Starting phenix.real_space_refine on Wed Jun 11 08:22:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwt_29518/06_2025/8fwt_29518.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwt_29518/06_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_29518/06_2025/8fwt_29518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwt_29518/06_2025/8fwt_29518.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwt_29518/06_2025/8fwt_29518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwt_29518/06_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-5710/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: 8.44, per 1000 atoms: 0.67 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: 2.99 Conformation dependent library (CDL) restraints added in 1.5 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: 1.42 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: 3.53 Time building geometry restraints manager: 3.57 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.490 Find NCS groups from input model: 0.520 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.950 ------------------------------------------------------------------------------- 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 : 1.331 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: 0.3366 time to fit residues: 140.6059 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 : 1.422 ------------------------------------------------------------------------------- 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 = 0.164166 restraints weight = 12746.948| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.93 r_work: 0.3493 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 PHE cc_start: 0.7617 (t80) cc_final: 0.7395 (m-80) REVERT: A 335 GLN cc_start: 0.6726 (tt0) cc_final: 0.6418 (tm-30) REVERT: A 351 LYS cc_start: 0.7804 (ttmp) cc_final: 0.7557 (tptt) REVERT: B 37 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7732 (ttm170) REVERT: B 82 LYS cc_start: 0.8765 (mttp) cc_final: 0.8462 (mttp) REVERT: B 133 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8198 (mmm160) REVERT: B 288 GLN cc_start: 0.5808 (mp10) cc_final: 0.5511 (mp10) REVERT: B 329 VAL cc_start: 0.8332 (t) cc_final: 0.8012 (m) REVERT: B 360 MET cc_start: 0.8572 (tpt) cc_final: 0.8293 (tpt) REVERT: C 262 PHE cc_start: 0.7655 (t80) cc_final: 0.7430 (m-80) REVERT: C 335 GLN cc_start: 0.6623 (tt0) cc_final: 0.6398 (tm-30) REVERT: C 351 LYS cc_start: 0.7826 (ttmp) cc_final: 0.7546 (tptt) REVERT: D 82 LYS cc_start: 0.8755 (mttp) cc_final: 0.8417 (mttp) REVERT: D 329 VAL cc_start: 0.8368 (t) cc_final: 0.8012 (m) REVERT: D 360 MET cc_start: 0.8580 (tpt) cc_final: 0.8292 (tpt) REVERT: D 400 GLU cc_start: 0.7293 (tt0) cc_final: 0.7085 (mm-30) outliers start: 14 outliers final: 7 residues processed: 213 average time/residue: 0.3002 time to fit residues: 87.3104 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 : 1.256 ------------------------------------------------------------------------------- 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: 0.1980 chunk 49 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.190940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.157707 restraints weight = 13051.282| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.90 r_work: 0.3460 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12920 Z= 0.152 Angle : 0.729 11.155 17548 Z= 0.336 Chirality : 0.048 0.395 2034 Planarity : 0.005 0.055 2180 Dihedral : 12.358 83.073 2274 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.42 % Allowed : 9.48 % Favored : 89.10 % 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: -2.68 (0.20), residues: 1524 helix: -0.83 (0.19), residues: 608 sheet: -2.05 (0.28), residues: 328 loop : -2.50 (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 0.018 0.002 PHE B 315 TYR 0.017 0.002 TYR C 252 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00923 ( 16) link_NAG-ASN : angle 3.53728 ( 48) link_BETA1-4 : bond 0.01347 ( 14) link_BETA1-4 : angle 4.26267 ( 42) hydrogen bonds : bond 0.04148 ( 412) hydrogen bonds : angle 4.46818 ( 1176) SS BOND : bond 0.00139 ( 4) SS BOND : angle 0.13097 ( 8) covalent geometry : bond 0.00350 (12886) covalent geometry : angle 0.67546 (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 214 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 GLN cc_start: 0.6827 (tt0) cc_final: 0.6618 (tm-30) REVERT: B 82 LYS cc_start: 0.8787 (mttp) cc_final: 0.8511 (mttp) REVERT: B 133 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8254 (mmm160) REVERT: B 160 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8659 (mt) REVERT: B 329 VAL cc_start: 0.8382 (t) cc_final: 0.7966 (m) REVERT: B 360 MET cc_start: 0.8617 (tpt) cc_final: 0.8283 (tpt) REVERT: C 335 GLN cc_start: 0.6848 (tt0) cc_final: 0.6633 (tm-30) REVERT: C 351 LYS cc_start: 0.7831 (ttmp) cc_final: 0.7616 (tptt) REVERT: D 82 LYS cc_start: 0.8803 (mttp) cc_final: 0.8524 (mttp) REVERT: D 160 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8663 (mt) REVERT: D 329 VAL cc_start: 0.8422 (t) cc_final: 0.7961 (m) REVERT: D 360 MET cc_start: 0.8617 (tpt) cc_final: 0.8270 (tpt) outliers start: 19 outliers final: 14 residues processed: 205 average time/residue: 0.2719 time to fit residues: 78.0684 Evaluate side-chains 188 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 120 SER Chi-restraints excluded: chain B residue 160 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 120 SER 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: 0.9980 chunk 54 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 34 HIS ** 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 = 0.4108 r_free = 0.4108 target = 0.194922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.162207 restraints weight = 12767.554| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.02 r_work: 0.3465 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12920 Z= 0.136 Angle : 0.694 10.797 17548 Z= 0.318 Chirality : 0.047 0.378 2034 Planarity : 0.004 0.054 2180 Dihedral : 10.282 73.795 2274 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.01 % Allowed : 10.22 % Favored : 87.76 % 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: -2.00 (0.21), residues: 1524 helix: -0.03 (0.21), residues: 608 sheet: -1.84 (0.29), residues: 328 loop : -2.32 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.004 0.001 HIS B 253 PHE 0.016 0.001 PHE D 315 TYR 0.023 0.002 TYR A 44 ARG 0.003 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00929 ( 16) link_NAG-ASN : angle 3.39530 ( 48) link_BETA1-4 : bond 0.01384 ( 14) link_BETA1-4 : angle 4.30064 ( 42) hydrogen bonds : bond 0.03545 ( 412) hydrogen bonds : angle 4.28712 ( 1176) SS BOND : bond 0.00133 ( 4) SS BOND : angle 0.15457 ( 8) covalent geometry : bond 0.00313 (12886) covalent geometry : angle 0.63834 (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 207 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 GLN cc_start: 0.6989 (tt0) cc_final: 0.6766 (tm-30) REVERT: B 82 LYS cc_start: 0.8815 (mttp) cc_final: 0.8586 (mttp) REVERT: B 133 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8239 (mmm160) REVERT: B 160 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8644 (mt) REVERT: B 248 MET cc_start: 0.8282 (mmm) cc_final: 0.7858 (mmm) REVERT: B 329 VAL cc_start: 0.8232 (t) cc_final: 0.7825 (m) REVERT: B 360 MET cc_start: 0.8610 (tpt) cc_final: 0.8156 (tpt) REVERT: C 335 GLN cc_start: 0.6979 (tt0) cc_final: 0.6739 (tm-30) REVERT: C 351 LYS cc_start: 0.7775 (ttmp) cc_final: 0.7427 (pttm) REVERT: D 82 LYS cc_start: 0.8840 (mttp) cc_final: 0.8600 (mttp) REVERT: D 160 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8630 (mt) REVERT: D 248 MET cc_start: 0.8294 (mmm) cc_final: 0.7888 (mmm) REVERT: D 329 VAL cc_start: 0.8257 (t) cc_final: 0.7840 (m) REVERT: D 360 MET cc_start: 0.8600 (tpt) cc_final: 0.8203 (tpt) outliers start: 27 outliers final: 14 residues processed: 200 average time/residue: 0.2806 time to fit residues: 77.7648 Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 87 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.181887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.147203 restraints weight = 12963.212| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.09 r_work: 0.3353 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 12920 Z= 0.249 Angle : 0.798 10.862 17548 Z= 0.370 Chirality : 0.051 0.378 2034 Planarity : 0.005 0.056 2180 Dihedral : 9.692 62.015 2274 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.31 % Allowed : 11.42 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.21), residues: 1524 helix: -0.06 (0.21), residues: 612 sheet: -2.05 (0.30), residues: 332 loop : -2.39 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 296 HIS 0.006 0.002 HIS D 253 PHE 0.025 0.002 PHE C 107 TYR 0.020 0.002 TYR C 44 ARG 0.004 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.01111 ( 16) link_NAG-ASN : angle 3.65057 ( 48) link_BETA1-4 : bond 0.01282 ( 14) link_BETA1-4 : angle 4.29358 ( 42) hydrogen bonds : bond 0.04009 ( 412) hydrogen bonds : angle 4.42802 ( 1176) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.24321 ( 8) covalent geometry : bond 0.00610 (12886) covalent geometry : angle 0.74839 (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 201 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.294 Fit side-chains REVERT: A 294 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 335 GLN cc_start: 0.7092 (tt0) cc_final: 0.6879 (tm-30) REVERT: B 82 LYS cc_start: 0.8900 (mttp) cc_final: 0.8642 (mttp) REVERT: B 133 ARG cc_start: 0.8670 (mmm-85) cc_final: 0.8364 (mmm160) REVERT: B 160 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8740 (mt) REVERT: B 329 VAL cc_start: 0.8526 (t) cc_final: 0.8030 (m) REVERT: B 340 MET cc_start: 0.7791 (ttm) cc_final: 0.7540 (ttp) REVERT: B 361 SER cc_start: 0.8018 (m) cc_final: 0.7816 (p) REVERT: C 335 GLN cc_start: 0.7121 (tt0) cc_final: 0.6918 (tm-30) REVERT: C 351 LYS cc_start: 0.7833 (ttmp) cc_final: 0.7473 (pttm) REVERT: D 82 LYS cc_start: 0.8923 (mttp) cc_final: 0.8631 (mttp) REVERT: D 160 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8739 (mt) REVERT: D 329 VAL cc_start: 0.8541 (t) cc_final: 0.8049 (m) REVERT: D 340 MET cc_start: 0.7852 (ttm) cc_final: 0.7613 (ttp) REVERT: D 361 SER cc_start: 0.8014 (m) cc_final: 0.7787 (p) outliers start: 31 outliers final: 19 residues processed: 193 average time/residue: 0.2850 time to fit residues: 75.8464 Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 87 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 124 optimal weight: 0.0020 chunk 24 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4065 r_free = 0.4065 target = 0.187597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161057 restraints weight = 12799.769| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.40 r_work: 0.3501 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12920 Z= 0.132 Angle : 0.680 10.376 17548 Z= 0.312 Chirality : 0.046 0.352 2034 Planarity : 0.004 0.057 2180 Dihedral : 8.552 55.318 2274 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.46 % Allowed : 11.87 % Favored : 85.67 % 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: -1.66 (0.22), residues: 1524 helix: 0.36 (0.21), residues: 612 sheet: -1.78 (0.30), residues: 328 loop : -2.21 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 296 HIS 0.005 0.001 HIS A 253 PHE 0.017 0.001 PHE D 315 TYR 0.016 0.001 TYR A 44 ARG 0.004 0.000 ARG B 194 Details of bonding type rmsd link_NAG-ASN : bond 0.01064 ( 16) link_NAG-ASN : angle 3.54324 ( 48) link_BETA1-4 : bond 0.01376 ( 14) link_BETA1-4 : angle 4.27497 ( 42) hydrogen bonds : bond 0.03385 ( 412) hydrogen bonds : angle 4.29564 ( 1176) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.11376 ( 8) covalent geometry : bond 0.00306 (12886) covalent geometry : angle 0.62148 (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 204 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 1.524 Fit side-chains revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: B 82 LYS cc_start: 0.8910 (mttp) cc_final: 0.8675 (mttp) REVERT: B 133 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8380 (mmm160) REVERT: B 329 VAL cc_start: 0.8431 (t) cc_final: 0.7986 (m) REVERT: B 340 MET cc_start: 0.7872 (ttm) cc_final: 0.7571 (ttp) REVERT: B 360 MET cc_start: 0.8737 (tpt) cc_final: 0.8332 (tpt) REVERT: C 351 LYS cc_start: 0.7775 (ttmp) cc_final: 0.7462 (pttm) REVERT: D 82 LYS cc_start: 0.8959 (mttp) cc_final: 0.8706 (mttp) REVERT: D 329 VAL cc_start: 0.8466 (t) cc_final: 0.8014 (m) REVERT: D 340 MET cc_start: 0.7963 (ttm) cc_final: 0.7652 (ttp) outliers start: 33 outliers final: 22 residues processed: 198 average time/residue: 0.2918 time to fit residues: 80.0407 Evaluate side-chains 175 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 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 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 198 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 ARG 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: 0.9990 chunk 26 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4044 r_free = 0.4044 target = 0.188294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.154963 restraints weight = 12944.665| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.90 r_work: 0.3449 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12920 Z= 0.141 Angle : 0.692 10.255 17548 Z= 0.316 Chirality : 0.046 0.352 2034 Planarity : 0.004 0.056 2180 Dihedral : 8.066 55.820 2274 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.87 % Allowed : 13.58 % Favored : 84.55 % 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: -1.51 (0.22), residues: 1524 helix: 0.49 (0.21), residues: 612 sheet: -1.69 (0.31), residues: 308 loop : -2.15 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.003 0.001 HIS B 232 PHE 0.017 0.001 PHE D 315 TYR 0.015 0.001 TYR A 146 ARG 0.004 0.000 ARG B 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00900 ( 16) link_NAG-ASN : angle 3.51908 ( 48) link_BETA1-4 : bond 0.01323 ( 14) link_BETA1-4 : angle 4.25183 ( 42) hydrogen bonds : bond 0.03257 ( 412) hydrogen bonds : angle 4.21981 ( 1176) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.34542 ( 8) covalent geometry : bond 0.00336 (12886) covalent geometry : angle 0.63528 (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: 25 poor density : 167 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 351 LYS cc_start: 0.8247 (tptt) cc_final: 0.7677 (pttm) REVERT: B 82 LYS cc_start: 0.8901 (mttp) cc_final: 0.8657 (mttp) REVERT: B 133 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8311 (mmm160) REVERT: B 329 VAL cc_start: 0.8411 (t) cc_final: 0.7932 (m) REVERT: B 340 MET cc_start: 0.7943 (ttm) cc_final: 0.7718 (ttp) REVERT: B 360 MET cc_start: 0.8587 (tpt) cc_final: 0.8211 (tpt) REVERT: C 217 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: C 351 LYS cc_start: 0.7748 (ttmp) cc_final: 0.7468 (pttm) REVERT: D 82 LYS cc_start: 0.8955 (mttp) cc_final: 0.8720 (mttp) REVERT: D 329 VAL cc_start: 0.8443 (t) cc_final: 0.7960 (m) REVERT: D 340 MET cc_start: 0.8002 (ttm) cc_final: 0.7780 (ttp) outliers start: 25 outliers final: 23 residues processed: 186 average time/residue: 0.3011 time to fit residues: 77.6541 Evaluate side-chains 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 220 ARG Chi-restraints excluded: chain A residue 380 THR 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 217 GLU Chi-restraints excluded: chain C residue 220 ARG 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: 0.3980 chunk 133 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 53 optimal weight: 0.0970 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 165 GLN A 339 GLN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.189014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.156698 restraints weight = 13029.043| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.86 r_work: 0.3485 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4025 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 : 0.673 10.140 17548 Z= 0.309 Chirality : 0.046 0.338 2034 Planarity : 0.004 0.056 2180 Dihedral : 7.649 55.813 2274 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.16 % Allowed : 13.36 % 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: -1.34 (0.22), residues: 1524 helix: 0.64 (0.21), residues: 612 sheet: -1.56 (0.31), residues: 304 loop : -2.10 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.004 0.001 HIS A 253 PHE 0.018 0.001 PHE D 315 TYR 0.017 0.001 TYR A 195 ARG 0.004 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00929 ( 16) link_NAG-ASN : angle 3.44610 ( 48) link_BETA1-4 : bond 0.01324 ( 14) link_BETA1-4 : angle 4.18469 ( 42) hydrogen bonds : bond 0.03133 ( 412) hydrogen bonds : angle 4.17010 ( 1176) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.29337 ( 8) covalent geometry : bond 0.00306 (12886) covalent geometry : angle 0.61733 (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 192 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.5986 (m-10) cc_final: 0.5704 (m-10) REVERT: A 294 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 351 LYS cc_start: 0.8158 (tptt) cc_final: 0.7546 (pttm) REVERT: B 82 LYS cc_start: 0.8931 (mttp) cc_final: 0.8647 (mttp) REVERT: B 133 ARG cc_start: 0.8715 (mmm-85) cc_final: 0.8317 (mmm160) REVERT: B 329 VAL cc_start: 0.8355 (t) cc_final: 0.7858 (m) REVERT: B 340 MET cc_start: 0.7926 (ttm) cc_final: 0.7691 (ttp) REVERT: B 360 MET cc_start: 0.8720 (tpt) cc_final: 0.8287 (tpt) REVERT: B 361 SER cc_start: 0.8004 (m) cc_final: 0.7797 (p) REVERT: B 379 LYS cc_start: 0.6880 (mmtm) cc_final: 0.6646 (mmtt) REVERT: C 217 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: C 294 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7508 (mm-30) REVERT: C 351 LYS cc_start: 0.7791 (ttmp) cc_final: 0.7443 (pttm) REVERT: D 82 LYS cc_start: 0.8968 (mttp) cc_final: 0.8681 (mttp) REVERT: D 329 VAL cc_start: 0.8385 (t) cc_final: 0.7908 (m) REVERT: D 340 MET cc_start: 0.8048 (ttm) cc_final: 0.7807 (ttp) REVERT: D 361 SER cc_start: 0.7952 (p) cc_final: 0.7703 (p) outliers start: 29 outliers final: 23 residues processed: 184 average time/residue: 0.3083 time to fit residues: 79.6550 Evaluate side-chains 178 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 140 ASP 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 217 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4041 r_free = 0.4041 target = 0.188041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.154787 restraints weight = 12926.477| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.84 r_work: 0.3482 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12920 Z= 0.149 Angle : 0.682 10.139 17548 Z= 0.315 Chirality : 0.046 0.337 2034 Planarity : 0.004 0.057 2180 Dihedral : 7.478 55.920 2274 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.79 % Allowed : 13.96 % Favored : 84.25 % 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: -1.30 (0.22), residues: 1524 helix: 0.66 (0.21), residues: 612 sheet: -1.54 (0.32), residues: 304 loop : -2.07 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS A 34 PHE 0.018 0.001 PHE D 315 TYR 0.017 0.001 TYR D 195 ARG 0.004 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00992 ( 16) link_NAG-ASN : angle 3.47763 ( 48) link_BETA1-4 : bond 0.01311 ( 14) link_BETA1-4 : angle 4.19333 ( 42) hydrogen bonds : bond 0.03163 ( 412) hydrogen bonds : angle 4.17555 ( 1176) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.29647 ( 8) covalent geometry : bond 0.00353 (12886) covalent geometry : angle 0.62613 (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 177 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.5714 (m-10) cc_final: 0.5457 (m-10) REVERT: A 294 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 351 LYS cc_start: 0.8191 (tptt) cc_final: 0.7598 (pttm) REVERT: B 82 LYS cc_start: 0.8924 (mttp) cc_final: 0.8625 (mttp) REVERT: B 133 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8342 (mmm160) REVERT: B 340 MET cc_start: 0.7955 (ttm) cc_final: 0.7736 (ttp) REVERT: B 379 LYS cc_start: 0.6878 (mmtm) cc_final: 0.6633 (mmtt) REVERT: C 217 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: C 294 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7562 (mm-30) REVERT: C 351 LYS cc_start: 0.7750 (ttmp) cc_final: 0.7481 (pttm) REVERT: D 82 LYS cc_start: 0.8995 (mttp) cc_final: 0.8698 (mttp) REVERT: D 340 MET cc_start: 0.8082 (ttm) cc_final: 0.7876 (ttp) REVERT: D 361 SER cc_start: 0.7924 (p) cc_final: 0.7674 (p) outliers start: 24 outliers final: 22 residues processed: 170 average time/residue: 0.3004 time to fit residues: 71.4791 Evaluate side-chains 172 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 345 LEU 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 217 GLU Chi-restraints excluded: chain C residue 345 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 143 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 117 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4047 r_free = 0.4047 target = 0.188590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.155679 restraints weight = 12930.174| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.87 r_work: 0.3489 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12920 Z= 0.137 Angle : 0.668 10.043 17548 Z= 0.309 Chirality : 0.045 0.333 2034 Planarity : 0.004 0.057 2180 Dihedral : 7.260 55.824 2274 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.94 % Allowed : 13.73 % Favored : 84.33 % 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: -1.17 (0.22), residues: 1524 helix: 0.78 (0.21), residues: 612 sheet: -1.61 (0.30), residues: 328 loop : -1.90 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.004 0.001 HIS A 34 PHE 0.018 0.001 PHE D 315 TYR 0.016 0.001 TYR D 195 ARG 0.004 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00926 ( 16) link_NAG-ASN : angle 3.41484 ( 48) link_BETA1-4 : bond 0.01322 ( 14) link_BETA1-4 : angle 4.14675 ( 42) hydrogen bonds : bond 0.03097 ( 412) hydrogen bonds : angle 4.17988 ( 1176) SS BOND : bond 0.00139 ( 4) SS BOND : angle 0.24332 ( 8) covalent geometry : bond 0.00323 (12886) covalent geometry : angle 0.61311 (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 178 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.5577 (m-10) cc_final: 0.5299 (m-10) REVERT: A 294 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 351 LYS cc_start: 0.8156 (tptt) cc_final: 0.7651 (pttm) REVERT: B 82 LYS cc_start: 0.8938 (mttp) cc_final: 0.8620 (mttp) REVERT: B 133 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8332 (mmm160) REVERT: B 340 MET cc_start: 0.7985 (ttm) cc_final: 0.7776 (ttp) REVERT: B 360 MET cc_start: 0.8694 (tpt) cc_final: 0.8320 (tpt) REVERT: B 379 LYS cc_start: 0.6883 (mmtm) cc_final: 0.6604 (mmtt) REVERT: C 217 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: C 294 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7577 (mm-30) REVERT: C 351 LYS cc_start: 0.7737 (ttmp) cc_final: 0.7491 (pttm) REVERT: D 82 LYS cc_start: 0.8966 (mttp) cc_final: 0.8679 (mttp) outliers start: 26 outliers final: 25 residues processed: 170 average time/residue: 0.3218 time to fit residues: 77.1807 Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 345 LEU Chi-restraints excluded: chain B residue 140 ASP 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 217 GLU Chi-restraints excluded: chain C residue 345 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.184864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151102 restraints weight = 12935.793| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.96 r_work: 0.3426 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12920 Z= 0.218 Angle : 0.744 10.426 17548 Z= 0.347 Chirality : 0.048 0.331 2034 Planarity : 0.005 0.057 2180 Dihedral : 7.424 57.027 2274 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.01 % Allowed : 13.96 % Favored : 84.03 % 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: -1.42 (0.22), residues: 1524 helix: 0.52 (0.21), residues: 612 sheet: -1.67 (0.31), residues: 304 loop : -2.02 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 296 HIS 0.006 0.001 HIS B 232 PHE 0.019 0.002 PHE D 315 TYR 0.018 0.002 TYR D 195 ARG 0.005 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00897 ( 16) link_NAG-ASN : angle 3.52092 ( 48) link_BETA1-4 : bond 0.01269 ( 14) link_BETA1-4 : angle 4.24179 ( 42) hydrogen bonds : bond 0.03525 ( 412) hydrogen bonds : angle 4.30249 ( 1176) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.39354 ( 8) covalent geometry : bond 0.00536 (12886) covalent geometry : angle 0.69211 (17450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7844.89 seconds wall clock time: 139 minutes 11.01 seconds (8351.01 seconds total)