Starting phenix.real_space_refine on Thu May 15 03:03:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwt_29518/05_2025/8fwt_29518.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwt_29518/05_2025/8fwt_29518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fwt_29518/05_2025/8fwt_29518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwt_29518/05_2025/8fwt_29518.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwt_29518/05_2025/8fwt_29518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwt_29518/05_2025/8fwt_29518.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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 8016 2.51 5 N 2100 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12606 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.90, per 1000 atoms: 0.71 Number of scatterers: 12606 At special positions: 0 Unit cell: (143.59, 113.71, 84.66, 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 2422 8.00 N 2100 7.00 C 8016 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 F 2 " - " BMA F 3 " " 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 J 2 " - " BMA J 3 " " 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: 3.76 Conformation dependent library (CDL) restraints added in 2.1 seconds 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, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.970A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.988A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.629A 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 removed outlier: 3.518A pdb=" N ILE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.666A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.989A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.867A pdb=" N ARG A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.542A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.838A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.970A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.988A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.629A 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 removed outlier: 3.519A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.667A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.989A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.867A pdb=" N ARG B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 301 removed outlier: 3.542A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.838A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.970A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.988A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.630A 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 removed outlier: 3.518A pdb=" N ILE C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.665A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.988A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.866A pdb=" N ARG C 270 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.542A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.838A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.970A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.987A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.629A 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 removed outlier: 3.518A pdb=" N ILE D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.667A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.989A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.866A pdb=" N ARG D 270 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 301 removed outlier: 3.543A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.838A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 7.070A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 203 removed outlier: 7.071A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 203 removed outlier: 7.070A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AB6, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 199 through 203 removed outlier: 7.070A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=AC2, first strand: chain 'D' and resid 392 through 394 412 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3904 1.34 - 1.46: 2145 1.46 - 1.57: 6711 1.57 - 1.69: 6 1.69 - 1.81: 120 Bond restraints: 12886 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.594 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 BMA K 3 " pdb=" C2 BMA K 3 " ideal model delta sigma weight residual 1.519 1.592 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " ideal model delta sigma weight residual 1.528 1.595 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 12881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 16237 1.83 - 3.65: 1017 3.65 - 5.48: 128 5.48 - 7.31: 51 7.31 - 9.13: 17 Bond angle restraints: 17450 Sorted by residual: angle pdb=" C ASN B 84 " pdb=" N LEU B 85 " pdb=" CA LEU B 85 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C ASN A 84 " pdb=" N LEU A 85 " pdb=" CA LEU A 85 " ideal model delta sigma weight residual 121.54 130.02 -8.48 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASN C 84 " pdb=" N LEU C 85 " pdb=" CA LEU C 85 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASN D 84 " pdb=" N LEU D 85 " pdb=" CA LEU D 85 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" N GLN B 302 " pdb=" CA GLN B 302 " pdb=" C GLN B 302 " ideal model delta sigma weight residual 111.17 116.31 -5.14 1.41e+00 5.03e-01 1.33e+01 ... (remaining 17445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.43: 7704 22.43 - 44.86: 231 44.86 - 67.29: 69 67.29 - 89.72: 56 89.72 - 112.15: 38 Dihedral angle restraints: 8098 sinusoidal: 3630 harmonic: 4468 Sorted by residual: dihedral pdb=" CA ARG A 300 " pdb=" C ARG A 300 " pdb=" N LEU A 301 " pdb=" CA LEU A 301 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG B 300 " pdb=" C ARG B 300 " pdb=" N LEU B 301 " pdb=" CA LEU B 301 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG C 300 " pdb=" C ARG C 300 " pdb=" N LEU C 301 " pdb=" CA LEU C 301 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 8095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 2016 0.224 - 0.448: 16 0.448 - 0.672: 0 0.672 - 0.897: 0 0.897 - 1.121: 2 Chirality restraints: 2034 Sorted by residual: chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 412 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 412 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.47e+01 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 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 2031 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 412 " 0.026 2.00e-02 2.50e+03 2.66e-02 8.82e+00 pdb=" CG ASN D 412 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN D 412 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN D 412 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG D1002 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 67 " 0.026 2.00e-02 2.50e+03 2.64e-02 8.69e+00 pdb=" CG ASN C 67 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN C 67 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 67 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 108 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO B 109 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 109 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 109 " -0.038 5.00e-02 4.00e+02 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4060 2.85 - 3.36: 10940 3.36 - 3.87: 20395 3.87 - 4.39: 23873 4.39 - 4.90: 41969 Nonbonded interactions: 101237 Sorted by model distance: nonbonded pdb=" OE1 GLN D 119 " pdb=" NZ LYS D 135 " model vdw 2.333 3.120 nonbonded pdb=" OE1 GLN B 119 " pdb=" NZ LYS B 135 " model vdw 2.333 3.120 nonbonded pdb=" OE1 GLN C 119 " pdb=" NZ LYS C 135 " model vdw 2.333 3.120 nonbonded pdb=" OE1 GLN A 119 " pdb=" NZ LYS A 135 " model vdw 2.333 3.120 nonbonded pdb=" NH1 ARG A 374 " pdb=" OD2 ASP A 386 " model vdw 2.345 3.120 ... (remaining 101232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'H' 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: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.520 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 0.081 12920 Z= 0.321 Angle : 1.133 15.430 17548 Z= 0.606 Chirality : 0.066 1.121 2034 Planarity : 0.007 0.069 2180 Dihedral : 16.224 112.152 5198 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.82 % Allowed : 3.06 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.70 (0.15), residues: 1524 helix: -4.46 (0.08), residues: 584 sheet: -2.71 (0.28), residues: 304 loop : -3.46 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 134 HIS 0.011 0.002 HIS C 253 PHE 0.022 0.003 PHE C 107 TYR 0.016 0.002 TYR A 146 ARG 0.011 0.001 ARG B 280 Details of bonding type rmsd link_NAG-ASN : bond 0.01706 ( 16) link_NAG-ASN : angle 6.54127 ( 48) link_BETA1-4 : bond 0.01783 ( 14) link_BETA1-4 : angle 5.92784 ( 42) hydrogen bonds : bond 0.28141 ( 412) hydrogen bonds : angle 9.61393 ( 1176) SS BOND : bond 0.00184 ( 4) SS BOND : angle 0.45377 ( 8) covalent geometry : bond 0.00694 (12886) covalent geometry : angle 1.04342 (17450) *********************** 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 317 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 306 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7607 (ttmt) REVERT: A 351 LYS cc_start: 0.7780 (ttmp) cc_final: 0.7259 (pttm) REVERT: B 82 LYS cc_start: 0.8721 (mttp) cc_final: 0.8239 (mttp) REVERT: B 112 SER cc_start: 0.8483 (m) cc_final: 0.8050 (t) REVERT: B 133 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7577 (mmm160) REVERT: B 360 MET cc_start: 0.8250 (tpt) cc_final: 0.8039 (tpt) REVERT: B 390 ASP cc_start: 0.7685 (m-30) cc_final: 0.7483 (m-30) REVERT: B 400 GLU cc_start: 0.6822 (tt0) cc_final: 0.6356 (mm-30) REVERT: C 200 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7606 (ttmt) REVERT: C 323 MET cc_start: 0.8870 (tpp) cc_final: 0.8666 (tpp) REVERT: C 325 ASP cc_start: 0.8078 (m-30) cc_final: 0.7859 (m-30) REVERT: C 351 LYS cc_start: 0.7751 (ttmp) cc_final: 0.7241 (pttm) REVERT: D 82 LYS cc_start: 0.8706 (mttp) cc_final: 0.8223 (mttp) REVERT: D 112 SER cc_start: 0.8471 (m) cc_final: 0.8030 (t) REVERT: D 223 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7738 (mt-10) REVERT: D 360 MET cc_start: 0.8253 (tpt) cc_final: 0.8020 (tpt) REVERT: D 400 GLU cc_start: 0.6867 (tt0) cc_final: 0.6367 (mm-30) outliers start: 11 outliers final: 0 residues processed: 317 average time/residue: 0.3302 time to fit residues: 137.8193 Evaluate side-chains 190 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 367 HIS ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 141 ASN B 367 HIS C 34 HIS C 367 HIS ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 98 GLN D 131 GLN D 141 ASN D 367 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.197614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.164165 restraints weight = 12746.945| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.93 r_work: 0.3492 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12920 Z= 0.169 Angle : 0.772 11.561 17548 Z= 0.362 Chirality : 0.051 0.472 2034 Planarity : 0.006 0.055 2180 Dihedral : 15.416 91.755 2274 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.04 % Allowed : 7.46 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.18), residues: 1524 helix: -2.42 (0.15), residues: 612 sheet: -2.27 (0.28), residues: 316 loop : -2.96 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 296 HIS 0.005 0.001 HIS B 253 PHE 0.021 0.002 PHE B 315 TYR 0.019 0.002 TYR D 195 ARG 0.006 0.001 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01161 ( 16) link_NAG-ASN : angle 3.71703 ( 48) link_BETA1-4 : bond 0.01648 ( 14) link_BETA1-4 : angle 4.14398 ( 42) hydrogen bonds : bond 0.04854 ( 412) hydrogen bonds : angle 4.89241 ( 1176) SS BOND : bond 0.00243 ( 4) SS BOND : angle 0.32382 ( 8) covalent geometry : bond 0.00380 (12886) covalent geometry : angle 0.72081 (17450) *********************** 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 217 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 PHE cc_start: 0.7613 (t80) cc_final: 0.7393 (m-80) REVERT: A 335 GLN cc_start: 0.6727 (tt0) cc_final: 0.6420 (tm-30) REVERT: A 351 LYS cc_start: 0.7800 (ttmp) cc_final: 0.7556 (tptt) REVERT: B 37 ARG cc_start: 0.7956 (ttp-110) cc_final: 0.7732 (ttm170) REVERT: B 82 LYS cc_start: 0.8764 (mttp) cc_final: 0.8462 (mttp) REVERT: B 133 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8197 (mmm160) REVERT: B 288 GLN cc_start: 0.5808 (mp10) cc_final: 0.5513 (mp10) REVERT: B 329 VAL cc_start: 0.8335 (t) cc_final: 0.8015 (m) REVERT: B 360 MET cc_start: 0.8571 (tpt) cc_final: 0.8292 (tpt) REVERT: C 262 PHE cc_start: 0.7652 (t80) cc_final: 0.7427 (m-80) REVERT: C 335 GLN cc_start: 0.6625 (tt0) cc_final: 0.6400 (tm-30) REVERT: C 351 LYS cc_start: 0.7821 (ttmp) cc_final: 0.7543 (tptt) REVERT: D 82 LYS cc_start: 0.8757 (mttp) cc_final: 0.8418 (mttp) REVERT: D 329 VAL cc_start: 0.8372 (t) cc_final: 0.8016 (m) REVERT: D 360 MET cc_start: 0.8578 (tpt) cc_final: 0.8292 (tpt) REVERT: D 400 GLU cc_start: 0.7295 (tt0) cc_final: 0.7085 (mm-30) outliers start: 14 outliers final: 7 residues processed: 213 average time/residue: 0.3071 time to fit residues: 88.8350 Evaluate side-chains 179 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 339 GLN B 34 HIS C 165 GLN C 335 GLN D 34 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.190335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.157322 restraints weight = 13046.816| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.91 r_work: 0.3446 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12920 Z= 0.161 Angle : 0.741 11.161 17548 Z= 0.342 Chirality : 0.049 0.403 2034 Planarity : 0.005 0.055 2180 Dihedral : 12.390 82.603 2274 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.42 % Allowed : 9.55 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.20), residues: 1524 helix: -0.78 (0.19), residues: 608 sheet: -2.05 (0.28), residues: 328 loop : -2.51 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 353 HIS 0.005 0.001 HIS B 253 PHE 0.020 0.002 PHE B 315 TYR 0.017 0.002 TYR A 252 ARG 0.004 0.000 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01139 ( 16) link_NAG-ASN : angle 3.58416 ( 48) link_BETA1-4 : bond 0.01337 ( 14) link_BETA1-4 : angle 4.24435 ( 42) hydrogen bonds : bond 0.04212 ( 412) hydrogen bonds : angle 4.47613 ( 1176) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.11907 ( 8) covalent geometry : bond 0.00371 (12886) covalent geometry : angle 0.68768 (17450) *********************** 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 212 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 GLN cc_start: 0.6829 (tt0) cc_final: 0.6615 (tm-30) REVERT: B 82 LYS cc_start: 0.8797 (mttp) cc_final: 0.8535 (mttp) REVERT: B 133 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8263 (mmm160) REVERT: B 160 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8674 (mt) REVERT: B 329 VAL cc_start: 0.8399 (t) cc_final: 0.7974 (m) REVERT: B 360 MET cc_start: 0.8628 (tpt) cc_final: 0.8260 (tpt) REVERT: C 335 GLN cc_start: 0.6847 (tt0) cc_final: 0.6625 (tm-30) REVERT: C 351 LYS cc_start: 0.7840 (ttmp) cc_final: 0.7626 (tptt) REVERT: D 82 LYS cc_start: 0.8806 (mttp) cc_final: 0.8523 (mttp) REVERT: D 160 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8664 (mt) REVERT: D 329 VAL cc_start: 0.8448 (t) cc_final: 0.7981 (m) REVERT: D 360 MET cc_start: 0.8630 (tpt) cc_final: 0.8241 (tpt) outliers start: 19 outliers final: 13 residues processed: 203 average time/residue: 0.2702 time to fit residues: 76.6894 Evaluate side-chains 186 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 146 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN B 336 GLN D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.193856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.161861 restraints weight = 12761.891| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.92 r_work: 0.3447 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12920 Z= 0.149 Angle : 0.708 10.788 17548 Z= 0.325 Chirality : 0.048 0.382 2034 Planarity : 0.005 0.055 2180 Dihedral : 10.317 73.258 2274 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.94 % Allowed : 10.97 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.21), residues: 1524 helix: -0.09 (0.20), residues: 612 sheet: -1.88 (0.29), residues: 328 loop : -2.39 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 353 HIS 0.004 0.001 HIS D 253 PHE 0.016 0.001 PHE A 107 TYR 0.023 0.002 TYR A 44 ARG 0.004 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00989 ( 16) link_NAG-ASN : angle 3.43445 ( 48) link_BETA1-4 : bond 0.01380 ( 14) link_BETA1-4 : angle 4.26667 ( 42) hydrogen bonds : bond 0.03605 ( 412) hydrogen bonds : angle 4.30530 ( 1176) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.17542 ( 8) covalent geometry : bond 0.00349 (12886) covalent geometry : angle 0.65365 (17450) *********************** 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 204 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7462 (mmm) cc_final: 0.7261 (mmm) REVERT: A 335 GLN cc_start: 0.6996 (tt0) cc_final: 0.6779 (tm-30) REVERT: B 82 LYS cc_start: 0.8831 (mttp) cc_final: 0.8596 (mttp) REVERT: B 133 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8249 (mmm160) REVERT: B 140 ASP cc_start: 0.7138 (m-30) cc_final: 0.6928 (m-30) REVERT: B 160 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (mt) REVERT: B 248 MET cc_start: 0.8337 (mmm) cc_final: 0.7866 (mmm) REVERT: B 329 VAL cc_start: 0.8285 (t) cc_final: 0.7878 (m) REVERT: B 360 MET cc_start: 0.8606 (tpt) cc_final: 0.8109 (tpt) REVERT: C 335 GLN cc_start: 0.6989 (tt0) cc_final: 0.6741 (tm-30) REVERT: C 351 LYS cc_start: 0.7786 (ttmp) cc_final: 0.7446 (pttm) REVERT: D 82 LYS cc_start: 0.8849 (mttp) cc_final: 0.8610 (mttp) REVERT: D 160 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8650 (mt) REVERT: D 248 MET cc_start: 0.8327 (mmm) cc_final: 0.7860 (mmm) REVERT: D 329 VAL cc_start: 0.8327 (t) cc_final: 0.7902 (m) REVERT: D 360 MET cc_start: 0.8607 (tpt) cc_final: 0.8167 (tpt) outliers start: 26 outliers final: 13 residues processed: 198 average time/residue: 0.2882 time to fit residues: 78.7142 Evaluate side-chains 180 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.187859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154832 restraints weight = 12922.119| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.02 r_work: 0.3424 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12920 Z= 0.159 Angle : 0.701 10.721 17548 Z= 0.322 Chirality : 0.047 0.357 2034 Planarity : 0.004 0.056 2180 Dihedral : 9.300 62.633 2274 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.16 % Allowed : 10.82 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1524 helix: 0.30 (0.21), residues: 612 sheet: -1.70 (0.31), residues: 304 loop : -2.33 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 296 HIS 0.004 0.001 HIS D 232 PHE 0.015 0.001 PHE A 107 TYR 0.018 0.002 TYR A 44 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00904 ( 16) link_NAG-ASN : angle 3.44863 ( 48) link_BETA1-4 : bond 0.01299 ( 14) link_BETA1-4 : angle 4.30102 ( 42) hydrogen bonds : bond 0.03540 ( 412) hydrogen bonds : angle 4.24657 ( 1176) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.11355 ( 8) covalent geometry : bond 0.00380 (12886) covalent geometry : angle 0.64601 (17450) *********************** 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 200 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7312 (mm-30) REVERT: A 335 GLN cc_start: 0.7091 (tt0) cc_final: 0.6886 (tm-30) REVERT: B 82 LYS cc_start: 0.8861 (mttp) cc_final: 0.8591 (mttp) REVERT: B 133 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8300 (mmm160) REVERT: B 160 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8696 (mt) REVERT: B 329 VAL cc_start: 0.8371 (t) cc_final: 0.7929 (m) REVERT: B 340 MET cc_start: 0.7822 (ttm) cc_final: 0.7443 (ttp) REVERT: C 335 GLN cc_start: 0.7065 (tt0) cc_final: 0.6849 (tm-30) REVERT: C 351 LYS cc_start: 0.7768 (ttmp) cc_final: 0.7442 (pttm) REVERT: D 82 LYS cc_start: 0.8908 (mttp) cc_final: 0.8639 (mttp) REVERT: D 160 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8676 (mt) REVERT: D 329 VAL cc_start: 0.8383 (t) cc_final: 0.7920 (m) REVERT: D 340 MET cc_start: 0.7814 (ttm) cc_final: 0.7434 (ttp) REVERT: D 360 MET cc_start: 0.8652 (tpt) cc_final: 0.8151 (tpt) outliers start: 29 outliers final: 21 residues processed: 195 average time/residue: 0.2721 time to fit residues: 74.7360 Evaluate side-chains 177 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 121 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 124 optimal weight: 0.0010 chunk 24 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN B 336 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.191623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.159175 restraints weight = 12976.088| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.94 r_work: 0.3458 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12920 Z= 0.127 Angle : 0.668 10.300 17548 Z= 0.306 Chirality : 0.046 0.348 2034 Planarity : 0.004 0.056 2180 Dihedral : 8.496 55.617 2274 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.09 % Allowed : 11.34 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.22), residues: 1524 helix: 0.52 (0.21), residues: 612 sheet: -1.55 (0.31), residues: 304 loop : -2.22 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 296 HIS 0.004 0.001 HIS C 253 PHE 0.016 0.001 PHE B 315 TYR 0.016 0.001 TYR C 44 ARG 0.004 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00881 ( 16) link_NAG-ASN : angle 3.48891 ( 48) link_BETA1-4 : bond 0.01350 ( 14) link_BETA1-4 : angle 4.26434 ( 42) hydrogen bonds : bond 0.03211 ( 412) hydrogen bonds : angle 4.18792 ( 1176) SS BOND : bond 0.00099 ( 4) SS BOND : angle 0.16043 ( 8) covalent geometry : bond 0.00291 (12886) covalent geometry : angle 0.60967 (17450) *********************** 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 200 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: B 82 LYS cc_start: 0.8891 (mttp) cc_final: 0.8621 (mttp) REVERT: B 133 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8254 (mmm160) REVERT: B 160 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8683 (mt) REVERT: B 329 VAL cc_start: 0.8326 (t) cc_final: 0.7921 (m) REVERT: B 360 MET cc_start: 0.8610 (tpt) cc_final: 0.8116 (tpt) REVERT: C 351 LYS cc_start: 0.7792 (ttmp) cc_final: 0.7451 (pttm) REVERT: D 82 LYS cc_start: 0.8933 (mttp) cc_final: 0.8668 (mttp) REVERT: D 329 VAL cc_start: 0.8335 (t) cc_final: 0.7869 (m) REVERT: D 360 MET cc_start: 0.8604 (tpt) cc_final: 0.8151 (tpt) outliers start: 28 outliers final: 22 residues processed: 195 average time/residue: 0.2583 time to fit residues: 70.6184 Evaluate side-chains 173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 123 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 36 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.195626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.162268 restraints weight = 12883.992| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.82 r_work: 0.3498 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12920 Z= 0.126 Angle : 0.666 10.251 17548 Z= 0.304 Chirality : 0.046 0.347 2034 Planarity : 0.004 0.055 2180 Dihedral : 7.909 55.980 2274 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.16 % Allowed : 12.46 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1524 helix: 0.70 (0.21), residues: 612 sheet: -1.51 (0.30), residues: 328 loop : -2.08 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS A 253 PHE 0.016 0.001 PHE D 315 TYR 0.016 0.001 TYR A 146 ARG 0.004 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00930 ( 16) link_NAG-ASN : angle 3.49672 ( 48) link_BETA1-4 : bond 0.01348 ( 14) link_BETA1-4 : angle 4.23927 ( 42) hydrogen bonds : bond 0.03129 ( 412) hydrogen bonds : angle 4.15836 ( 1176) SS BOND : bond 0.00097 ( 4) SS BOND : angle 0.17708 ( 8) covalent geometry : bond 0.00290 (12886) covalent geometry : angle 0.60709 (17450) *********************** 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 192 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 82 LYS cc_start: 0.8921 (mttp) cc_final: 0.8699 (mttp) REVERT: B 133 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.8241 (mmm160) REVERT: B 329 VAL cc_start: 0.8334 (t) cc_final: 0.7871 (m) REVERT: B 400 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7059 (mm-30) REVERT: C 351 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7476 (pttm) REVERT: D 82 LYS cc_start: 0.8933 (mttp) cc_final: 0.8705 (mttp) REVERT: D 329 VAL cc_start: 0.8360 (t) cc_final: 0.7889 (m) REVERT: D 400 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7072 (mm-30) outliers start: 29 outliers final: 24 residues processed: 185 average time/residue: 0.2833 time to fit residues: 72.4162 Evaluate side-chains 173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 35 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.185737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.154032 restraints weight = 13121.735| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.77 r_work: 0.3467 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12920 Z= 0.156 Angle : 0.683 10.052 17548 Z= 0.315 Chirality : 0.046 0.340 2034 Planarity : 0.004 0.056 2180 Dihedral : 7.683 56.182 2274 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.24 % Allowed : 13.28 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.22), residues: 1524 helix: 0.69 (0.21), residues: 612 sheet: -1.54 (0.30), residues: 328 loop : -2.06 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS B 232 PHE 0.017 0.001 PHE D 315 TYR 0.015 0.001 TYR A 146 ARG 0.005 0.000 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00872 ( 16) link_NAG-ASN : angle 3.49928 ( 48) link_BETA1-4 : bond 0.01343 ( 14) link_BETA1-4 : angle 4.18984 ( 42) hydrogen bonds : bond 0.03261 ( 412) hydrogen bonds : angle 4.18920 ( 1176) SS BOND : bond 0.00133 ( 4) SS BOND : angle 0.23361 ( 8) covalent geometry : bond 0.00373 (12886) covalent geometry : angle 0.62714 (17450) *********************** 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 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: A 294 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 82 LYS cc_start: 0.8974 (mttp) cc_final: 0.8704 (mttp) REVERT: B 133 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8341 (mmm160) REVERT: B 329 VAL cc_start: 0.8388 (t) cc_final: 0.7903 (m) REVERT: B 360 MET cc_start: 0.8725 (tpt) cc_final: 0.8286 (tpt) REVERT: B 400 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7400 (mm-30) REVERT: C 351 LYS cc_start: 0.7742 (ttmp) cc_final: 0.7537 (pttm) REVERT: D 82 LYS cc_start: 0.8965 (mttp) cc_final: 0.8682 (mttp) REVERT: D 329 VAL cc_start: 0.8393 (t) cc_final: 0.7935 (m) REVERT: D 360 MET cc_start: 0.8703 (tpt) cc_final: 0.8241 (tpt) REVERT: D 400 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7447 (mm-30) outliers start: 30 outliers final: 27 residues processed: 177 average time/residue: 0.2804 time to fit residues: 68.7044 Evaluate side-chains 181 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.185343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.153121 restraints weight = 13031.698| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.89 r_work: 0.3453 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12920 Z= 0.154 Angle : 0.678 10.077 17548 Z= 0.314 Chirality : 0.046 0.331 2034 Planarity : 0.004 0.055 2180 Dihedral : 7.332 55.955 2274 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.09 % Allowed : 13.96 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1524 helix: 0.76 (0.21), residues: 612 sheet: -1.52 (0.31), residues: 328 loop : -1.99 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.006 0.001 HIS A 232 PHE 0.017 0.001 PHE B 315 TYR 0.015 0.001 TYR A 146 ARG 0.004 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00964 ( 16) link_NAG-ASN : angle 3.39609 ( 48) link_BETA1-4 : bond 0.01307 ( 14) link_BETA1-4 : angle 4.15877 ( 42) hydrogen bonds : bond 0.03221 ( 412) hydrogen bonds : angle 4.18936 ( 1176) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.25602 ( 8) covalent geometry : bond 0.00368 (12886) covalent geometry : angle 0.62332 (17450) *********************** 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 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7591 (mm-30) REVERT: B 82 LYS cc_start: 0.8950 (mttp) cc_final: 0.8651 (mttp) REVERT: B 133 ARG cc_start: 0.8770 (mmm-85) cc_final: 0.8369 (mmm160) REVERT: B 400 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 351 LYS cc_start: 0.7831 (ttmp) cc_final: 0.7460 (pttm) REVERT: D 82 LYS cc_start: 0.8973 (mttp) cc_final: 0.8656 (mttp) REVERT: D 195 TYR cc_start: 0.6996 (m-10) cc_final: 0.6746 (m-10) REVERT: D 400 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7471 (mm-30) outliers start: 28 outliers final: 27 residues processed: 178 average time/residue: 0.2851 time to fit residues: 71.0405 Evaluate side-chains 175 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.194255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.162063 restraints weight = 12840.210| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.80 r_work: 0.3500 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12920 Z= 0.127 Angle : 0.656 9.913 17548 Z= 0.304 Chirality : 0.045 0.328 2034 Planarity : 0.004 0.056 2180 Dihedral : 7.146 55.830 2274 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.87 % Allowed : 14.40 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1524 helix: 0.90 (0.21), residues: 612 sheet: -1.31 (0.31), residues: 308 loop : -2.01 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.004 0.001 HIS A 34 PHE 0.017 0.001 PHE D 315 TYR 0.016 0.001 TYR A 146 ARG 0.004 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00914 ( 16) link_NAG-ASN : angle 3.34329 ( 48) link_BETA1-4 : bond 0.01329 ( 14) link_BETA1-4 : angle 4.11799 ( 42) hydrogen bonds : bond 0.03065 ( 412) hydrogen bonds : angle 4.15036 ( 1176) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.22565 ( 8) covalent geometry : bond 0.00295 (12886) covalent geometry : angle 0.60134 (17450) ********************** 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 173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7529 (mm-30) REVERT: B 82 LYS cc_start: 0.8966 (mttp) cc_final: 0.8651 (mttp) REVERT: B 133 ARG cc_start: 0.8729 (mmm-85) cc_final: 0.8340 (mmm160) REVERT: C 351 LYS cc_start: 0.7717 (ttmp) cc_final: 0.7469 (pttm) REVERT: D 82 LYS cc_start: 0.8988 (mttp) cc_final: 0.8699 (mttp) REVERT: D 294 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6996 (mm-30) REVERT: D 400 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7418 (mm-30) outliers start: 25 outliers final: 23 residues processed: 167 average time/residue: 0.2821 time to fit residues: 65.5841 Evaluate side-chains 171 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.194319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.162742 restraints weight = 12797.403| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.74 r_work: 0.3504 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12920 Z= 0.131 Angle : 0.653 9.878 17548 Z= 0.302 Chirality : 0.045 0.326 2034 Planarity : 0.004 0.055 2180 Dihedral : 7.044 55.926 2274 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.01 % Allowed : 14.40 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1524 helix: 0.98 (0.21), residues: 612 sheet: -1.29 (0.31), residues: 308 loop : -1.95 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.004 0.001 HIS A 34 PHE 0.018 0.001 PHE D 359 TYR 0.016 0.001 TYR A 146 ARG 0.004 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00907 ( 16) link_NAG-ASN : angle 3.30589 ( 48) link_BETA1-4 : bond 0.01308 ( 14) link_BETA1-4 : angle 4.09645 ( 42) hydrogen bonds : bond 0.03027 ( 412) hydrogen bonds : angle 4.11785 ( 1176) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.22423 ( 8) covalent geometry : bond 0.00307 (12886) covalent geometry : angle 0.59880 (17450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6645.26 seconds wall clock time: 116 minutes 24.55 seconds (6984.55 seconds total)