259 (mmt90) cc_final: 0.8592 (mtm-85) REVERT: D 101 ASN cc_start: 0.8782 (m110) cc_final: 0.8401 (t0) REVERT: D 112 PHE cc_start: 0.7979 (p90) cc_final: 0.7158 (p90) REVERT: D 115 ASN cc_start: 0.8615 (p0) cc_final: 0.8330 (p0) REVERT: D 139 VAL cc_start: 0.9643 (t) cc_final: 0.9426 (p) REVERT: D 172 TYR cc_start: 0.7450 (t80) cc_final: 0.7233 (t80) REVERT: D 207 ARG cc_start: 0.8825 (ptt90) cc_final: 0.8384 (ptt90) REVERT: D 214 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8592 (tppt) REVERT: D 219 ASP cc_start: 0.9085 (t0) cc_final: 0.8864 (t0) REVERT: D 223 MET cc_start: 0.8586 (mmm) cc_final: 0.7951 (mmm) REVERT: D 226 TYR cc_start: 0.8953 (m-10) cc_final: 0.8465 (m-10) REVERT: D 239 GLN cc_start: 0.8698 (mt0) cc_final: 0.8287 (pt0) REVERT: C 25 TYR cc_start: 0.8554 (t80) cc_final: 0.8032 (t80) REVERT: C 55 HIS cc_start: 0.8543 (t-90) cc_final: 0.8176 (m-70) REVERT: C 58 GLU cc_start: 0.8484 (pp20) cc_final: 0.8101 (pp20) REVERT: C 70 LYS cc_start: 0.8076 (tmtm) cc_final: 0.7770 (tmtm) REVERT: C 100 PHE cc_start: 0.9346 (m-80) cc_final: 0.9075 (m-80) REVERT: C 102 ASN cc_start: 0.8350 (p0) cc_final: 0.7016 (t0) REVERT: C 285 MET cc_start: 0.7159 (mtt) cc_final: 0.6958 (mpp) REVERT: A 57 MET cc_start: 0.8365 (tpp) cc_final: 0.8136 (tpt) REVERT: A 77 LYS cc_start: 0.9314 (mtmt) cc_final: 0.8956 (mppt) REVERT: A 92 LYS cc_start: 0.8327 (mtmm) cc_final: 0.8011 (mtmt) REVERT: A 102 ASN cc_start: 0.8181 (t0) cc_final: 0.7860 (t0) REVERT: A 105 LYS cc_start: 0.8764 (tptt) cc_final: 0.8202 (pttp) REVERT: A 107 VAL cc_start: 0.7917 (m) cc_final: 0.7656 (p) REVERT: A 113 MET cc_start: 0.8882 (mmm) cc_final: 0.8513 (mmm) REVERT: A 137 GLU cc_start: 0.8909 (pp20) cc_final: 0.8477 (pp20) REVERT: A 144 ASP cc_start: 0.8240 (p0) cc_final: 0.7719 (p0) REVERT: A 167 VAL cc_start: 0.8860 (t) cc_final: 0.8247 (p) REVERT: A 209 TYR cc_start: 0.7959 (m-10) cc_final: 0.7283 (m-10) REVERT: A 241 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8622 (tp-100) REVERT: A 287 TRP cc_start: 0.8830 (m100) cc_final: 0.8316 (m-10) REVERT: E 28 ARG cc_start: 0.8776 (ptm160) cc_final: 0.8339 (ppt170) REVERT: E 40 MET cc_start: 0.8665 (mtt) cc_final: 0.8178 (mmt) REVERT: E 41 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7758 (ttp-170) REVERT: E 61 MET cc_start: 0.8002 (ppp) cc_final: 0.7789 (ppp) REVERT: E 64 GLN cc_start: 0.9064 (tt0) cc_final: 0.8657 (tt0) REVERT: E 68 LYS cc_start: 0.9394 (mmmm) cc_final: 0.9000 (mmmm) REVERT: E 90 GLN cc_start: 0.8817 (mt0) cc_final: 0.8392 (pt0) REVERT: E 112 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8924 (ttmm) REVERT: E 129 ARG cc_start: 0.8443 (ttt-90) cc_final: 0.7372 (ttp80) REVERT: E 133 THR cc_start: 0.9129 (m) cc_final: 0.8820 (p) REVERT: E 181 ILE cc_start: 0.9120 (mm) cc_final: 0.8884 (mm) REVERT: E 216 ARG cc_start: 0.8806 (ttp-170) cc_final: 0.8589 (ttm-80) REVERT: E 299 TYR cc_start: 0.7440 (t80) cc_final: 0.7122 (t80) REVERT: B 13 LYS cc_start: 0.9080 (tttm) cc_final: 0.8687 (ttmm) REVERT: B 17 ASP cc_start: 0.9213 (m-30) cc_final: 0.8862 (m-30) REVERT: B 18 ARG cc_start: 0.9417 (ptm-80) cc_final: 0.9157 (ttp-110) REVERT: B 41 ARG cc_start: 0.8657 (mtt90) cc_final: 0.8217 (mtt90) REVERT: B 55 MET cc_start: 0.8833 (mmm) cc_final: 0.8283 (tpt) REVERT: B 56 ASP cc_start: 0.8651 (p0) cc_final: 0.8261 (p0) REVERT: B 61 MET cc_start: 0.8427 (ppp) cc_final: 0.7310 (ppp) REVERT: B 63 PHE cc_start: 0.9089 (t80) cc_final: 0.8644 (t80) REVERT: B 89 ASP cc_start: 0.9060 (m-30) cc_final: 0.8711 (t0) REVERT: B 90 GLN cc_start: 0.9109 (mm110) cc_final: 0.8766 (mm110) REVERT: B 126 TYR cc_start: 0.8760 (t80) cc_final: 0.8295 (t80) REVERT: B 137 MET cc_start: 0.8590 (mmm) cc_final: 0.8125 (mmm) REVERT: B 142 ARG cc_start: 0.8356 (mtp180) cc_final: 0.7947 (mtm180) REVERT: B 153 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8086 (mp0) REVERT: B 216 ARG cc_start: 0.8747 (mtm180) cc_final: 0.7783 (mtm180) outliers start: 69 outliers final: 64 residues processed: 645 average time/residue: 0.2287 time to fit residues: 208.0194 Evaluate side-chains 695 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 631 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 42 LEU 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 128 ASN Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 180 VAL 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 C residue 33 LEU 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 162 THR 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 293 TYR Chi-restraints excluded: chain A residue 15 THR 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 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 239 LEU Chi-restraints excluded: chain A residue 291 VAL 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 58 THR Chi-restraints excluded: chain E residue 66 SER 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 189 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 332 PHE Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 44 VAL 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 222 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU 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 41 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** A 215 HIS ** A 228 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** ** 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 = 0.3969 r_free = 0.3969 target = 0.153541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114169 restraints weight = 22355.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118796 restraints weight = 12235.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121931 restraints weight = 8066.056| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12202 Z= 0.175 Angle : 0.948 14.465 16687 Z= 0.449 Chirality : 0.049 0.252 2058 Planarity : 0.005 0.052 2046 Dihedral : 6.593 49.470 2087 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.65 % Allowed : 34.40 % Favored : 59.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1515 helix: 0.44 (0.24), residues: 459 sheet: -1.16 (0.25), residues: 411 loop : -1.54 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP B 168 HIS 0.006 0.001 HIS D 156 PHE 0.018 0.002 PHE C 64 TYR 0.028 0.002 TYR B 167 ARG 0.009 0.001 ARG D 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 6) link_NAG-ASN : angle 1.85145 ( 18) link_ALPHA1-6 : bond 0.00562 ( 1) link_ALPHA1-6 : angle 1.89649 ( 3) link_BETA1-4 : bond 0.00437 ( 10) link_BETA1-4 : angle 2.01691 ( 30) link_ALPHA1-2 : bond 0.00500 ( 1) link_ALPHA1-2 : angle 1.40770 ( 3) link_ALPHA1-3 : bond 0.00633 ( 3) link_ALPHA1-3 : angle 1.46521 ( 9) hydrogen bonds : bond 0.03670 ( 517) hydrogen bonds : angle 5.27225 ( 1755) SS BOND : bond 0.00373 ( 5) SS BOND : angle 2.47594 ( 10) covalent geometry : bond 0.00398 (12176) covalent geometry : angle 0.94150 (16614) ********************** 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 707 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 638 time to evaluate : 1.388 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: 0.9171 (t0) cc_final: 0.8810 (t70) REVERT: D 40 ASN cc_start: 0.8565 (m-40) cc_final: 0.8248 (m-40) REVERT: D 54 HIS cc_start: 0.9010 (m-70) cc_final: 0.8793 (m-70) REVERT: D 77 PHE cc_start: 0.9311 (m-80) cc_final: 0.9052 (m-80) REVERT: D 97 ARG cc_start: 0.9240 (mmt90) cc_final: 0.8668 (mtm-85) REVERT: D 101 ASN cc_start: 0.8949 (m110) cc_final: 0.8289 (t0) REVERT: D 112 PHE cc_start: 0.8132 (p90) cc_final: 0.7285 (p90) REVERT: D 115 ASN cc_start: 0.8666 (p0) cc_final: 0.8419 (p0) REVERT: D 172 TYR cc_start: 0.7453 (t80) cc_final: 0.7235 (t80) REVERT: D 207 ARG cc_start: 0.8870 (ptt90) cc_final: 0.8493 (ptt90) REVERT: D 214 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8576 (tppt) REVERT: D 219 ASP cc_start: 0.9124 (t0) cc_final: 0.8908 (t0) REVERT: D 223 MET cc_start: 0.8622 (mmm) cc_final: 0.7988 (mmm) REVERT: D 226 TYR cc_start: 0.8901 (m-10) cc_final: 0.8383 (m-10) REVERT: D 239 GLN cc_start: 0.8674 (mt0) cc_final: 0.8262 (pt0) REVERT: C 55 HIS cc_start: 0.8630 (t-90) cc_final: 0.8244 (m-70) REVERT: C 58 GLU cc_start: 0.8566 (pp20) cc_final: 0.8169 (pp20) REVERT: C 70 LYS cc_start: 0.8042 (tmtm) cc_final: 0.7736 (tmtm) REVERT: C 102 ASN cc_start: 0.8347 (p0) cc_final: 0.7018 (t0) REVERT: C 213 THR cc_start: 0.8610 (m) cc_final: 0.8075 (p) REVERT: C 285 MET cc_start: 0.7296 (mtt) cc_final: 0.7087 (mpp) REVERT: A 57 MET cc_start: 0.8552 (tpp) cc_final: 0.8338 (tpt) REVERT: A 77 LYS cc_start: 0.9319 (mtmt) cc_final: 0.8965 (mppt) REVERT: A 80 MET cc_start: 0.7669 (tpp) cc_final: 0.7454 (tpt) REVERT: A 102 ASN cc_start: 0.8201 (t0) cc_final: 0.7853 (t0) REVERT: A 105 LYS cc_start: 0.8758 (tptt) cc_final: 0.8199 (pttp) REVERT: A 107 VAL cc_start: 0.7900 (m) cc_final: 0.7627 (p) REVERT: A 113 MET cc_start: 0.8879 (mmm) cc_final: 0.8484 (mmm) REVERT: A 137 GLU cc_start: 0.8921 (pp20) cc_final: 0.8494 (pp20) REVERT: A 144 ASP cc_start: 0.8074 (p0) cc_final: 0.7595 (p0) REVERT: A 167 VAL cc_start: 0.8832 (t) cc_final: 0.8235 (p) REVERT: A 209 TYR cc_start: 0.7772 (m-10) cc_final: 0.7004 (m-10) REVERT: A 221 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7789 (mmmm) REVERT: A 241 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8006 (tp-100) REVERT: A 245 TRP cc_start: 0.7243 (m100) cc_final: 0.6075 (m100) REVERT: A 287 TRP cc_start: 0.8892 (m100) cc_final: 0.8355 (m-10) REVERT: E 18 ARG cc_start: 0.9360 (ttp80) cc_final: 0.8614 (tpm170) REVERT: E 21 LYS cc_start: 0.9162 (tmtm) cc_final: 0.8548 (tppt) REVERT: E 40 MET cc_start: 0.8729 (mtt) cc_final: 0.8237 (mmt) REVERT: E 41 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7680 (ttp-170) REVERT: E 64 GLN cc_start: 0.9073 (tt0) cc_final: 0.8645 (tt0) REVERT: E 68 LYS cc_start: 0.9384 (mmmm) cc_final: 0.8987 (mmmm) REVERT: E 69 ASP cc_start: 0.8607 (t70) cc_final: 0.8300 (t70) REVERT: E 90 GLN cc_start: 0.8912 (mt0) cc_final: 0.8516 (pt0) REVERT: E 91 LEU cc_start: 0.9329 (mm) cc_final: 0.9001 (mm) REVERT: E 112 LYS cc_start: 0.9201 (ttmm) cc_final: 0.8881 (ttmm) REVERT: E 133 THR cc_start: 0.9082 (m) cc_final: 0.8767 (p) REVERT: E 181 ILE cc_start: 0.9143 (mm) cc_final: 0.8911 (mm) REVERT: E 216 ARG cc_start: 0.8754 (ttp-170) cc_final: 0.8520 (ttm-80) REVERT: E 299 TYR cc_start: 0.7451 (t80) cc_final: 0.7149 (t80) REVERT: B 13 LYS cc_start: 0.9109 (tttm) cc_final: 0.8707 (ttmm) REVERT: B 17 ASP cc_start: 0.9224 (m-30) cc_final: 0.8896 (m-30) REVERT: B 18 ARG cc_start: 0.9413 (ptm-80) cc_final: 0.9156 (ttp-110) REVERT: B 41 ARG cc_start: 0.8564 (mtt90) cc_final: 0.8165 (mtt90) REVERT: B 55 MET cc_start: 0.8850 (mmm) cc_final: 0.8329 (tpt) REVERT: B 56 ASP cc_start: 0.8622 (p0) cc_final: 0.8231 (p0) REVERT: B 61 MET cc_start: 0.8437 (ppp) cc_final: 0.7323 (ppp) REVERT: B 63 PHE cc_start: 0.9081 (t80) cc_final: 0.8626 (t80) REVERT: B 89 ASP cc_start: 0.9029 (m-30) cc_final: 0.8686 (t0) REVERT: B 90 GLN cc_start: 0.9047 (mm110) cc_final: 0.8701 (mm110) REVERT: B 126 TYR cc_start: 0.8761 (t80) cc_final: 0.8267 (t80) REVERT: B 137 MET cc_start: 0.8671 (mmm) cc_final: 0.8269 (mmm) REVERT: B 142 ARG cc_start: 0.8367 (mtp180) cc_final: 0.8136 (mtm180) REVERT: B 148 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7795 (mm110) REVERT: B 153 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8115 (mp0) REVERT: B 205 TYR cc_start: 0.8531 (m-10) cc_final: 0.8263 (m-10) REVERT: B 216 ARG cc_start: 0.8837 (mtm180) cc_final: 0.7827 (mtm180) outliers start: 69 outliers final: 67 residues processed: 658 average time/residue: 0.2646 time to fit residues: 250.7512 Evaluate side-chains 701 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 634 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 42 LEU 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 128 ASN Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 180 VAL 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 C residue 33 LEU 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 162 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 198 ASP 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 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 SER 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 239 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 291 VAL 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 58 THR Chi-restraints excluded: chain E residue 66 SER 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 189 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 332 PHE Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 44 VAL 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 185 GLN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU 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 109 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 0.0170 chunk 5 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3982 r_free = 0.3982 target = 0.154727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115599 restraints weight = 22331.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120271 restraints weight = 12320.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123431 restraints weight = 8142.281| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5643 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= 0.161 Angle : 0.940 14.479 16687 Z= 0.444 Chirality : 0.049 0.234 2058 Planarity : 0.004 0.053 2046 Dihedral : 6.275 43.146 2087 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.81 % Allowed : 34.23 % Favored : 59.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1515 helix: 0.47 (0.24), residues: 459 sheet: -1.15 (0.25), residues: 412 loop : -1.45 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP B 168 HIS 0.011 0.001 HIS C 150 PHE 0.021 0.002 PHE E 31 TYR 0.030 0.002 TYR B 167 ARG 0.012 0.001 ARG D 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 6) link_NAG-ASN : angle 1.86880 ( 18) link_ALPHA1-6 : bond 0.00591 ( 1) link_ALPHA1-6 : angle 1.73893 ( 3) link_BETA1-4 : bond 0.00412 ( 10) link_BETA1-4 : angle 1.91776 ( 30) link_ALPHA1-2 : bond 0.00495 ( 1) link_ALPHA1-2 : angle 1.41686 ( 3) link_ALPHA1-3 : bond 0.00631 ( 3) link_ALPHA1-3 : angle 1.46009 ( 9) hydrogen bonds : bond 0.03519 ( 517) hydrogen bonds : angle 5.25216 ( 1755) SS BOND : bond 0.00350 ( 5) SS BOND : angle 2.25194 ( 10) covalent geometry : bond 0.00371 (12176) covalent geometry : angle 0.93379 (16614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6032.05 seconds wall clock time: 108 minutes 22.22 seconds (6502.22 seconds total)