Starting phenix.real_space_refine on Fri Jul 3 06:50:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fwv_29520/07_2026/8fwv_29520.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwv_29520/07_2026/8fwv_29520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fwv_29520/07_2026/8fwv_29520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwv_29520/07_2026/8fwv_29520.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fwv_29520/07_2026/8fwv_29520.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fwv_29520/07_2026/8fwv_29520.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fwv_29520/07_2026/8fwv_29520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwv_29520/07_2026/8fwv_29520.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 68 5.16 5 C 8004 2.51 5 N 2100 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12584 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "E" 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 chiralities: 3 Chain: "F" 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 chiralities: 2 Chain: "G" 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 chiralities: 3 Chain: "H" 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 chiralities: 2 Chain: "I" 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 chiralities: 3 Chain: "J" 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 chiralities: 2 Chain: "K" 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 chiralities: 3 Chain: "L" 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 chiralities: 2 Chain: "A" 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 chiralities: 2 Chain: "B" 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 chiralities: 2 Chain: "C" 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 chiralities: 2 Chain: "D" 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 chiralities: 2 Time building chain proxies: 3.09, per 1000 atoms: 0.25 Number of scatterers: 12584 At special positions: 0 Unit cell: (104, 160.576, 85.696, 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 68 16.00 O 2412 8.00 N 2100 7.00 C 8004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1001 " - " ASN A 275 " " NAG A1002 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG C1001 " - " ASN C 275 " " NAG C1002 " - " ASN C 412 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN A 67 " " NAG G 1 " - " ASN B 378 " " NAG H 1 " - " ASN B 67 " " NAG I 1 " - " ASN C 378 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN D 378 " " NAG L 1 " - " ASN D 67 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 559.4 milliseconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 20 sheets defined 39.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.957A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.525A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.664A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.630A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.957A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.525A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.631A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.958A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 161 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.597A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.526A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.630A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.747A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.958A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.526A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.631A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY A 40 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS A 129 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 149 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN A 131 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG A 384 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER A 148 " --> pdb=" O ARG A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.813A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 395 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY B 40 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS B 129 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU B 149 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N GLN B 131 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.813A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 395 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY C 40 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU C 149 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN C 131 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG C 384 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N SER C 148 " --> pdb=" O ARG C 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.812A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 392 through 395 Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY D 40 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS D 129 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU D 149 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN D 131 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.812A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 392 through 395 428 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3741 1.33 - 1.45: 2114 1.45 - 1.57: 6882 1.57 - 1.69: 7 1.69 - 1.81: 120 Bond restraints: 12864 Sorted by residual: bond pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " ideal model delta sigma weight residual 1.406 1.558 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.659 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.647 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.645 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.530 -0.124 2.00e-02 2.50e+03 3.81e+01 ... (remaining 12859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 16711 2.38 - 4.75: 610 4.75 - 7.13: 81 7.13 - 9.50: 9 9.50 - 11.88: 9 Bond angle restraints: 17420 Sorted by residual: angle pdb=" N THR B 414 " pdb=" CA THR B 414 " pdb=" C THR B 414 " ideal model delta sigma weight residual 112.88 107.59 5.29 1.29e+00 6.01e-01 1.68e+01 angle pdb=" N THR C 414 " pdb=" CA THR C 414 " pdb=" C THR C 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" N THR A 414 " pdb=" CA THR A 414 " pdb=" C THR A 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" N THR D 414 " pdb=" CA THR D 414 " pdb=" C THR D 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " pdb=" C5 NAG D1002 " ideal model delta sigma weight residual 113.21 125.09 -11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 17415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 6996 14.30 - 28.59: 355 28.59 - 42.89: 109 42.89 - 57.19: 8 57.19 - 71.49: 12 Dihedral angle restraints: 7480 sinusoidal: 3012 harmonic: 4468 Sorted by residual: dihedral pdb=" CA GLY C 310 " pdb=" C GLY C 310 " pdb=" N LEU C 311 " pdb=" CA LEU C 311 " ideal model delta harmonic sigma weight residual -180.00 -119.43 -60.57 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLY A 310 " pdb=" C GLY A 310 " pdb=" N LEU A 311 " pdb=" CA LEU A 311 " ideal model delta harmonic sigma weight residual -180.00 -119.44 -60.56 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLY B 310 " pdb=" C GLY B 310 " pdb=" N LEU B 311 " pdb=" CA LEU B 311 " ideal model delta harmonic sigma weight residual 180.00 -119.49 -60.51 0 5.00e+00 4.00e-02 1.46e+02 ... (remaining 7477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.373: 2018 0.373 - 0.747: 2 0.747 - 1.120: 0 1.120 - 1.493: 0 1.493 - 1.866: 4 Chirality restraints: 2024 Sorted by residual: chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 275 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.53 -1.87 2.00e-01 2.50e+01 8.71e+01 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 275 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.60 -1.80 2.00e-01 2.50e+01 8.14e+01 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 275 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.16e+01 ... (remaining 2021 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 191 " -0.066 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO B 192 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 191 " 0.066 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO D 192 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 191 " -0.066 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO A 192 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.055 5.00e-02 4.00e+02 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4072 2.85 - 3.36: 10859 3.36 - 3.87: 20453 3.87 - 4.39: 23789 4.39 - 4.90: 41544 Nonbonded interactions: 100717 Sorted by model distance: nonbonded pdb=" OG1 THR A 173 " pdb=" OE1 GLU A 223 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLU B 223 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR D 173 " pdb=" OE1 GLU D 223 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR C 173 " pdb=" OE1 GLU C 223 " model vdw 2.335 3.040 nonbonded pdb=" OE1 GLU D 46 " pdb=" OG SER D 47 " model vdw 2.350 3.040 ... (remaining 100712 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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 individual isotropic 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: 8.490 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.370 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.007 0.152 12896 Z= 0.329 Angle : 1.238 29.065 17512 Z= 0.624 Chirality : 0.095 1.866 2024 Planarity : 0.008 0.100 2180 Dihedral : 10.316 71.487 4580 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.35 % Favored : 92.39 % Rotamer: Outliers : 1.19 % Allowed : 4.78 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.20 (0.16), residues: 1524 helix: -4.16 (0.10), residues: 568 sheet: -2.50 (0.27), residues: 328 loop : -3.06 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 158 TYR 0.016 0.002 TYR D 252 PHE 0.024 0.003 PHE A 107 TRP 0.028 0.004 TRP A 353 HIS 0.010 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.33 (12864) covalent geometry : angle 1.06588 / 0.59 (17420) SS BOND : bond 0.00151 / 0.07 ( 4) SS BOND : angle 0.48138 / 0.27 ( 8) hydrogen bonds : bond 0.28591 / 18.93 ( 428) hydrogen bonds : angle 9.69215 / 6.61 ( 1236) link_BETA1-4 : bond 0.02842 / 1.87 ( 12) link_BETA1-4 : angle 7.57409 / 5.62 ( 36) link_NAG-ASN : bond 0.01481 / 1.01 ( 16) link_NAG-ASN : angle 10.18381 / 7.13 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 311 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8632 (m) cc_final: 0.8192 (p) REVERT: A 156 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 222 LYS cc_start: 0.7945 (mttm) cc_final: 0.7692 (mmtm) REVERT: A 262 PHE cc_start: 0.7324 (t80) cc_final: 0.7036 (p90) REVERT: A 291 SER cc_start: 0.7469 (t) cc_final: 0.7240 (m) REVERT: A 360 MET cc_start: 0.7834 (tpt) cc_final: 0.7147 (tpt) REVERT: B 262 PHE cc_start: 0.7190 (t80) cc_final: 0.6935 (p90) REVERT: B 267 GLU cc_start: 0.7154 (tp30) cc_final: 0.6951 (tp30) REVERT: B 351 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7860 (mppt) REVERT: B 360 MET cc_start: 0.8370 (tpt) cc_final: 0.8166 (tpt) REVERT: C 113 SER cc_start: 0.8636 (m) cc_final: 0.8201 (p) REVERT: C 156 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8297 (tp) REVERT: C 222 LYS cc_start: 0.7938 (mttm) cc_final: 0.7684 (mmtm) REVERT: C 262 PHE cc_start: 0.7303 (t80) cc_final: 0.7048 (p90) REVERT: C 291 SER cc_start: 0.7465 (t) cc_final: 0.7236 (m) REVERT: C 360 MET cc_start: 0.7832 (tpt) cc_final: 0.7148 (tpt) REVERT: D 152 ASP cc_start: 0.7924 (t0) cc_final: 0.7627 (t0) REVERT: D 198 ARG cc_start: 0.7349 (tmt-80) cc_final: 0.7052 (tpt90) REVERT: D 200 LYS cc_start: 0.7855 (mttp) cc_final: 0.7610 (mtpt) REVERT: D 247 MET cc_start: 0.9125 (mtp) cc_final: 0.8886 (mtp) REVERT: D 262 PHE cc_start: 0.7139 (t80) cc_final: 0.6876 (p90) REVERT: D 351 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7823 (mppt) outliers start: 16 outliers final: 4 residues processed: 325 average time/residue: 0.1434 time to fit residues: 63.2081 Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 286 ASN A 335 GLN A 336 GLN A 346 GLN A 350 HIS B 98 GLN B 288 GLN B 335 GLN B 336 GLN B 350 HIS C 196 ASN C 286 ASN C 335 GLN C 336 GLN C 346 GLN C 350 HIS D 288 GLN D 335 GLN D 336 GLN D 350 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136992 restraints weight = 13497.453| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.24 r_work: 0.3332 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12896 Z= 0.158 Angle : 0.841 23.389 17512 Z= 0.380 Chirality : 0.059 1.044 2024 Planarity : 0.006 0.084 2180 Dihedral : 6.349 49.034 1664 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.81 % Allowed : 9.70 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.18), residues: 1524 helix: -2.30 (0.16), residues: 568 sheet: -2.45 (0.27), residues: 328 loop : -2.73 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 37 TYR 0.007 0.001 TYR B 252 PHE 0.014 0.002 PHE B 107 TRP 0.013 0.002 TRP C 353 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (12864) covalent geometry : angle 0.72679 / 0.35 (17420) SS BOND : bond 0.00208 / 0.10 ( 4) SS BOND : angle 0.38610 / 0.24 ( 8) hydrogen bonds : bond 0.04566 / 3.03 ( 428) hydrogen bonds : angle 4.97522 / 3.46 ( 1236) link_BETA1-4 : bond 0.02390 / 1.61 ( 12) link_BETA1-4 : angle 4.94527 / 3.44 ( 36) link_NAG-ASN : bond 0.01303 / 0.83 ( 16) link_NAG-ASN : angle 6.92991 / 4.65 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7042 (mm) REVERT: A 113 SER cc_start: 0.8860 (m) cc_final: 0.8499 (p) REVERT: A 156 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8005 (mt) REVERT: A 177 ASP cc_start: 0.8320 (t70) cc_final: 0.8089 (t0) REVERT: A 222 LYS cc_start: 0.8071 (mttm) cc_final: 0.7651 (mmtm) REVERT: A 262 PHE cc_start: 0.7764 (t80) cc_final: 0.7157 (p90) REVERT: A 291 SER cc_start: 0.7649 (t) cc_final: 0.7354 (m) REVERT: B 262 PHE cc_start: 0.7947 (t80) cc_final: 0.7098 (p90) REVERT: B 288 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7613 (mm110) REVERT: B 351 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7936 (mppt) REVERT: C 55 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7057 (mm) REVERT: C 113 SER cc_start: 0.8845 (m) cc_final: 0.8481 (p) REVERT: C 156 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7990 (mt) REVERT: C 177 ASP cc_start: 0.8329 (t70) cc_final: 0.8099 (t0) REVERT: C 222 LYS cc_start: 0.8060 (mttm) cc_final: 0.7636 (mmtm) REVERT: C 262 PHE cc_start: 0.7762 (t80) cc_final: 0.7100 (p90) REVERT: C 291 SER cc_start: 0.7640 (t) cc_final: 0.7362 (m) REVERT: D 198 ARG cc_start: 0.7928 (tmt-80) cc_final: 0.7475 (tpt90) REVERT: D 218 MET cc_start: 0.8953 (mtp) cc_final: 0.8690 (mtm) REVERT: D 247 MET cc_start: 0.9200 (mtp) cc_final: 0.8967 (mtp) REVERT: D 262 PHE cc_start: 0.7945 (t80) cc_final: 0.7085 (p90) REVERT: D 351 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7700 (mppt) outliers start: 51 outliers final: 23 residues processed: 207 average time/residue: 0.1108 time to fit residues: 32.9146 Evaluate side-chains 179 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 97 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 113 optimal weight: 0.0770 chunk 151 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 346 GLN C 196 ASN C 346 GLN D 165 GLN D 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138483 restraints weight = 13707.251| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.17 r_work: 0.3349 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12896 Z= 0.122 Angle : 0.750 21.182 17512 Z= 0.331 Chirality : 0.056 0.903 2024 Planarity : 0.005 0.077 2180 Dihedral : 5.807 55.175 1664 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.66 % Allowed : 9.40 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.19), residues: 1524 helix: -0.46 (0.20), residues: 572 sheet: -2.34 (0.28), residues: 312 loop : -2.73 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 37 TYR 0.017 0.001 TYR C 195 PHE 0.011 0.001 PHE B 359 TRP 0.016 0.001 TRP C 296 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (12864) covalent geometry : angle 0.64558 / 0.31 (17420) SS BOND : bond 0.00166 / 0.08 ( 4) SS BOND : angle 0.14088 / 0.09 ( 8) hydrogen bonds : bond 0.03609 / 2.39 ( 428) hydrogen bonds : angle 4.23757 / 2.95 ( 1236) link_BETA1-4 : bond 0.02057 / 1.38 ( 12) link_BETA1-4 : angle 4.51413 / 3.13 ( 36) link_NAG-ASN : bond 0.01331 / 0.84 ( 16) link_NAG-ASN : angle 6.20209 / 4.20 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6875 (mm) REVERT: A 113 SER cc_start: 0.8599 (m) cc_final: 0.8196 (p) REVERT: A 156 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7680 (mt) REVERT: A 177 ASP cc_start: 0.8066 (t70) cc_final: 0.7854 (t0) REVERT: A 220 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7706 (mtm110) REVERT: A 222 LYS cc_start: 0.7935 (mttm) cc_final: 0.7598 (mmtm) REVERT: A 262 PHE cc_start: 0.7794 (t80) cc_final: 0.7117 (p90) REVERT: A 283 ASN cc_start: 0.7148 (t0) cc_final: 0.6840 (t0) REVERT: A 291 SER cc_start: 0.7617 (t) cc_final: 0.7332 (m) REVERT: B 262 PHE cc_start: 0.7830 (t80) cc_final: 0.7094 (p90) REVERT: B 288 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7547 (mm110) REVERT: B 351 LYS cc_start: 0.8237 (mtmt) cc_final: 0.8019 (mptt) REVERT: C 55 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6884 (mm) REVERT: C 113 SER cc_start: 0.8573 (m) cc_final: 0.8163 (p) REVERT: C 156 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7680 (mt) REVERT: C 177 ASP cc_start: 0.8055 (t70) cc_final: 0.7844 (t0) REVERT: C 222 LYS cc_start: 0.7950 (mttm) cc_final: 0.7621 (mmtm) REVERT: C 262 PHE cc_start: 0.7810 (t80) cc_final: 0.7100 (p90) REVERT: C 283 ASN cc_start: 0.7150 (t0) cc_final: 0.6824 (t0) REVERT: C 291 SER cc_start: 0.7641 (t) cc_final: 0.7356 (m) REVERT: D 50 MET cc_start: 0.7459 (ptp) cc_final: 0.7201 (ptt) REVERT: D 198 ARG cc_start: 0.7639 (tmt-80) cc_final: 0.7338 (tpt90) REVERT: D 218 MET cc_start: 0.8882 (mtp) cc_final: 0.8677 (mtm) REVERT: D 247 MET cc_start: 0.9154 (mtp) cc_final: 0.8932 (mtp) REVERT: D 262 PHE cc_start: 0.7813 (t80) cc_final: 0.7129 (p90) REVERT: D 288 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7447 (mm-40) outliers start: 49 outliers final: 23 residues processed: 209 average time/residue: 0.0956 time to fit residues: 29.1018 Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 139 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN C 196 ASN D 98 GLN D 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.172274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134515 restraints weight = 13548.193| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.25 r_work: 0.3288 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12896 Z= 0.173 Angle : 0.788 21.891 17512 Z= 0.351 Chirality : 0.060 1.017 2024 Planarity : 0.005 0.076 2180 Dihedral : 5.826 58.583 1664 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.51 % Allowed : 10.82 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.20), residues: 1524 helix: 0.18 (0.21), residues: 560 sheet: -2.27 (0.27), residues: 332 loop : -2.65 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 37 TYR 0.015 0.002 TYR C 195 PHE 0.017 0.002 PHE B 107 TRP 0.013 0.001 TRP C 296 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (12864) covalent geometry : angle 0.68867 / 0.33 (17420) SS BOND : bond 0.00095 / 0.05 ( 4) SS BOND : angle 0.20723 / 0.13 ( 8) hydrogen bonds : bond 0.03522 / 2.33 ( 428) hydrogen bonds : angle 4.09174 / 2.84 ( 1236) link_BETA1-4 : bond 0.01946 / 1.31 ( 12) link_BETA1-4 : angle 4.43449 / 3.08 ( 36) link_NAG-ASN : bond 0.00891 / 0.58 ( 16) link_NAG-ASN : angle 6.30049 / 4.29 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6622 (t) cc_final: 0.6412 (p) REVERT: A 55 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7146 (mm) REVERT: A 113 SER cc_start: 0.8798 (m) cc_final: 0.8379 (p) REVERT: A 220 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7810 (mtm110) REVERT: A 222 LYS cc_start: 0.8099 (mttm) cc_final: 0.7578 (mtmt) REVERT: A 262 PHE cc_start: 0.8013 (t80) cc_final: 0.7075 (p90) REVERT: A 283 ASN cc_start: 0.7283 (t0) cc_final: 0.6960 (t0) REVERT: A 298 MET cc_start: 0.6462 (tmm) cc_final: 0.6260 (tmm) REVERT: B 50 MET cc_start: 0.7653 (ptt) cc_final: 0.7371 (ptt) REVERT: B 262 PHE cc_start: 0.8177 (t80) cc_final: 0.7142 (p90) REVERT: B 288 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7588 (mm110) REVERT: B 351 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8012 (mptt) REVERT: C 45 VAL cc_start: 0.6607 (t) cc_final: 0.6398 (p) REVERT: C 55 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7131 (mm) REVERT: C 113 SER cc_start: 0.8802 (m) cc_final: 0.8371 (p) REVERT: C 194 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7425 (ptp-170) REVERT: C 222 LYS cc_start: 0.8021 (mttm) cc_final: 0.7677 (mmtm) REVERT: C 262 PHE cc_start: 0.7998 (t80) cc_final: 0.7037 (p90) REVERT: C 400 GLU cc_start: 0.7659 (tt0) cc_final: 0.6947 (mm-30) REVERT: D 198 ARG cc_start: 0.7903 (tmt-80) cc_final: 0.7481 (tpt90) REVERT: D 218 MET cc_start: 0.9037 (mtp) cc_final: 0.8773 (mtm) REVERT: D 247 MET cc_start: 0.9208 (mtp) cc_final: 0.9005 (mtp) REVERT: D 262 PHE cc_start: 0.8159 (t80) cc_final: 0.7136 (p90) REVERT: D 288 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7444 (mm-40) outliers start: 47 outliers final: 31 residues processed: 197 average time/residue: 0.1126 time to fit residues: 32.4783 Evaluate side-chains 187 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.173146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134740 restraints weight = 13634.001| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.34 r_work: 0.3299 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12896 Z= 0.136 Angle : 0.731 20.463 17512 Z= 0.324 Chirality : 0.059 1.073 2024 Planarity : 0.005 0.078 2180 Dihedral : 5.262 33.598 1660 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.66 % Allowed : 11.19 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.20), residues: 1524 helix: 0.75 (0.21), residues: 564 sheet: -2.17 (0.28), residues: 292 loop : -2.51 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 37 TYR 0.013 0.001 TYR C 195 PHE 0.014 0.002 PHE C 107 TRP 0.014 0.001 TRP D 296 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (12864) covalent geometry : angle 0.63099 / 0.30 (17420) SS BOND : bond 0.00148 / 0.07 ( 4) SS BOND : angle 0.57898 / 0.35 ( 8) hydrogen bonds : bond 0.03215 / 2.11 ( 428) hydrogen bonds : angle 3.96993 / 2.75 ( 1236) link_BETA1-4 : bond 0.01935 / 1.30 ( 12) link_BETA1-4 : angle 4.31862 / 3.03 ( 36) link_NAG-ASN : bond 0.01062 / 0.67 ( 16) link_NAG-ASN : angle 6.04750 / 4.09 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6550 (t) cc_final: 0.6330 (p) REVERT: A 55 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7047 (mm) REVERT: A 113 SER cc_start: 0.8760 (m) cc_final: 0.8312 (p) REVERT: A 160 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 220 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7773 (mtm110) REVERT: A 222 LYS cc_start: 0.8067 (mttm) cc_final: 0.7533 (mtmt) REVERT: A 262 PHE cc_start: 0.8053 (t80) cc_final: 0.7045 (p90) REVERT: A 275 ASN cc_start: 0.5303 (m-40) cc_final: 0.5086 (m-40) REVERT: A 351 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7807 (mptt) REVERT: A 400 GLU cc_start: 0.7665 (tt0) cc_final: 0.6914 (mm-30) REVERT: B 50 MET cc_start: 0.7553 (ptt) cc_final: 0.7291 (ptt) REVERT: B 262 PHE cc_start: 0.8239 (t80) cc_final: 0.7132 (p90) REVERT: B 288 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7530 (mm110) REVERT: B 351 LYS cc_start: 0.8336 (mtmt) cc_final: 0.7988 (mppt) REVERT: C 45 VAL cc_start: 0.6581 (t) cc_final: 0.6368 (p) REVERT: C 55 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7087 (mm) REVERT: C 113 SER cc_start: 0.8757 (m) cc_final: 0.8314 (p) REVERT: C 160 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8222 (mp) REVERT: C 222 LYS cc_start: 0.8090 (mttm) cc_final: 0.7734 (mmtm) REVERT: C 262 PHE cc_start: 0.8037 (t80) cc_final: 0.7009 (p90) REVERT: C 275 ASN cc_start: 0.5315 (m-40) cc_final: 0.5102 (m-40) REVERT: C 400 GLU cc_start: 0.7674 (tt0) cc_final: 0.6930 (mm-30) REVERT: D 198 ARG cc_start: 0.7884 (tmt-80) cc_final: 0.7441 (tpt90) REVERT: D 218 MET cc_start: 0.9026 (mtp) cc_final: 0.8773 (mtm) REVERT: D 262 PHE cc_start: 0.8199 (t80) cc_final: 0.7148 (p90) REVERT: D 288 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7406 (mm-40) outliers start: 49 outliers final: 35 residues processed: 201 average time/residue: 0.1006 time to fit residues: 29.3285 Evaluate side-chains 194 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 0.0870 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 150 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.175182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135800 restraints weight = 13532.859| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.21 r_work: 0.3312 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12896 Z= 0.123 Angle : 0.690 19.208 17512 Z= 0.308 Chirality : 0.055 0.890 2024 Planarity : 0.005 0.078 2180 Dihedral : 5.012 31.250 1660 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.21 % Allowed : 11.64 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.21), residues: 1524 helix: 1.26 (0.22), residues: 564 sheet: -2.01 (0.29), residues: 292 loop : -2.42 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 37 TYR 0.016 0.001 TYR B 86 PHE 0.012 0.001 PHE D 107 TRP 0.015 0.001 TRP D 296 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (12864) covalent geometry : angle 0.60039 / 0.29 (17420) SS BOND : bond 0.00066 / 0.03 ( 4) SS BOND : angle 0.22995 / 0.14 ( 8) hydrogen bonds : bond 0.02970 / 1.95 ( 428) hydrogen bonds : angle 3.84564 / 2.67 ( 1236) link_BETA1-4 : bond 0.01833 / 1.23 ( 12) link_BETA1-4 : angle 4.12230 / 2.92 ( 36) link_NAG-ASN : bond 0.00803 / 0.53 ( 16) link_NAG-ASN : angle 5.47620 / 3.69 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6518 (t) cc_final: 0.6298 (p) REVERT: A 55 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7069 (mm) REVERT: A 160 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 222 LYS cc_start: 0.8071 (mttm) cc_final: 0.7519 (mtmt) REVERT: A 262 PHE cc_start: 0.8067 (t80) cc_final: 0.7050 (p90) REVERT: A 335 GLN cc_start: 0.6795 (tp40) cc_final: 0.6503 (tt0) REVERT: A 351 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7810 (mptt) REVERT: B 194 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7535 (ptm160) REVERT: B 262 PHE cc_start: 0.8266 (t80) cc_final: 0.7159 (p90) REVERT: B 288 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7519 (mm110) REVERT: B 351 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7943 (mppt) REVERT: C 45 VAL cc_start: 0.6573 (t) cc_final: 0.6351 (p) REVERT: C 55 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7111 (mm) REVERT: C 160 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8209 (mp) REVERT: C 222 LYS cc_start: 0.8091 (mttm) cc_final: 0.7679 (mmtm) REVERT: C 262 PHE cc_start: 0.8052 (t80) cc_final: 0.7030 (p90) REVERT: C 335 GLN cc_start: 0.6787 (tp40) cc_final: 0.6506 (tt0) REVERT: C 351 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7807 (mptt) REVERT: D 198 ARG cc_start: 0.7851 (tmt-80) cc_final: 0.7420 (tpt90) REVERT: D 218 MET cc_start: 0.9021 (mtp) cc_final: 0.8767 (mtm) REVERT: D 262 PHE cc_start: 0.8239 (t80) cc_final: 0.7166 (p90) REVERT: D 288 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7385 (mm-40) outliers start: 43 outliers final: 31 residues processed: 202 average time/residue: 0.1104 time to fit residues: 31.7724 Evaluate side-chains 191 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138436 restraints weight = 13498.768| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.45 r_work: 0.3341 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12896 Z= 0.119 Angle : 0.759 24.307 17512 Z= 0.326 Chirality : 0.047 0.762 2024 Planarity : 0.005 0.076 2180 Dihedral : 4.956 32.887 1660 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.06 % Allowed : 11.42 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1524 helix: 1.47 (0.22), residues: 564 sheet: -1.96 (0.27), residues: 312 loop : -2.35 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 37 TYR 0.021 0.001 TYR B 86 PHE 0.013 0.001 PHE A 107 TRP 0.014 0.001 TRP D 296 HIS 0.003 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12864) covalent geometry : angle 0.61522 / 0.29 (17420) SS BOND : bond 0.00061 / 0.03 ( 4) SS BOND : angle 0.12817 / 0.08 ( 8) hydrogen bonds : bond 0.02776 / 1.85 ( 428) hydrogen bonds : angle 3.78858 / 2.62 ( 1236) link_BETA1-4 : bond 0.01741 / 1.16 ( 12) link_BETA1-4 : angle 3.96708 / 2.84 ( 36) link_NAG-ASN : bond 0.00828 / 0.53 ( 16) link_NAG-ASN : angle 7.80390 / 5.06 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6565 (t) cc_final: 0.6329 (p) REVERT: A 55 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7162 (mm) REVERT: A 160 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8281 (mp) REVERT: A 222 LYS cc_start: 0.8042 (mttm) cc_final: 0.7607 (mmtm) REVERT: A 248 MET cc_start: 0.7996 (mmm) cc_final: 0.7764 (mmm) REVERT: A 262 PHE cc_start: 0.8132 (t80) cc_final: 0.7168 (p90) REVERT: A 335 GLN cc_start: 0.6811 (tp40) cc_final: 0.6538 (tt0) REVERT: A 351 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7822 (mptt) REVERT: B 262 PHE cc_start: 0.8345 (t80) cc_final: 0.7209 (p90) REVERT: B 288 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7561 (mm110) REVERT: B 351 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7977 (mppt) REVERT: C 45 VAL cc_start: 0.6611 (t) cc_final: 0.6379 (p) REVERT: C 55 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7165 (mm) REVERT: C 160 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8270 (mp) REVERT: C 222 LYS cc_start: 0.8110 (mttm) cc_final: 0.7704 (mmtm) REVERT: C 262 PHE cc_start: 0.8119 (t80) cc_final: 0.7145 (p90) REVERT: C 335 GLN cc_start: 0.6817 (tp40) cc_final: 0.6544 (tt0) REVERT: C 351 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7814 (mptt) REVERT: D 50 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7244 (ptt) REVERT: D 198 ARG cc_start: 0.7936 (tmt-80) cc_final: 0.7518 (tpt90) REVERT: D 218 MET cc_start: 0.9002 (mtp) cc_final: 0.8768 (mtm) REVERT: D 262 PHE cc_start: 0.8305 (t80) cc_final: 0.7205 (p90) REVERT: D 288 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7427 (mm-40) outliers start: 41 outliers final: 28 residues processed: 186 average time/residue: 0.1250 time to fit residues: 33.4266 Evaluate side-chains 182 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 HIS D 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.174431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135343 restraints weight = 13446.473| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.42 r_work: 0.3309 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12896 Z= 0.155 Angle : 0.726 19.767 17512 Z= 0.322 Chirality : 0.050 0.789 2024 Planarity : 0.005 0.075 2180 Dihedral : 5.037 31.841 1660 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.91 % Allowed : 12.09 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1524 helix: 1.41 (0.22), residues: 564 sheet: -1.94 (0.28), residues: 312 loop : -2.28 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 37 TYR 0.015 0.001 TYR B 86 PHE 0.016 0.002 PHE A 107 TRP 0.010 0.001 TRP A 296 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (12864) covalent geometry : angle 0.61848 / 0.30 (17420) SS BOND : bond 0.00018 / 0.01 ( 4) SS BOND : angle 0.11414 / 0.07 ( 8) hydrogen bonds : bond 0.02936 / 1.94 ( 428) hydrogen bonds : angle 3.84503 / 2.66 ( 1236) link_BETA1-4 : bond 0.01647 / 1.10 ( 12) link_BETA1-4 : angle 3.88887 / 2.81 ( 36) link_NAG-ASN : bond 0.00863 / 0.56 ( 16) link_NAG-ASN : angle 6.50646 / 4.30 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6606 (t) cc_final: 0.6385 (p) REVERT: A 55 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7368 (mt) REVERT: A 160 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 222 LYS cc_start: 0.8070 (mttm) cc_final: 0.7524 (mtmt) REVERT: A 262 PHE cc_start: 0.8184 (t80) cc_final: 0.7180 (p90) REVERT: A 335 GLN cc_start: 0.6777 (tp40) cc_final: 0.6536 (tt0) REVERT: A 351 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7802 (mptt) REVERT: B 50 MET cc_start: 0.7431 (ptt) cc_final: 0.7041 (ptt) REVERT: B 262 PHE cc_start: 0.8413 (t80) cc_final: 0.7227 (p90) REVERT: B 288 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7612 (mm110) REVERT: B 351 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7923 (mppt) REVERT: C 45 VAL cc_start: 0.6643 (t) cc_final: 0.6430 (p) REVERT: C 55 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7380 (mt) REVERT: C 160 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 195 TYR cc_start: 0.6847 (m-10) cc_final: 0.6628 (m-10) REVERT: C 222 LYS cc_start: 0.8058 (mttm) cc_final: 0.7622 (mmtm) REVERT: C 262 PHE cc_start: 0.8174 (t80) cc_final: 0.7163 (p90) REVERT: C 335 GLN cc_start: 0.6790 (tp40) cc_final: 0.6533 (tt0) REVERT: C 351 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7811 (mptt) REVERT: D 50 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7263 (ptt) REVERT: D 198 ARG cc_start: 0.7959 (tmt-80) cc_final: 0.7480 (tpt90) REVERT: D 200 LYS cc_start: 0.8523 (mttp) cc_final: 0.8259 (mttt) REVERT: D 218 MET cc_start: 0.9024 (mtp) cc_final: 0.8740 (mtm) REVERT: D 234 MET cc_start: 0.9015 (ttm) cc_final: 0.8803 (mtp) REVERT: D 262 PHE cc_start: 0.8419 (t80) cc_final: 0.7221 (p90) REVERT: D 288 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7431 (mm-40) outliers start: 39 outliers final: 28 residues processed: 186 average time/residue: 0.1232 time to fit residues: 32.7266 Evaluate side-chains 186 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.5980 chunk 144 optimal weight: 0.0980 chunk 101 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.176840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138159 restraints weight = 13479.629| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.40 r_work: 0.3341 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12896 Z= 0.113 Angle : 0.658 18.494 17512 Z= 0.295 Chirality : 0.048 0.684 2024 Planarity : 0.005 0.076 2180 Dihedral : 4.838 31.929 1660 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.39 % Allowed : 12.69 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.22), residues: 1524 helix: 1.71 (0.22), residues: 576 sheet: -1.82 (0.28), residues: 312 loop : -2.17 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 37 TYR 0.023 0.001 TYR B 86 PHE 0.009 0.001 PHE D 107 TRP 0.015 0.001 TRP B 296 HIS 0.003 0.000 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (12864) covalent geometry : angle 0.56495 / 0.27 (17420) SS BOND : bond 0.00034 / 0.02 ( 4) SS BOND : angle 0.12984 / 0.08 ( 8) hydrogen bonds : bond 0.02682 / 1.77 ( 428) hydrogen bonds : angle 3.75952 / 2.60 ( 1236) link_BETA1-4 : bond 0.01557 / 1.02 ( 12) link_BETA1-4 : angle 3.59686 / 2.66 ( 36) link_NAG-ASN : bond 0.00905 / 0.58 ( 16) link_NAG-ASN : angle 5.67324 / 3.75 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6574 (t) cc_final: 0.6335 (p) REVERT: A 55 LEU cc_start: 0.7634 (mm) cc_final: 0.7387 (mt) REVERT: A 160 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A 194 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7828 (ptm160) REVERT: A 195 TYR cc_start: 0.6899 (m-10) cc_final: 0.6663 (m-10) REVERT: A 222 LYS cc_start: 0.8114 (mttm) cc_final: 0.7695 (mmtm) REVERT: A 262 PHE cc_start: 0.8289 (t80) cc_final: 0.7184 (p90) REVERT: A 335 GLN cc_start: 0.6736 (tp40) cc_final: 0.6500 (tt0) REVERT: A 351 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7817 (mptt) REVERT: B 50 MET cc_start: 0.7357 (ptt) cc_final: 0.7047 (ptt) REVERT: B 133 ARG cc_start: 0.8851 (ttt-90) cc_final: 0.8377 (mtp85) REVERT: B 262 PHE cc_start: 0.8431 (t80) cc_final: 0.7231 (p90) REVERT: B 288 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7601 (mm-40) REVERT: B 351 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7850 (mppt) REVERT: C 45 VAL cc_start: 0.6560 (t) cc_final: 0.6314 (p) REVERT: C 55 LEU cc_start: 0.7636 (mm) cc_final: 0.7381 (mt) REVERT: C 160 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8224 (mp) REVERT: C 222 LYS cc_start: 0.8011 (mttm) cc_final: 0.7587 (mmtm) REVERT: C 262 PHE cc_start: 0.8268 (t80) cc_final: 0.7164 (p90) REVERT: C 335 GLN cc_start: 0.6780 (tp40) cc_final: 0.6519 (tt0) REVERT: C 351 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7831 (mptt) REVERT: D 50 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7129 (ptt) REVERT: D 133 ARG cc_start: 0.8840 (ttt-90) cc_final: 0.8355 (mtp85) REVERT: D 165 GLN cc_start: 0.8275 (mt0) cc_final: 0.8068 (mm-40) REVERT: D 198 ARG cc_start: 0.7918 (tmt-80) cc_final: 0.7449 (tpt90) REVERT: D 200 LYS cc_start: 0.8482 (mttp) cc_final: 0.8236 (mttt) REVERT: D 218 MET cc_start: 0.8982 (mtp) cc_final: 0.8772 (mtm) REVERT: D 234 MET cc_start: 0.8982 (ttm) cc_final: 0.8761 (mtp) REVERT: D 262 PHE cc_start: 0.8461 (t80) cc_final: 0.7239 (p90) REVERT: D 288 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7404 (mm-40) outliers start: 32 outliers final: 25 residues processed: 186 average time/residue: 0.1232 time to fit residues: 32.8571 Evaluate side-chains 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135194 restraints weight = 13548.591| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.44 r_work: 0.3298 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12896 Z= 0.153 Angle : 0.687 17.784 17512 Z= 0.313 Chirality : 0.050 0.734 2024 Planarity : 0.005 0.075 2180 Dihedral : 4.964 31.108 1660 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.16 % Allowed : 13.06 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1524 helix: 1.57 (0.22), residues: 576 sheet: -1.81 (0.28), residues: 312 loop : -2.09 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 37 TYR 0.024 0.001 TYR B 86 PHE 0.018 0.002 PHE C 107 TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (12864) covalent geometry : angle 0.60712 / 0.29 (17420) SS BOND : bond 0.00037 / 0.01 ( 4) SS BOND : angle 0.10801 / 0.06 ( 8) hydrogen bonds : bond 0.02915 / 1.93 ( 428) hydrogen bonds : angle 3.82858 / 2.65 ( 1236) link_BETA1-4 : bond 0.01438 / 0.95 ( 12) link_BETA1-4 : angle 3.58082 / 2.65 ( 36) link_NAG-ASN : bond 0.00852 / 0.55 ( 16) link_NAG-ASN : angle 5.38571 / 3.56 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6633 (t) cc_final: 0.6379 (p) REVERT: A 55 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7433 (mt) REVERT: A 160 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8238 (mp) REVERT: A 194 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7829 (ptm160) REVERT: A 222 LYS cc_start: 0.8184 (mttm) cc_final: 0.7665 (mtmt) REVERT: A 262 PHE cc_start: 0.8321 (t80) cc_final: 0.7268 (p90) REVERT: A 335 GLN cc_start: 0.6781 (tp40) cc_final: 0.6520 (tt0) REVERT: A 351 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7791 (mptt) REVERT: B 50 MET cc_start: 0.7386 (ptt) cc_final: 0.7098 (ptt) REVERT: B 133 ARG cc_start: 0.8868 (ttt-90) cc_final: 0.8399 (mtp85) REVERT: B 262 PHE cc_start: 0.8498 (t80) cc_final: 0.7303 (p90) REVERT: B 288 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7623 (mm-40) REVERT: B 351 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7868 (mppt) REVERT: C 45 VAL cc_start: 0.6660 (t) cc_final: 0.6402 (p) REVERT: C 55 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7454 (mt) REVERT: C 160 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8240 (mp) REVERT: C 222 LYS cc_start: 0.8068 (mttm) cc_final: 0.7554 (mtmt) REVERT: C 262 PHE cc_start: 0.8312 (t80) cc_final: 0.7259 (p90) REVERT: C 335 GLN cc_start: 0.6793 (tp40) cc_final: 0.6530 (tt0) REVERT: C 351 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7837 (mptt) REVERT: D 50 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7108 (ptt) REVERT: D 198 ARG cc_start: 0.7964 (tmt-80) cc_final: 0.7518 (tpt90) REVERT: D 200 LYS cc_start: 0.8551 (mttp) cc_final: 0.8313 (mttt) REVERT: D 218 MET cc_start: 0.9033 (mtp) cc_final: 0.8762 (mtm) REVERT: D 234 MET cc_start: 0.9024 (ttm) cc_final: 0.8814 (mtp) REVERT: D 262 PHE cc_start: 0.8530 (t80) cc_final: 0.7268 (p90) REVERT: D 288 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7567 (mm110) outliers start: 29 outliers final: 24 residues processed: 182 average time/residue: 0.1270 time to fit residues: 33.3232 Evaluate side-chains 186 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 134 optimal weight: 0.0370 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137080 restraints weight = 13505.554| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.36 r_work: 0.3331 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12896 Z= 0.112 Angle : 0.640 16.610 17512 Z= 0.293 Chirality : 0.048 0.659 2024 Planarity : 0.005 0.079 2180 Dihedral : 4.831 31.538 1660 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.39 % Allowed : 13.06 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.22), residues: 1524 helix: 1.72 (0.22), residues: 580 sheet: -1.71 (0.28), residues: 312 loop : -1.98 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 37 TYR 0.023 0.001 TYR B 86 PHE 0.010 0.001 PHE C 107 TRP 0.013 0.001 TRP B 296 HIS 0.003 0.000 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (12864) covalent geometry : angle 0.56378 / 0.28 (17420) SS BOND : bond 0.00032 / 0.02 ( 4) SS BOND : angle 0.11999 / 0.07 ( 8) hydrogen bonds : bond 0.02707 / 1.78 ( 428) hydrogen bonds : angle 3.75612 / 2.60 ( 1236) link_BETA1-4 : bond 0.01411 / 0.92 ( 12) link_BETA1-4 : angle 3.39281 / 2.56 ( 36) link_NAG-ASN : bond 0.00900 / 0.58 ( 16) link_NAG-ASN : angle 5.03561 / 3.33 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3391.08 seconds wall clock time: 58 minutes 57.38 seconds (3537.38 seconds total)