Starting phenix.real_space_refine on Sat Aug 23 14:37:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwr_29516/08_2025/8fwr_29516.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwr_29516/08_2025/8fwr_29516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fwr_29516/08_2025/8fwr_29516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwr_29516/08_2025/8fwr_29516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fwr_29516/08_2025/8fwr_29516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwr_29516/08_2025/8fwr_29516.map" } resolution = 3.1 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= 0.002 sd= 0.107 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 8028 2.51 5 N 2100 2.21 5 O 2432 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: 12628 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 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: 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: "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: 3.32, per 1000 atoms: 0.26 Number of scatterers: 12628 At special positions: 0 Unit cell: (165.575, 102.675, 84.175, 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 2432 8.00 N 2100 7.00 C 8028 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=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.04 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.04 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.04 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 H 2 " - " BMA H 3 " " 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 L 2 " - " BMA L 3 " 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: 1.07 Conformation dependent library (CDL) restraints added in 592.6 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: 52 helices and 20 sheets defined 40.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 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 125 removed outlier: 3.951A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.918A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 removed outlier: 3.594A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.580A pdb=" N SER A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 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 125 removed outlier: 3.952A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.919A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 removed outlier: 3.594A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU B 264 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.579A pdb=" N SER B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 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 125 removed outlier: 3.951A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.919A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.593A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU C 264 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.580A pdb=" N SER C 297 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 364 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 125 removed outlier: 3.951A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.919A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.594A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU D 264 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.579A pdb=" N SER D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 43 removed outlier: 6.398A pdb=" N HIS A 34 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 77 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 203 removed outlier: 7.865A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 6.407A 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 removed outlier: 3.562A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) 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 34 through 43 removed outlier: 6.398A pdb=" N HIS B 34 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR B 77 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 removed outlier: 7.866A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 6.407A 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 removed outlier: 3.563A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) 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 34 through 43 removed outlier: 6.398A pdb=" N HIS C 34 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR C 77 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.866A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 6.407A 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 removed outlier: 3.562A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 373 " --> pdb=" O GLY C 370 " (cutoff:3.500A) 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 34 through 43 removed outlier: 6.399A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AB9, first strand: chain 'D' and resid 202 through 203 removed outlier: 7.866A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 6.407A 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 removed outlier: 3.563A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D 373 " --> pdb=" O GLY D 370 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 392 through 394 404 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.43 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: 3887 1.34 - 1.46: 2223 1.46 - 1.57: 6669 1.57 - 1.69: 9 1.69 - 1.81: 120 Bond restraints: 12908 Sorted by residual: bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " ideal model delta sigma weight residual 1.406 1.536 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C ALA A 191 " pdb=" N PRO A 192 " ideal model delta sigma weight residual 1.337 1.387 -0.050 9.80e-03 1.04e+04 2.62e+01 bond pdb=" C ALA D 191 " pdb=" N PRO D 192 " ideal model delta sigma weight residual 1.337 1.386 -0.050 9.80e-03 1.04e+04 2.55e+01 bond pdb=" C ALA B 191 " pdb=" N PRO B 192 " ideal model delta sigma weight residual 1.337 1.386 -0.049 9.80e-03 1.04e+04 2.51e+01 ... (remaining 12903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 16894 2.62 - 5.24: 495 5.24 - 7.85: 79 7.85 - 10.47: 10 10.47 - 13.09: 2 Bond angle restraints: 17480 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 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C ASN A 84 " pdb=" N LEU A 85 " pdb=" CA LEU A 85 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASN D 84 " pdb=" N LEU D 85 " pdb=" CA LEU D 85 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C ASN C 84 " pdb=" N LEU C 85 " pdb=" CA LEU C 85 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N VAL A 266 " pdb=" CA VAL A 266 " pdb=" C VAL A 266 " ideal model delta sigma weight residual 112.29 108.15 4.14 9.40e-01 1.13e+00 1.94e+01 ... (remaining 17475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.46: 7698 24.46 - 48.92: 224 48.92 - 73.37: 97 73.37 - 97.83: 83 97.83 - 122.29: 34 Dihedral angle restraints: 8136 sinusoidal: 3668 harmonic: 4468 Sorted by residual: dihedral pdb=" CA GLY C 246 " pdb=" C GLY C 246 " pdb=" N MET C 247 " pdb=" CA MET C 247 " ideal model delta harmonic sigma weight residual -180.00 -139.86 -40.14 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" CA GLY A 246 " pdb=" C GLY A 246 " pdb=" N MET A 247 " pdb=" CA MET A 247 " ideal model delta harmonic sigma weight residual 180.00 -139.86 -40.14 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" CA GLY B 246 " pdb=" C GLY B 246 " pdb=" N MET B 247 " pdb=" CA MET B 247 " ideal model delta harmonic sigma weight residual -180.00 -139.87 -40.13 0 5.00e+00 4.00e-02 6.44e+01 ... (remaining 8133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1954 0.118 - 0.235: 66 0.235 - 0.353: 18 0.353 - 0.470: 2 0.470 - 0.587: 4 Chirality restraints: 2044 Sorted by residual: 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 -1.81 -0.59 2.00e-01 2.50e+01 8.63e+00 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 -1.82 -0.58 2.00e-01 2.50e+01 8.36e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 67 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.95e+00 ... (remaining 2041 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 67 " -0.034 2.00e-02 2.50e+03 3.49e-02 1.53e+01 pdb=" CG ASN A 67 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 67 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 67 " 0.052 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 67 " 0.034 2.00e-02 2.50e+03 3.40e-02 1.45e+01 pdb=" CG ASN C 67 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 67 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 67 " -0.050 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 275 " 0.000 2.00e-02 2.50e+03 2.97e-02 1.11e+01 pdb=" CG ASN C 275 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN C 275 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN C 275 " -0.050 2.00e-02 2.50e+03 pdb=" C1 NAG C1001 " 0.033 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4104 2.85 - 3.36: 11074 3.36 - 3.87: 20440 3.87 - 4.39: 23830 4.39 - 4.90: 41134 Nonbonded interactions: 100582 Sorted by model distance: nonbonded pdb=" OD1 ASN C 378 " pdb=" OG1 THR C 385 " model vdw 2.334 3.040 nonbonded pdb=" OD1 ASN A 378 " pdb=" OG1 THR A 385 " model vdw 2.335 3.040 nonbonded pdb=" OD1 ASN D 378 " pdb=" OG1 THR D 385 " model vdw 2.335 3.040 nonbonded pdb=" OD1 ASN B 378 " pdb=" OG1 THR B 385 " model vdw 2.335 3.040 nonbonded pdb=" ND2 ASN C 123 " pdb=" OD1 ASP C 143 " model vdw 2.401 3.120 ... (remaining 100577 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: 0.03 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 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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: 5.060 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.800 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 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 : 0.008 0.142 12944 Z= 0.351 Angle : 1.240 23.682 17584 Z= 0.637 Chirality : 0.066 0.587 2044 Planarity : 0.007 0.069 2180 Dihedral : 19.319 122.290 5236 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.74 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -5.62 (0.14), residues: 1524 helix: -4.07 (0.09), residues: 580 sheet: -3.43 (0.25), residues: 304 loop : -3.33 (0.18), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 58 TYR 0.014 0.002 TYR B 146 PHE 0.023 0.003 PHE B 359 TRP 0.031 0.004 TRP D 353 HIS 0.009 0.002 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00758 (12908) covalent geometry : angle 1.09996 (17480) SS BOND : bond 0.00685 ( 4) SS BOND : angle 1.23300 ( 8) hydrogen bonds : bond 0.28813 ( 404) hydrogen bonds : angle 9.12031 ( 1188) link_BETA1-4 : bond 0.02464 ( 16) link_BETA1-4 : angle 7.23841 ( 48) link_NAG-ASN : bond 0.01770 ( 16) link_NAG-ASN : angle 8.36398 ( 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 325 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.7965 (mttp) cc_final: 0.7704 (mtmt) REVERT: A 234 MET cc_start: 0.6886 (mtp) cc_final: 0.6643 (mtt) REVERT: B 55 LEU cc_start: 0.7187 (mm) cc_final: 0.6838 (mp) REVERT: B 84 ASN cc_start: 0.7593 (t0) cc_final: 0.7244 (t0) REVERT: B 154 SER cc_start: 0.8195 (m) cc_final: 0.7961 (m) REVERT: B 240 LYS cc_start: 0.7578 (mttm) cc_final: 0.7350 (mtpp) REVERT: B 262 PHE cc_start: 0.6866 (t80) cc_final: 0.6518 (p90) REVERT: B 267 GLU cc_start: 0.7583 (tt0) cc_final: 0.7351 (tm-30) REVERT: B 271 TYR cc_start: 0.7148 (m-80) cc_final: 0.6842 (m-80) REVERT: B 296 TRP cc_start: 0.7670 (t-100) cc_final: 0.7324 (t-100) REVERT: B 316 MET cc_start: 0.7898 (mtm) cc_final: 0.7652 (mtt) REVERT: B 361 SER cc_start: 0.8025 (t) cc_final: 0.7715 (p) REVERT: C 78 TYR cc_start: 0.6914 (p90) cc_final: 0.6572 (p90) REVERT: C 170 LYS cc_start: 0.7981 (mttp) cc_final: 0.7715 (mtmt) REVERT: C 234 MET cc_start: 0.6903 (mtp) cc_final: 0.6561 (mtt) REVERT: C 323 MET cc_start: 0.8580 (tpp) cc_final: 0.8377 (tpp) REVERT: C 360 MET cc_start: 0.8172 (tpt) cc_final: 0.7621 (tpt) REVERT: D 55 LEU cc_start: 0.7406 (mm) cc_final: 0.7128 (mp) REVERT: D 144 SER cc_start: 0.8092 (p) cc_final: 0.7799 (t) REVERT: D 200 LYS cc_start: 0.7387 (mttp) cc_final: 0.7091 (ttmt) REVERT: D 240 LYS cc_start: 0.7724 (mttm) cc_final: 0.7493 (mtpp) REVERT: D 262 PHE cc_start: 0.7036 (t80) cc_final: 0.6664 (p90) REVERT: D 296 TRP cc_start: 0.7762 (t-100) cc_final: 0.7418 (t-100) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1499 time to fit residues: 65.9599 Evaluate side-chains 182 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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: 0.6980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 141 ASN A 288 GLN C 98 GLN C 141 ASN C 288 GLN D 84 ASN D 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.174300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133087 restraints weight = 13156.857| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.44 r_work: 0.3242 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12944 Z= 0.166 Angle : 0.844 15.439 17584 Z= 0.375 Chirality : 0.051 0.352 2044 Planarity : 0.006 0.063 2180 Dihedral : 18.009 84.196 2312 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.72 % Allowed : 8.13 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -3.92 (0.18), residues: 1524 helix: -1.78 (0.17), residues: 604 sheet: -3.14 (0.25), residues: 316 loop : -2.98 (0.21), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 66 TYR 0.015 0.001 TYR A 252 PHE 0.017 0.002 PHE C 228 TRP 0.018 0.002 TRP A 353 HIS 0.009 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00368 (12908) covalent geometry : angle 0.75670 (17480) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.44125 ( 8) hydrogen bonds : bond 0.04465 ( 404) hydrogen bonds : angle 4.24725 ( 1188) link_BETA1-4 : bond 0.01444 ( 16) link_BETA1-4 : angle 4.82665 ( 48) link_NAG-ASN : bond 0.01435 ( 16) link_NAG-ASN : angle 5.38516 ( 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 222 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8042 (mttp) cc_final: 0.7433 (mtmt) REVERT: A 234 MET cc_start: 0.5994 (mtp) cc_final: 0.5601 (mtt) REVERT: A 294 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6402 (mm-30) REVERT: A 312 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.5965 (mp) REVERT: A 360 MET cc_start: 0.7787 (tpt) cc_final: 0.7533 (tpt) REVERT: B 82 LYS cc_start: 0.8458 (mmtp) cc_final: 0.7800 (mmtm) REVERT: B 84 ASN cc_start: 0.7670 (t0) cc_final: 0.7374 (t0) REVERT: B 240 LYS cc_start: 0.7246 (mttm) cc_final: 0.6997 (mtpp) REVERT: B 262 PHE cc_start: 0.7048 (t80) cc_final: 0.6212 (p90) REVERT: B 271 TYR cc_start: 0.7464 (m-80) cc_final: 0.6694 (m-80) REVERT: B 288 GLN cc_start: 0.6797 (tp-100) cc_final: 0.6325 (mp10) REVERT: B 312 LEU cc_start: 0.7644 (mt) cc_final: 0.7326 (mt) REVERT: B 361 SER cc_start: 0.7750 (t) cc_final: 0.7357 (p) REVERT: C 78 TYR cc_start: 0.6971 (p90) cc_final: 0.6537 (p90) REVERT: C 170 LYS cc_start: 0.8033 (mttp) cc_final: 0.7437 (mtmt) REVERT: C 234 MET cc_start: 0.6042 (mtp) cc_final: 0.5625 (mtt) REVERT: C 250 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: C 294 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6488 (mm-30) REVERT: C 312 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5977 (mp) REVERT: D 35 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8198 (p) REVERT: D 82 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8359 (mmtm) REVERT: D 137 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6934 (mm-40) REVERT: D 240 LYS cc_start: 0.7172 (mttm) cc_final: 0.6912 (mtpp) REVERT: D 248 MET cc_start: 0.8801 (mmm) cc_final: 0.8538 (mmm) REVERT: D 262 PHE cc_start: 0.7210 (t80) cc_final: 0.6189 (p90) REVERT: D 286 ASN cc_start: 0.6976 (t0) cc_final: 0.6604 (t0) REVERT: D 288 GLN cc_start: 0.6821 (tp-100) cc_final: 0.6311 (mp10) REVERT: D 296 TRP cc_start: 0.7422 (t-100) cc_final: 0.7065 (t-100) REVERT: D 312 LEU cc_start: 0.7646 (mt) cc_final: 0.7336 (mt) outliers start: 23 outliers final: 8 residues processed: 215 average time/residue: 0.1286 time to fit residues: 39.0624 Evaluate side-chains 177 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 357 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 0.6980 chunk 112 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 103 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN C 346 GLN D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.172306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130814 restraints weight = 13206.332| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.52 r_work: 0.3205 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12944 Z= 0.149 Angle : 0.750 14.181 17584 Z= 0.334 Chirality : 0.048 0.306 2044 Planarity : 0.005 0.058 2180 Dihedral : 13.804 82.605 2312 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 2.24 % Allowed : 8.66 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -2.57 (0.20), residues: 1524 helix: -0.26 (0.20), residues: 600 sheet: -2.93 (0.26), residues: 312 loop : -2.40 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 68 TYR 0.013 0.001 TYR A 146 PHE 0.016 0.001 PHE C 337 TRP 0.016 0.001 TRP A 353 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00341 (12908) covalent geometry : angle 0.68739 (17480) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.22118 ( 8) hydrogen bonds : bond 0.03800 ( 404) hydrogen bonds : angle 3.75855 ( 1188) link_BETA1-4 : bond 0.01297 ( 16) link_BETA1-4 : angle 4.49137 ( 48) link_NAG-ASN : bond 0.01224 ( 16) link_NAG-ASN : angle 3.71096 ( 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 200 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8195 (mttp) cc_final: 0.7642 (mtmt) REVERT: A 234 MET cc_start: 0.6245 (mtp) cc_final: 0.5862 (mtt) REVERT: A 360 MET cc_start: 0.7652 (tpt) cc_final: 0.7422 (tpt) REVERT: B 82 LYS cc_start: 0.8509 (mmtp) cc_final: 0.7850 (mmtm) REVERT: B 240 LYS cc_start: 0.7308 (mttm) cc_final: 0.7054 (mtpp) REVERT: B 248 MET cc_start: 0.9039 (mmm) cc_final: 0.8630 (mmm) REVERT: B 262 PHE cc_start: 0.7343 (t80) cc_final: 0.6260 (p90) REVERT: B 288 GLN cc_start: 0.6792 (tp-100) cc_final: 0.6430 (mp10) REVERT: B 335 GLN cc_start: 0.6867 (tt0) cc_final: 0.6666 (tt0) REVERT: B 361 SER cc_start: 0.7742 (t) cc_final: 0.7377 (p) REVERT: C 170 LYS cc_start: 0.8156 (mttp) cc_final: 0.7591 (mtmt) REVERT: C 234 MET cc_start: 0.6196 (mtp) cc_final: 0.5791 (mtt) REVERT: C 245 MET cc_start: 0.7184 (mtp) cc_final: 0.6846 (ttm) REVERT: C 250 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: C 251 TYR cc_start: 0.6822 (m-80) cc_final: 0.6306 (m-80) REVERT: C 294 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6461 (mm-30) REVERT: D 35 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8204 (p) REVERT: D 82 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8045 (mmtm) REVERT: D 84 ASN cc_start: 0.7314 (t0) cc_final: 0.7046 (t0) REVERT: D 240 LYS cc_start: 0.7260 (mttm) cc_final: 0.7017 (mtpp) REVERT: D 248 MET cc_start: 0.8969 (mmm) cc_final: 0.8563 (mmm) REVERT: D 262 PHE cc_start: 0.7425 (t80) cc_final: 0.6334 (p90) REVERT: D 288 GLN cc_start: 0.6720 (tp-100) cc_final: 0.6309 (mp10) outliers start: 30 outliers final: 15 residues processed: 193 average time/residue: 0.1199 time to fit residues: 33.3516 Evaluate side-chains 176 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 144 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 overall best weight: 1.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 136 HIS D 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.168007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125621 restraints weight = 13137.330| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.54 r_work: 0.3294 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12944 Z= 0.202 Angle : 0.749 13.694 17584 Z= 0.337 Chirality : 0.048 0.287 2044 Planarity : 0.005 0.068 2180 Dihedral : 12.463 131.042 2312 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 2.39 % Allowed : 8.96 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.06 (0.21), residues: 1524 helix: 0.28 (0.21), residues: 600 sheet: -2.83 (0.26), residues: 312 loop : -2.14 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 270 TYR 0.019 0.002 TYR A 44 PHE 0.017 0.002 PHE C 337 TRP 0.016 0.001 TRP C 353 HIS 0.005 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00495 (12908) covalent geometry : angle 0.68865 (17480) SS BOND : bond 0.00069 ( 4) SS BOND : angle 0.20790 ( 8) hydrogen bonds : bond 0.03739 ( 404) hydrogen bonds : angle 3.78518 ( 1188) link_BETA1-4 : bond 0.01253 ( 16) link_BETA1-4 : angle 4.38850 ( 48) link_NAG-ASN : bond 0.01006 ( 16) link_NAG-ASN : angle 3.71401 ( 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 192 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7159 (mptt) cc_final: 0.6890 (mtmm) REVERT: A 170 LYS cc_start: 0.8272 (mttp) cc_final: 0.7739 (mtmt) REVERT: A 198 ARG cc_start: 0.7228 (ttt-90) cc_final: 0.6986 (tpt170) REVERT: A 234 MET cc_start: 0.6539 (mtp) cc_final: 0.6095 (mtt) REVERT: A 248 MET cc_start: 0.8025 (mmm) cc_final: 0.7790 (mmm) REVERT: A 294 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6466 (mm-30) REVERT: B 82 LYS cc_start: 0.8611 (mmtp) cc_final: 0.8020 (mmtm) REVERT: B 85 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6977 (mp) REVERT: B 240 LYS cc_start: 0.7468 (mttm) cc_final: 0.7212 (mtpp) REVERT: B 262 PHE cc_start: 0.7630 (t80) cc_final: 0.6415 (p90) REVERT: B 271 TYR cc_start: 0.8078 (m-80) cc_final: 0.7657 (m-80) REVERT: B 335 GLN cc_start: 0.7020 (tt0) cc_final: 0.6763 (tt0) REVERT: B 361 SER cc_start: 0.7875 (t) cc_final: 0.7481 (p) REVERT: C 168 LYS cc_start: 0.7205 (mptt) cc_final: 0.6903 (mtmm) REVERT: C 170 LYS cc_start: 0.8241 (mttp) cc_final: 0.7733 (mtmt) REVERT: C 234 MET cc_start: 0.6486 (mtp) cc_final: 0.6026 (mtt) REVERT: C 250 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: C 251 TYR cc_start: 0.7006 (m-80) cc_final: 0.6427 (m-80) REVERT: C 294 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6599 (mm-30) REVERT: D 35 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8353 (m) REVERT: D 82 LYS cc_start: 0.8800 (mmtp) cc_final: 0.8223 (mmtm) REVERT: D 137 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6962 (mp10) REVERT: D 240 LYS cc_start: 0.7421 (mttm) cc_final: 0.7206 (mtpp) REVERT: D 262 PHE cc_start: 0.7710 (t80) cc_final: 0.6535 (p90) REVERT: D 288 GLN cc_start: 0.6654 (tp-100) cc_final: 0.6391 (mp10) REVERT: D 365 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7287 (mm-30) outliers start: 32 outliers final: 17 residues processed: 185 average time/residue: 0.1255 time to fit residues: 33.1762 Evaluate side-chains 171 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 350 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 132 optimal weight: 0.0470 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN D 84 ASN D 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.168729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.126109 restraints weight = 13219.278| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.53 r_work: 0.3141 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12944 Z= 0.156 Angle : 0.709 14.737 17584 Z= 0.317 Chirality : 0.046 0.263 2044 Planarity : 0.005 0.066 2180 Dihedral : 11.516 126.991 2312 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 1.94 % Allowed : 10.00 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.21), residues: 1524 helix: 0.77 (0.21), residues: 600 sheet: -2.69 (0.26), residues: 312 loop : -2.08 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.015 0.001 TYR C 44 PHE 0.015 0.001 PHE C 337 TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00373 (12908) covalent geometry : angle 0.64231 (17480) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.19392 ( 8) hydrogen bonds : bond 0.03413 ( 404) hydrogen bonds : angle 3.68051 ( 1188) link_BETA1-4 : bond 0.01164 ( 16) link_BETA1-4 : angle 4.30280 ( 48) link_NAG-ASN : bond 0.01012 ( 16) link_NAG-ASN : angle 3.95227 ( 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 179 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7074 (mptt) cc_final: 0.6756 (mtmm) REVERT: A 170 LYS cc_start: 0.8167 (mttp) cc_final: 0.7615 (mtmt) REVERT: A 234 MET cc_start: 0.6375 (mtp) cc_final: 0.5927 (mtt) REVERT: A 248 MET cc_start: 0.8149 (mmm) cc_final: 0.7823 (mmm) REVERT: A 294 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6482 (mm-30) REVERT: B 82 LYS cc_start: 0.8544 (mmtp) cc_final: 0.7874 (mmtm) REVERT: B 85 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6770 (mp) REVERT: B 240 LYS cc_start: 0.7229 (mttm) cc_final: 0.6979 (mtpp) REVERT: B 248 MET cc_start: 0.9028 (mmm) cc_final: 0.8664 (mmm) REVERT: B 262 PHE cc_start: 0.7708 (t80) cc_final: 0.6397 (p90) REVERT: B 271 TYR cc_start: 0.7920 (m-80) cc_final: 0.7546 (m-80) REVERT: B 335 GLN cc_start: 0.6758 (tt0) cc_final: 0.6524 (tt0) REVERT: B 361 SER cc_start: 0.7705 (t) cc_final: 0.7264 (p) REVERT: C 168 LYS cc_start: 0.7081 (mptt) cc_final: 0.6745 (mtmm) REVERT: C 170 LYS cc_start: 0.8158 (mttp) cc_final: 0.7585 (mtmt) REVERT: C 234 MET cc_start: 0.6341 (mtp) cc_final: 0.5889 (mtt) REVERT: C 251 TYR cc_start: 0.6975 (m-80) cc_final: 0.6457 (m-80) REVERT: C 294 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6599 (mm-30) REVERT: D 35 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8342 (m) REVERT: D 82 LYS cc_start: 0.8665 (mmtp) cc_final: 0.7997 (mmtm) REVERT: D 137 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: D 240 LYS cc_start: 0.7243 (mttm) cc_final: 0.7015 (mtpp) REVERT: D 248 MET cc_start: 0.9176 (mmm) cc_final: 0.8778 (mmm) REVERT: D 262 PHE cc_start: 0.7735 (t80) cc_final: 0.6366 (p90) REVERT: D 365 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7204 (mm-30) outliers start: 26 outliers final: 19 residues processed: 170 average time/residue: 0.1195 time to fit residues: 29.4766 Evaluate side-chains 168 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 109 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.169030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.126586 restraints weight = 13131.796| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.53 r_work: 0.3270 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12944 Z= 0.141 Angle : 0.686 14.548 17584 Z= 0.306 Chirality : 0.045 0.253 2044 Planarity : 0.005 0.065 2180 Dihedral : 10.824 126.638 2312 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 2.31 % Allowed : 10.60 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.22), residues: 1524 helix: 1.13 (0.22), residues: 600 sheet: -2.59 (0.26), residues: 312 loop : -1.97 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 349 TYR 0.014 0.001 TYR C 44 PHE 0.012 0.001 PHE C 337 TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00332 (12908) covalent geometry : angle 0.62107 (17480) SS BOND : bond 0.00052 ( 4) SS BOND : angle 0.14057 ( 8) hydrogen bonds : bond 0.03212 ( 404) hydrogen bonds : angle 3.60337 ( 1188) link_BETA1-4 : bond 0.01154 ( 16) link_BETA1-4 : angle 4.25292 ( 48) link_NAG-ASN : bond 0.00942 ( 16) link_NAG-ASN : angle 3.73150 ( 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 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7185 (mptt) cc_final: 0.6942 (mtmm) REVERT: A 170 LYS cc_start: 0.8238 (mttp) cc_final: 0.7723 (mtmt) REVERT: A 234 MET cc_start: 0.6572 (mtp) cc_final: 0.6124 (mtt) REVERT: A 248 MET cc_start: 0.8039 (mmm) cc_final: 0.7709 (mmm) REVERT: A 294 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6512 (mm-30) REVERT: B 82 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8034 (mmtm) REVERT: B 85 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.7019 (mp) REVERT: B 240 LYS cc_start: 0.7403 (mttm) cc_final: 0.7156 (mtpp) REVERT: B 248 MET cc_start: 0.8946 (mmm) cc_final: 0.8600 (mmm) REVERT: B 262 PHE cc_start: 0.7828 (t80) cc_final: 0.6519 (p90) REVERT: B 335 GLN cc_start: 0.6914 (tt0) cc_final: 0.6662 (tt0) REVERT: B 361 SER cc_start: 0.7744 (t) cc_final: 0.7333 (p) REVERT: C 168 LYS cc_start: 0.7207 (mptt) cc_final: 0.6918 (mtmm) REVERT: C 170 LYS cc_start: 0.8220 (mttp) cc_final: 0.7697 (mtmt) REVERT: C 234 MET cc_start: 0.6506 (mtp) cc_final: 0.6054 (mtt) REVERT: C 251 TYR cc_start: 0.7029 (m-80) cc_final: 0.6486 (m-80) REVERT: C 294 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6657 (mm-30) REVERT: D 35 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8345 (m) REVERT: D 82 LYS cc_start: 0.8742 (mmtp) cc_final: 0.8119 (mmtm) REVERT: D 137 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6601 (mm-40) REVERT: D 240 LYS cc_start: 0.7433 (mttm) cc_final: 0.7193 (mtpp) REVERT: D 248 MET cc_start: 0.9085 (mmm) cc_final: 0.8704 (mmm) REVERT: D 262 PHE cc_start: 0.7854 (t80) cc_final: 0.6542 (p90) REVERT: D 365 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7211 (mm-30) outliers start: 31 outliers final: 22 residues processed: 173 average time/residue: 0.1169 time to fit residues: 29.5878 Evaluate side-chains 173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 146 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 109 optimal weight: 0.0470 chunk 145 optimal weight: 6.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.168718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127380 restraints weight = 13218.553| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.54 r_work: 0.3285 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12944 Z= 0.140 Angle : 0.677 14.086 17584 Z= 0.303 Chirality : 0.045 0.245 2044 Planarity : 0.005 0.064 2180 Dihedral : 10.340 126.267 2312 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.17 % Favored : 93.70 % Rotamer: Outliers : 2.61 % Allowed : 10.75 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.15 (0.22), residues: 1524 helix: 1.27 (0.22), residues: 600 sheet: -2.40 (0.27), residues: 304 loop : -1.92 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 349 TYR 0.012 0.001 TYR A 44 PHE 0.011 0.001 PHE C 337 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00332 (12908) covalent geometry : angle 0.61299 (17480) SS BOND : bond 0.00040 ( 4) SS BOND : angle 0.16385 ( 8) hydrogen bonds : bond 0.03155 ( 404) hydrogen bonds : angle 3.57691 ( 1188) link_BETA1-4 : bond 0.01125 ( 16) link_BETA1-4 : angle 4.21687 ( 48) link_NAG-ASN : bond 0.00917 ( 16) link_NAG-ASN : angle 3.64657 ( 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 192 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7096 (mptt) cc_final: 0.6802 (mtmm) REVERT: A 170 LYS cc_start: 0.8194 (mttp) cc_final: 0.7679 (mtmt) REVERT: A 234 MET cc_start: 0.6491 (mtp) cc_final: 0.6023 (mtt) REVERT: A 294 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6501 (mm-30) REVERT: B 82 LYS cc_start: 0.8542 (mmtp) cc_final: 0.7951 (mmtm) REVERT: B 85 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.7029 (mp) REVERT: B 240 LYS cc_start: 0.7323 (mttm) cc_final: 0.7064 (mtpp) REVERT: B 262 PHE cc_start: 0.7876 (t80) cc_final: 0.6502 (p90) REVERT: B 335 GLN cc_start: 0.6860 (tt0) cc_final: 0.6619 (tt0) REVERT: B 361 SER cc_start: 0.7770 (t) cc_final: 0.7305 (p) REVERT: C 168 LYS cc_start: 0.7324 (mptt) cc_final: 0.6919 (mtmm) REVERT: C 170 LYS cc_start: 0.8214 (mttp) cc_final: 0.7651 (mtmt) REVERT: C 234 MET cc_start: 0.6442 (mtp) cc_final: 0.5963 (mtt) REVERT: C 251 TYR cc_start: 0.6964 (m-80) cc_final: 0.6403 (m-80) REVERT: C 267 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6833 (mm-30) REVERT: C 294 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6636 (mm-30) REVERT: D 35 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8371 (m) REVERT: D 82 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8040 (mmtm) REVERT: D 137 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6555 (mm-40) REVERT: D 240 LYS cc_start: 0.7302 (mttm) cc_final: 0.7062 (mtpp) REVERT: D 248 MET cc_start: 0.9088 (mmm) cc_final: 0.8710 (mmm) REVERT: D 262 PHE cc_start: 0.7916 (t80) cc_final: 0.6479 (p90) REVERT: D 315 PHE cc_start: 0.6851 (p90) cc_final: 0.4951 (m-80) REVERT: D 365 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7143 (mm-30) outliers start: 35 outliers final: 23 residues processed: 182 average time/residue: 0.1185 time to fit residues: 31.7860 Evaluate side-chains 182 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 121 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.168248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125898 restraints weight = 13142.245| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.63 r_work: 0.3138 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12944 Z= 0.158 Angle : 0.681 13.505 17584 Z= 0.305 Chirality : 0.045 0.249 2044 Planarity : 0.005 0.065 2180 Dihedral : 10.013 125.844 2312 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 2.46 % Allowed : 11.12 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.09 (0.22), residues: 1524 helix: 1.27 (0.22), residues: 600 sheet: -2.32 (0.27), residues: 304 loop : -1.86 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 349 TYR 0.011 0.001 TYR A 44 PHE 0.012 0.001 PHE B 359 TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00382 (12908) covalent geometry : angle 0.61914 (17480) SS BOND : bond 0.00020 ( 4) SS BOND : angle 0.18769 ( 8) hydrogen bonds : bond 0.03212 ( 404) hydrogen bonds : angle 3.59486 ( 1188) link_BETA1-4 : bond 0.01093 ( 16) link_BETA1-4 : angle 4.19584 ( 48) link_NAG-ASN : bond 0.00901 ( 16) link_NAG-ASN : angle 3.55527 ( 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 193 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7403 (mptt) cc_final: 0.6977 (mtmm) REVERT: A 170 LYS cc_start: 0.8208 (mttp) cc_final: 0.7679 (mtmt) REVERT: A 234 MET cc_start: 0.6629 (mtp) cc_final: 0.6158 (mtt) REVERT: A 248 MET cc_start: 0.8037 (mmm) cc_final: 0.7769 (mmm) REVERT: A 294 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6602 (mm-30) REVERT: B 82 LYS cc_start: 0.8528 (mmtp) cc_final: 0.7866 (mmtm) REVERT: B 85 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6990 (mp) REVERT: B 240 LYS cc_start: 0.7388 (mttm) cc_final: 0.7130 (mtpp) REVERT: B 248 MET cc_start: 0.9000 (mmm) cc_final: 0.8629 (mmm) REVERT: B 262 PHE cc_start: 0.8001 (t80) cc_final: 0.6536 (p90) REVERT: B 294 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7011 (mm-30) REVERT: B 335 GLN cc_start: 0.6928 (tt0) cc_final: 0.6694 (tt0) REVERT: B 361 SER cc_start: 0.7752 (t) cc_final: 0.7317 (p) REVERT: C 154 SER cc_start: 0.7501 (m) cc_final: 0.7218 (p) REVERT: C 168 LYS cc_start: 0.7335 (mptt) cc_final: 0.6902 (mtmm) REVERT: C 170 LYS cc_start: 0.8202 (mttp) cc_final: 0.7664 (mtmt) REVERT: C 234 MET cc_start: 0.6605 (mtp) cc_final: 0.6106 (mtt) REVERT: C 251 TYR cc_start: 0.6902 (m-80) cc_final: 0.6297 (m-80) REVERT: C 267 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6876 (mm-30) REVERT: C 294 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6676 (mm-30) REVERT: D 35 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8411 (m) REVERT: D 82 LYS cc_start: 0.8667 (mmtp) cc_final: 0.8014 (mmtm) REVERT: D 240 LYS cc_start: 0.7378 (mttm) cc_final: 0.7131 (mtpp) REVERT: D 248 MET cc_start: 0.9153 (mmm) cc_final: 0.8831 (mmm) REVERT: D 262 PHE cc_start: 0.8013 (t80) cc_final: 0.6493 (p90) REVERT: D 315 PHE cc_start: 0.6876 (p90) cc_final: 0.4971 (m-80) REVERT: D 365 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7203 (mm-30) outliers start: 33 outliers final: 23 residues processed: 184 average time/residue: 0.1147 time to fit residues: 31.0623 Evaluate side-chains 180 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.169074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127050 restraints weight = 13192.706| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.59 r_work: 0.3304 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12944 Z= 0.140 Angle : 0.664 13.182 17584 Z= 0.298 Chirality : 0.044 0.245 2044 Planarity : 0.005 0.065 2180 Dihedral : 9.548 125.556 2312 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.17 % Favored : 93.70 % Rotamer: Outliers : 2.09 % Allowed : 11.42 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.97 (0.22), residues: 1524 helix: 1.38 (0.22), residues: 600 sheet: -2.23 (0.27), residues: 304 loop : -1.80 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 349 TYR 0.011 0.001 TYR A 44 PHE 0.010 0.001 PHE A 337 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00335 (12908) covalent geometry : angle 0.60321 (17480) SS BOND : bond 0.00052 ( 4) SS BOND : angle 0.21783 ( 8) hydrogen bonds : bond 0.03098 ( 404) hydrogen bonds : angle 3.57613 ( 1188) link_BETA1-4 : bond 0.01066 ( 16) link_BETA1-4 : angle 4.15341 ( 48) link_NAG-ASN : bond 0.00875 ( 16) link_NAG-ASN : angle 3.43902 ( 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 189 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 SER cc_start: 0.7366 (m) cc_final: 0.7075 (p) REVERT: A 168 LYS cc_start: 0.7279 (mptt) cc_final: 0.6831 (mtmm) REVERT: A 170 LYS cc_start: 0.8195 (mttp) cc_final: 0.7620 (mtmt) REVERT: A 234 MET cc_start: 0.6570 (mtp) cc_final: 0.6151 (mtt) REVERT: A 248 MET cc_start: 0.8045 (mmm) cc_final: 0.7758 (mmm) REVERT: A 294 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6617 (mm-30) REVERT: A 337 PHE cc_start: 0.7340 (t80) cc_final: 0.7096 (t80) REVERT: B 82 LYS cc_start: 0.8541 (mmtp) cc_final: 0.7883 (mmtm) REVERT: B 85 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6925 (mp) REVERT: B 240 LYS cc_start: 0.7205 (mttm) cc_final: 0.6959 (mtpp) REVERT: B 248 MET cc_start: 0.8982 (mmm) cc_final: 0.8589 (mmm) REVERT: B 262 PHE cc_start: 0.8071 (t80) cc_final: 0.6486 (p90) REVERT: B 294 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6966 (mm-30) REVERT: B 335 GLN cc_start: 0.6849 (tt0) cc_final: 0.6596 (tt0) REVERT: B 361 SER cc_start: 0.7739 (t) cc_final: 0.7253 (p) REVERT: C 154 SER cc_start: 0.7396 (m) cc_final: 0.7105 (p) REVERT: C 168 LYS cc_start: 0.7303 (mptt) cc_final: 0.6844 (mtmm) REVERT: C 170 LYS cc_start: 0.8200 (mttp) cc_final: 0.7628 (mtmt) REVERT: C 234 MET cc_start: 0.6527 (mtp) cc_final: 0.6028 (mtt) REVERT: C 251 TYR cc_start: 0.6878 (m-80) cc_final: 0.6287 (m-80) REVERT: C 267 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6962 (mm-30) REVERT: C 294 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6664 (mm-30) REVERT: D 82 LYS cc_start: 0.8597 (mmtp) cc_final: 0.7995 (mmtm) REVERT: D 240 LYS cc_start: 0.7190 (mttm) cc_final: 0.6976 (mtpp) REVERT: D 248 MET cc_start: 0.9135 (mmm) cc_final: 0.8735 (mmm) REVERT: D 262 PHE cc_start: 0.8095 (t80) cc_final: 0.6466 (p90) REVERT: D 294 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6924 (mm-30) REVERT: D 315 PHE cc_start: 0.6782 (p90) cc_final: 0.4925 (m-80) REVERT: D 365 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7122 (mm-30) outliers start: 28 outliers final: 23 residues processed: 181 average time/residue: 0.1175 time to fit residues: 31.3170 Evaluate side-chains 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 125 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 147 optimal weight: 0.0970 chunk 99 optimal weight: 5.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.170804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128088 restraints weight = 13143.992| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.45 r_work: 0.3352 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12944 Z= 0.109 Angle : 0.638 12.928 17584 Z= 0.288 Chirality : 0.043 0.234 2044 Planarity : 0.004 0.061 2180 Dihedral : 8.932 125.182 2312 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.72 % Allowed : 11.94 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.71 (0.22), residues: 1524 helix: 1.64 (0.23), residues: 600 sheet: -2.07 (0.28), residues: 304 loop : -1.74 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 349 TYR 0.015 0.001 TYR B 86 PHE 0.019 0.001 PHE A 337 TRP 0.009 0.001 TRP C 353 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00245 (12908) covalent geometry : angle 0.57756 (17480) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.18750 ( 8) hydrogen bonds : bond 0.02831 ( 404) hydrogen bonds : angle 3.47659 ( 1188) link_BETA1-4 : bond 0.01052 ( 16) link_BETA1-4 : angle 4.08264 ( 48) link_NAG-ASN : bond 0.00828 ( 16) link_NAG-ASN : angle 3.29613 ( 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 192 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7421 (mptt) cc_final: 0.6919 (mtmm) REVERT: A 170 LYS cc_start: 0.8250 (mttp) cc_final: 0.7766 (mtmt) REVERT: A 248 MET cc_start: 0.7915 (mmm) cc_final: 0.7679 (mmm) REVERT: A 294 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6658 (mm-30) REVERT: B 82 LYS cc_start: 0.8542 (mmtp) cc_final: 0.8073 (mmtm) REVERT: B 85 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7081 (mp) REVERT: B 240 LYS cc_start: 0.7447 (mttm) cc_final: 0.7212 (mtpp) REVERT: B 248 MET cc_start: 0.8851 (mmm) cc_final: 0.8464 (mmm) REVERT: B 262 PHE cc_start: 0.8110 (t80) cc_final: 0.6636 (p90) REVERT: B 271 TYR cc_start: 0.8149 (m-80) cc_final: 0.7832 (m-80) REVERT: B 315 PHE cc_start: 0.6898 (p90) cc_final: 0.5113 (m-80) REVERT: B 335 GLN cc_start: 0.7032 (tt0) cc_final: 0.6776 (tt0) REVERT: B 361 SER cc_start: 0.7670 (t) cc_final: 0.7245 (p) REVERT: C 168 LYS cc_start: 0.7471 (mptt) cc_final: 0.6915 (mtmm) REVERT: C 170 LYS cc_start: 0.8253 (mttp) cc_final: 0.7749 (mtmt) REVERT: C 234 MET cc_start: 0.6619 (mtp) cc_final: 0.6159 (mtt) REVERT: C 251 TYR cc_start: 0.6898 (m-80) cc_final: 0.6343 (m-80) REVERT: C 294 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6752 (mm-30) REVERT: D 82 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8121 (mmtm) REVERT: D 248 MET cc_start: 0.9068 (mmm) cc_final: 0.8715 (mmm) REVERT: D 262 PHE cc_start: 0.8122 (t80) cc_final: 0.6671 (p90) REVERT: D 294 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7073 (mm-30) REVERT: D 315 PHE cc_start: 0.6888 (p90) cc_final: 0.5139 (m-80) REVERT: D 365 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7277 (mm-30) outliers start: 23 outliers final: 21 residues processed: 186 average time/residue: 0.1220 time to fit residues: 33.2061 Evaluate side-chains 178 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 17 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 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 = 0.3834 r_free = 0.3834 target = 0.169294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127445 restraints weight = 13208.641| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.41 r_work: 0.3344 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12944 Z= 0.140 Angle : 0.659 12.635 17584 Z= 0.298 Chirality : 0.044 0.236 2044 Planarity : 0.005 0.063 2180 Dihedral : 8.711 124.937 2312 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 1.64 % Allowed : 12.46 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.70 (0.22), residues: 1524 helix: 1.60 (0.22), residues: 600 sheet: -2.00 (0.28), residues: 304 loop : -1.71 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 37 TYR 0.012 0.001 TYR D 86 PHE 0.025 0.001 PHE A 337 TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00336 (12908) covalent geometry : angle 0.60277 (17480) SS BOND : bond 0.00046 ( 4) SS BOND : angle 0.27493 ( 8) hydrogen bonds : bond 0.03024 ( 404) hydrogen bonds : angle 3.51589 ( 1188) link_BETA1-4 : bond 0.00997 ( 16) link_BETA1-4 : angle 4.02856 ( 48) link_NAG-ASN : bond 0.00816 ( 16) link_NAG-ASN : angle 3.26113 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2905.15 seconds wall clock time: 51 minutes 1.79 seconds (3061.79 seconds total)