Starting phenix.real_space_refine on Sat Aug 23 14:17:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwt_29518/08_2025/8fwt_29518.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwt_29518/08_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_29518/08_2025/8fwt_29518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwt_29518/08_2025/8fwt_29518.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwt_29518/08_2025/8fwt_29518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwt_29518/08_2025/8fwt_29518.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.53, per 1000 atoms: 0.28 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: 1.19 Conformation dependent library (CDL) restraints added in 661.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.42 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: 2.08 Time building geometry restraints manager: 1.57 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain '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: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.690 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG B 280 TYR 0.016 0.002 TYR A 146 PHE 0.022 0.003 PHE C 107 TRP 0.026 0.003 TRP C 134 HIS 0.011 0.002 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00694 (12886) covalent geometry : angle 1.04342 (17450) SS BOND : bond 0.00184 ( 4) SS BOND : angle 0.45377 ( 8) hydrogen bonds : bond 0.28141 ( 412) hydrogen bonds : angle 9.61393 ( 1176) link_BETA1-4 : bond 0.01783 ( 14) link_BETA1-4 : angle 5.92784 ( 42) link_NAG-ASN : bond 0.01706 ( 16) link_NAG-ASN : angle 6.54127 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 306 time to evaluate : 0.415 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: 0.1656 time to fit residues: 69.0971 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 : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.191138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.155837 restraints weight = 12835.777| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.03 r_work: 0.3422 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12920 Z= 0.233 Angle : 0.823 11.528 17548 Z= 0.390 Chirality : 0.052 0.476 2034 Planarity : 0.006 0.056 2180 Dihedral : 15.508 90.169 2274 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.97 % Allowed : 8.21 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.16 (0.18), residues: 1524 helix: -2.57 (0.15), residues: 612 sheet: -2.49 (0.27), residues: 328 loop : -2.90 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 66 TYR 0.019 0.002 TYR D 195 PHE 0.022 0.002 PHE B 315 TRP 0.019 0.002 TRP C 296 HIS 0.007 0.002 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00562 (12886) covalent geometry : angle 0.77556 (17450) SS BOND : bond 0.00277 ( 4) SS BOND : angle 0.50301 ( 8) hydrogen bonds : bond 0.04893 ( 412) hydrogen bonds : angle 4.99713 ( 1176) link_BETA1-4 : bond 0.01456 ( 14) link_BETA1-4 : angle 4.10310 ( 42) link_NAG-ASN : bond 0.01051 ( 16) link_NAG-ASN : angle 3.78722 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8386 (m-30) cc_final: 0.8179 (m-30) REVERT: A 335 GLN cc_start: 0.6804 (tt0) cc_final: 0.6534 (tm-30) REVERT: A 351 LYS cc_start: 0.7835 (ttmp) cc_final: 0.7624 (tptt) REVERT: B 37 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.7884 (ttm170) REVERT: B 82 LYS cc_start: 0.8794 (mttp) cc_final: 0.8511 (mttp) REVERT: B 133 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8248 (mmm160) REVERT: B 288 GLN cc_start: 0.5932 (mp10) cc_final: 0.5638 (mp10) REVERT: B 329 VAL cc_start: 0.8515 (t) cc_final: 0.8166 (m) REVERT: B 360 MET cc_start: 0.8685 (tpt) cc_final: 0.8304 (tpt) REVERT: C 325 ASP cc_start: 0.8383 (m-30) cc_final: 0.8170 (m-30) REVERT: C 351 LYS cc_start: 0.7888 (ttmp) cc_final: 0.7643 (tptt) REVERT: D 82 LYS cc_start: 0.8807 (mttp) cc_final: 0.8507 (mttp) REVERT: D 329 VAL cc_start: 0.8513 (t) cc_final: 0.8135 (m) REVERT: D 360 MET cc_start: 0.8672 (tpt) cc_final: 0.8275 (tpt) outliers start: 13 outliers final: 7 residues processed: 208 average time/residue: 0.1426 time to fit residues: 41.1784 Evaluate side-chains 173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 139 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 146 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 335 GLN A 339 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN C 34 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.195152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.165171 restraints weight = 12878.976| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.80 r_work: 0.3240 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3004 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= 0.143 Angle : 0.724 11.276 17548 Z= 0.335 Chirality : 0.048 0.387 2034 Planarity : 0.005 0.056 2180 Dihedral : 11.896 79.222 2274 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.94 % Allowed : 8.51 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.20), residues: 1524 helix: -0.90 (0.19), residues: 608 sheet: -2.09 (0.29), residues: 324 loop : -2.50 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.019 0.002 TYR A 86 PHE 0.019 0.001 PHE B 315 TRP 0.015 0.001 TRP C 353 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00323 (12886) covalent geometry : angle 0.66919 (17450) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.09178 ( 8) hydrogen bonds : bond 0.04161 ( 412) hydrogen bonds : angle 4.45690 ( 1176) link_BETA1-4 : bond 0.01382 ( 14) link_BETA1-4 : angle 4.34540 ( 42) link_NAG-ASN : bond 0.01026 ( 16) link_NAG-ASN : angle 3.49244 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: A 335 GLN cc_start: 0.6956 (tt0) cc_final: 0.6665 (tm-30) REVERT: A 351 LYS cc_start: 0.7649 (ttmp) cc_final: 0.7390 (tptt) REVERT: B 82 LYS cc_start: 0.8788 (mttp) cc_final: 0.8436 (mttp) REVERT: B 97 ASP cc_start: 0.7421 (m-30) cc_final: 0.7191 (m-30) REVERT: B 133 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8357 (mmm160) REVERT: B 329 VAL cc_start: 0.8289 (t) cc_final: 0.7834 (m) REVERT: B 360 MET cc_start: 0.8636 (tpt) cc_final: 0.8332 (tpt) REVERT: B 361 SER cc_start: 0.8091 (m) cc_final: 0.7819 (p) REVERT: C 217 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: C 351 LYS cc_start: 0.7785 (ttmp) cc_final: 0.7455 (tptt) REVERT: D 82 LYS cc_start: 0.8793 (mttp) cc_final: 0.8440 (mttp) REVERT: D 329 VAL cc_start: 0.8330 (t) cc_final: 0.7854 (m) REVERT: D 360 MET cc_start: 0.8636 (tpt) cc_final: 0.8304 (tpt) REVERT: D 361 SER cc_start: 0.8055 (m) cc_final: 0.7782 (p) outliers start: 26 outliers final: 13 residues processed: 210 average time/residue: 0.1245 time to fit residues: 36.6450 Evaluate side-chains 186 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 185 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 262 PHE 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 217 GLU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 120 SER 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 146 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN ** D 34 HIS ** 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 = 0.3989 r_free = 0.3989 target = 0.183648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150454 restraints weight = 12983.877| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.00 r_work: 0.3383 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12920 Z= 0.209 Angle : 0.755 11.019 17548 Z= 0.349 Chirality : 0.050 0.393 2034 Planarity : 0.005 0.057 2180 Dihedral : 10.623 71.981 2274 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.09 % Allowed : 10.07 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.21), residues: 1524 helix: -0.39 (0.20), residues: 612 sheet: -2.07 (0.29), residues: 332 loop : -2.40 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 354 TYR 0.010 0.002 TYR A 86 PHE 0.016 0.002 PHE B 315 TRP 0.014 0.001 TRP A 296 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00505 (12886) covalent geometry : angle 0.70179 (17450) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.23338 ( 8) hydrogen bonds : bond 0.03850 ( 412) hydrogen bonds : angle 4.37826 ( 1176) link_BETA1-4 : bond 0.01330 ( 14) link_BETA1-4 : angle 4.33924 ( 42) link_NAG-ASN : bond 0.00912 ( 16) link_NAG-ASN : angle 3.57963 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 GLN cc_start: 0.7057 (tt0) cc_final: 0.6840 (tm-30) REVERT: A 351 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7441 (pttm) REVERT: B 82 LYS cc_start: 0.8839 (mttp) cc_final: 0.8611 (mttp) REVERT: B 133 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8342 (mmm160) REVERT: B 140 ASP cc_start: 0.7243 (m-30) cc_final: 0.7017 (m-30) REVERT: B 329 VAL cc_start: 0.8510 (t) cc_final: 0.8076 (m) REVERT: B 360 MET cc_start: 0.8698 (tpt) cc_final: 0.8154 (tpt) REVERT: D 82 LYS cc_start: 0.8868 (mttp) cc_final: 0.8620 (mttp) REVERT: D 329 VAL cc_start: 0.8504 (t) cc_final: 0.8066 (m) REVERT: D 361 SER cc_start: 0.7993 (m) cc_final: 0.7791 (p) outliers start: 28 outliers final: 16 residues processed: 194 average time/residue: 0.1372 time to fit residues: 36.7759 Evaluate side-chains 175 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 B residue 238 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 141 optimal weight: 0.0040 chunk 111 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4035 r_free = 0.4035 target = 0.187882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152807 restraints weight = 12963.321| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.02 r_work: 0.3429 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3595 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= 0.140 Angle : 0.692 10.738 17548 Z= 0.318 Chirality : 0.047 0.372 2034 Planarity : 0.004 0.057 2180 Dihedral : 9.418 62.526 2274 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.79 % Allowed : 10.75 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.22), residues: 1524 helix: 0.12 (0.21), residues: 612 sheet: -1.86 (0.29), residues: 328 loop : -2.28 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 194 TYR 0.020 0.001 TYR C 44 PHE 0.015 0.001 PHE B 315 TRP 0.012 0.001 TRP C 353 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00325 (12886) covalent geometry : angle 0.63439 (17450) SS BOND : bond 0.00101 ( 4) SS BOND : angle 0.11192 ( 8) hydrogen bonds : bond 0.03428 ( 412) hydrogen bonds : angle 4.26453 ( 1176) link_BETA1-4 : bond 0.01390 ( 14) link_BETA1-4 : angle 4.28914 ( 42) link_NAG-ASN : bond 0.01069 ( 16) link_NAG-ASN : angle 3.56044 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.424 Fit side-chains REVERT: A 217 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: A 335 GLN cc_start: 0.7051 (tt0) cc_final: 0.6827 (tm-30) REVERT: A 351 LYS cc_start: 0.7713 (ttmp) cc_final: 0.7412 (pttm) REVERT: B 82 LYS cc_start: 0.8887 (mttp) cc_final: 0.8618 (mttp) REVERT: B 133 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8290 (mmm160) REVERT: B 140 ASP cc_start: 0.7279 (m-30) cc_final: 0.7058 (m-30) REVERT: B 248 MET cc_start: 0.8309 (mmm) cc_final: 0.7994 (mmm) REVERT: B 329 VAL cc_start: 0.8382 (t) cc_final: 0.7939 (m) REVERT: B 340 MET cc_start: 0.7860 (ttm) cc_final: 0.7498 (ttp) REVERT: B 360 MET cc_start: 0.8623 (tpt) cc_final: 0.8095 (tpt) REVERT: C 195 TYR cc_start: 0.6621 (m-80) cc_final: 0.6408 (m-80) REVERT: C 217 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: D 82 LYS cc_start: 0.8924 (mttp) cc_final: 0.8659 (mttp) REVERT: D 248 MET cc_start: 0.8301 (mmm) cc_final: 0.8015 (mmm) REVERT: D 329 VAL cc_start: 0.8413 (t) cc_final: 0.7967 (m) REVERT: D 340 MET cc_start: 0.7973 (ttm) cc_final: 0.7578 (ttp) REVERT: D 361 SER cc_start: 0.7966 (m) cc_final: 0.7753 (p) outliers start: 24 outliers final: 16 residues processed: 181 average time/residue: 0.1290 time to fit residues: 33.2420 Evaluate side-chains 169 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 217 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4045 r_free = 0.4045 target = 0.189092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.156926 restraints weight = 12998.309| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.05 r_work: 0.3454 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12920 Z= 0.121 Angle : 0.670 10.431 17548 Z= 0.305 Chirality : 0.046 0.352 2034 Planarity : 0.004 0.056 2180 Dihedral : 8.558 55.655 2274 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.79 % Allowed : 11.42 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.22), residues: 1524 helix: 0.49 (0.21), residues: 612 sheet: -1.66 (0.30), residues: 328 loop : -2.12 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 194 TYR 0.014 0.001 TYR C 44 PHE 0.012 0.001 PHE B 315 TRP 0.012 0.001 TRP A 353 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00275 (12886) covalent geometry : angle 0.60934 (17450) SS BOND : bond 0.00099 ( 4) SS BOND : angle 0.14877 ( 8) hydrogen bonds : bond 0.03166 ( 412) hydrogen bonds : angle 4.16169 ( 1176) link_BETA1-4 : bond 0.01382 ( 14) link_BETA1-4 : angle 4.28750 ( 42) link_NAG-ASN : bond 0.00967 ( 16) link_NAG-ASN : angle 3.60538 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: A 294 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 351 LYS cc_start: 0.7738 (ttmp) cc_final: 0.7442 (pttm) REVERT: B 82 LYS cc_start: 0.8920 (mttp) cc_final: 0.8650 (mttp) REVERT: B 133 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8279 (mmm160) REVERT: B 140 ASP cc_start: 0.7283 (m-30) cc_final: 0.7052 (m-30) REVERT: B 248 MET cc_start: 0.8284 (mmm) cc_final: 0.8064 (mmm) REVERT: B 329 VAL cc_start: 0.8318 (t) cc_final: 0.7888 (m) REVERT: B 340 MET cc_start: 0.7965 (ttm) cc_final: 0.7590 (ttp) REVERT: B 360 MET cc_start: 0.8646 (tpt) cc_final: 0.8191 (tpt) REVERT: B 361 SER cc_start: 0.8006 (m) cc_final: 0.7797 (p) REVERT: C 217 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: D 82 LYS cc_start: 0.8922 (mttp) cc_final: 0.8647 (mttp) REVERT: D 248 MET cc_start: 0.8273 (mmm) cc_final: 0.8063 (mmm) REVERT: D 329 VAL cc_start: 0.8313 (t) cc_final: 0.7845 (m) REVERT: D 361 SER cc_start: 0.7964 (m) cc_final: 0.7758 (p) outliers start: 24 outliers final: 18 residues processed: 200 average time/residue: 0.1255 time to fit residues: 35.2774 Evaluate side-chains 178 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 217 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 30 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.188384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158869 restraints weight = 12699.634| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.67 r_work: 0.3483 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12920 Z= 0.146 Angle : 0.680 10.138 17548 Z= 0.311 Chirality : 0.046 0.351 2034 Planarity : 0.004 0.057 2180 Dihedral : 8.147 56.018 2274 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.24 % Allowed : 12.16 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.22), residues: 1524 helix: 0.55 (0.21), residues: 612 sheet: -1.52 (0.32), residues: 304 loop : -2.15 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 270 TYR 0.014 0.001 TYR A 195 PHE 0.016 0.001 PHE B 315 TRP 0.011 0.001 TRP C 296 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00347 (12886) covalent geometry : angle 0.62105 (17450) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.20156 ( 8) hydrogen bonds : bond 0.03189 ( 412) hydrogen bonds : angle 4.17578 ( 1176) link_BETA1-4 : bond 0.01315 ( 14) link_BETA1-4 : angle 4.24621 ( 42) link_NAG-ASN : bond 0.00922 ( 16) link_NAG-ASN : angle 3.59265 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: A 294 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 351 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7469 (pttm) REVERT: B 82 LYS cc_start: 0.8945 (mttp) cc_final: 0.8686 (mttp) REVERT: B 133 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8364 (mmm160) REVERT: B 140 ASP cc_start: 0.7433 (m-30) cc_final: 0.7187 (m-30) REVERT: B 248 MET cc_start: 0.8360 (mmm) cc_final: 0.8071 (mmm) REVERT: B 329 VAL cc_start: 0.8397 (t) cc_final: 0.7929 (m) REVERT: B 340 MET cc_start: 0.7998 (ttm) cc_final: 0.7676 (ttp) REVERT: B 361 SER cc_start: 0.8088 (m) cc_final: 0.7870 (p) REVERT: B 400 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 217 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: C 294 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7457 (mm-30) REVERT: D 82 LYS cc_start: 0.8936 (mttp) cc_final: 0.8642 (mttp) REVERT: D 248 MET cc_start: 0.8377 (mmm) cc_final: 0.8108 (mmm) REVERT: D 329 VAL cc_start: 0.8375 (t) cc_final: 0.7920 (m) REVERT: D 340 MET cc_start: 0.7908 (ttm) cc_final: 0.7553 (ttp) REVERT: D 361 SER cc_start: 0.8024 (m) cc_final: 0.7795 (p) outliers start: 30 outliers final: 26 residues processed: 191 average time/residue: 0.1396 time to fit residues: 37.1923 Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 197 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 197 LEU 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 380 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 378 ASN 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 32 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4096 r_free = 0.4096 target = 0.193128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.158105 restraints weight = 12832.909| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.98 r_work: 0.3455 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12920 Z= 0.154 Angle : 0.684 10.186 17548 Z= 0.316 Chirality : 0.047 0.347 2034 Planarity : 0.004 0.057 2180 Dihedral : 7.743 56.071 2274 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.39 % Allowed : 12.16 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.22), residues: 1524 helix: 0.61 (0.21), residues: 612 sheet: -1.49 (0.32), residues: 304 loop : -2.07 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.018 0.001 TYR A 44 PHE 0.017 0.001 PHE B 315 TRP 0.012 0.001 TRP A 353 HIS 0.004 0.001 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00366 (12886) covalent geometry : angle 0.62672 (17450) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.24944 ( 8) hydrogen bonds : bond 0.03232 ( 412) hydrogen bonds : angle 4.19163 ( 1176) link_BETA1-4 : bond 0.01364 ( 14) link_BETA1-4 : angle 4.21977 ( 42) link_NAG-ASN : bond 0.01013 ( 16) link_NAG-ASN : angle 3.56079 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: A 294 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 351 LYS cc_start: 0.7725 (ttmp) cc_final: 0.7436 (pttm) REVERT: B 82 LYS cc_start: 0.8933 (mttp) cc_final: 0.8643 (mttp) REVERT: B 133 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.8370 (mmm160) REVERT: B 140 ASP cc_start: 0.7573 (m-30) cc_final: 0.7334 (m-30) REVERT: B 248 MET cc_start: 0.8453 (mmm) cc_final: 0.8103 (mmm) REVERT: B 329 VAL cc_start: 0.8389 (t) cc_final: 0.7923 (m) REVERT: B 340 MET cc_start: 0.7995 (ttm) cc_final: 0.7727 (ttp) REVERT: B 361 SER cc_start: 0.8074 (m) cc_final: 0.7870 (p) REVERT: B 400 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7479 (mm-30) REVERT: C 217 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: C 294 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7479 (mm-30) REVERT: D 82 LYS cc_start: 0.8961 (mttp) cc_final: 0.8655 (mttp) REVERT: D 248 MET cc_start: 0.8478 (mmm) cc_final: 0.8149 (mmm) REVERT: D 329 VAL cc_start: 0.8406 (t) cc_final: 0.7931 (m) REVERT: D 340 MET cc_start: 0.7936 (ttm) cc_final: 0.7656 (ttp) outliers start: 32 outliers final: 27 residues processed: 191 average time/residue: 0.1430 time to fit residues: 37.9370 Evaluate side-chains 187 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 197 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 A residue 345 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 151 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 chunk 33 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 165 GLN A 339 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4102 r_free = 0.4102 target = 0.193625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.161477 restraints weight = 12900.274| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.79 r_work: 0.3493 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12920 Z= 0.142 Angle : 0.668 10.031 17548 Z= 0.310 Chirality : 0.046 0.335 2034 Planarity : 0.004 0.056 2180 Dihedral : 7.392 55.785 2274 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.39 % Allowed : 12.61 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.22), residues: 1524 helix: 0.70 (0.21), residues: 612 sheet: -1.55 (0.31), residues: 328 loop : -1.91 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.019 0.001 TYR D 195 PHE 0.017 0.001 PHE B 315 TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00338 (12886) covalent geometry : angle 0.61128 (17450) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.22227 ( 8) hydrogen bonds : bond 0.03159 ( 412) hydrogen bonds : angle 4.21117 ( 1176) link_BETA1-4 : bond 0.01321 ( 14) link_BETA1-4 : angle 4.17258 ( 42) link_NAG-ASN : bond 0.00966 ( 16) link_NAG-ASN : angle 3.49208 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: A 294 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7540 (mm-30) REVERT: A 351 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7470 (pttm) REVERT: B 82 LYS cc_start: 0.8924 (mttp) cc_final: 0.8630 (mttp) REVERT: B 133 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.8328 (mmm160) REVERT: B 248 MET cc_start: 0.8387 (mmm) cc_final: 0.8108 (mmm) REVERT: B 340 MET cc_start: 0.8009 (ttm) cc_final: 0.7789 (ttp) REVERT: B 361 SER cc_start: 0.8085 (m) cc_final: 0.7884 (p) REVERT: B 400 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7409 (mm-30) REVERT: C 217 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: C 294 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7550 (mm-30) REVERT: D 82 LYS cc_start: 0.8954 (mttp) cc_final: 0.8642 (mttp) REVERT: D 248 MET cc_start: 0.8419 (mmm) cc_final: 0.8141 (mmm) REVERT: D 340 MET cc_start: 0.7974 (ttm) cc_final: 0.7771 (ttp) REVERT: D 360 MET cc_start: 0.8685 (tpt) cc_final: 0.8277 (tpt) outliers start: 32 outliers final: 28 residues processed: 186 average time/residue: 0.1410 time to fit residues: 36.5597 Evaluate side-chains 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 150 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.194358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.161317 restraints weight = 12884.356| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.82 r_work: 0.3518 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12920 Z= 0.128 Angle : 0.657 10.015 17548 Z= 0.304 Chirality : 0.045 0.340 2034 Planarity : 0.004 0.055 2180 Dihedral : 7.190 55.739 2274 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.16 % Allowed : 12.84 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.22), residues: 1524 helix: 0.87 (0.21), residues: 612 sheet: -1.47 (0.30), residues: 332 loop : -1.85 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.017 0.001 TYR D 195 PHE 0.017 0.001 PHE D 315 TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00300 (12886) covalent geometry : angle 0.60060 (17450) SS BOND : bond 0.00119 ( 4) SS BOND : angle 0.21179 ( 8) hydrogen bonds : bond 0.03062 ( 412) hydrogen bonds : angle 4.20191 ( 1176) link_BETA1-4 : bond 0.01353 ( 14) link_BETA1-4 : angle 4.13449 ( 42) link_NAG-ASN : bond 0.00932 ( 16) link_NAG-ASN : angle 3.44959 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: A 294 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 351 LYS cc_start: 0.7725 (ttmp) cc_final: 0.7472 (pttm) REVERT: B 82 LYS cc_start: 0.8942 (mttp) cc_final: 0.8624 (mttp) REVERT: B 133 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8327 (mmm160) REVERT: B 248 MET cc_start: 0.8335 (mmm) cc_final: 0.8123 (mmm) REVERT: B 294 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7003 (mm-30) REVERT: B 360 MET cc_start: 0.8697 (tpt) cc_final: 0.8253 (tpt) REVERT: B 361 SER cc_start: 0.8076 (m) cc_final: 0.7873 (p) REVERT: B 400 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7382 (mm-30) REVERT: C 217 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: C 294 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7551 (mm-30) REVERT: D 82 LYS cc_start: 0.8936 (mttp) cc_final: 0.8642 (mttp) REVERT: D 248 MET cc_start: 0.8380 (mmm) cc_final: 0.8152 (mmm) REVERT: D 294 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6996 (mm-30) outliers start: 29 outliers final: 25 residues processed: 180 average time/residue: 0.1347 time to fit residues: 33.8306 Evaluate side-chains 180 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.193109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161488 restraints weight = 12897.133| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.78 r_work: 0.3490 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12920 Z= 0.150 Angle : 0.668 10.000 17548 Z= 0.310 Chirality : 0.045 0.331 2034 Planarity : 0.004 0.055 2180 Dihedral : 7.143 55.998 2274 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.94 % Allowed : 13.43 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.22), residues: 1524 helix: 0.84 (0.21), residues: 612 sheet: -1.49 (0.30), residues: 332 loop : -1.79 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.016 0.001 TYR D 195 PHE 0.017 0.001 PHE B 315 TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00358 (12886) covalent geometry : angle 0.61325 (17450) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.24234 ( 8) hydrogen bonds : bond 0.03128 ( 412) hydrogen bonds : angle 4.19435 ( 1176) link_BETA1-4 : bond 0.01318 ( 14) link_BETA1-4 : angle 4.13034 ( 42) link_NAG-ASN : bond 0.00887 ( 16) link_NAG-ASN : angle 3.40147 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.51 seconds wall clock time: 62 minutes 13.21 seconds (3733.21 seconds total)