Starting phenix.real_space_refine on Thu May 15 05:11:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwr_29516/05_2025/8fwr_29516.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwr_29516/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fwr_29516/05_2025/8fwr_29516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwr_29516/05_2025/8fwr_29516.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwr_29516/05_2025/8fwr_29516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwr_29516/05_2025/8fwr_29516.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.87, per 1000 atoms: 0.70 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: 3.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 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: 1.44 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: 3.71 Time building geometry restraints manager: 3.87 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain '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: 2.810 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.260 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.62 (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 TRP 0.031 0.004 TRP D 353 HIS 0.009 0.002 HIS D 111 PHE 0.023 0.003 PHE B 359 TYR 0.014 0.002 TYR B 146 ARG 0.010 0.001 ARG A 58 Details of bonding type rmsd link_NAG-ASN : bond 0.01770 ( 16) link_NAG-ASN : angle 8.36398 ( 48) link_BETA1-4 : bond 0.02464 ( 16) link_BETA1-4 : angle 7.23841 ( 48) hydrogen bonds : bond 0.28813 ( 404) hydrogen bonds : angle 9.12031 ( 1188) SS BOND : bond 0.00685 ( 4) SS BOND : angle 1.23300 ( 8) covalent geometry : bond 0.00758 (12908) covalent geometry : angle 1.09996 (17480) *********************** 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 : 1.342 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: 0.2842 time to fit residues: 124.7039 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 : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 88 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.173837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132507 restraints weight = 13075.855| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.40 r_work: 0.3392 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12944 Z= 0.167 Angle : 0.848 15.605 17584 Z= 0.378 Chirality : 0.052 0.580 2044 Planarity : 0.006 0.064 2180 Dihedral : 18.222 86.228 2312 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.72 % Allowed : 8.21 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.18), residues: 1524 helix: -1.82 (0.17), residues: 604 sheet: -3.16 (0.25), residues: 316 loop : -2.98 (0.21), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 353 HIS 0.009 0.001 HIS D 253 PHE 0.017 0.002 PHE C 228 TYR 0.015 0.001 TYR A 252 ARG 0.009 0.001 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01129 ( 16) link_NAG-ASN : angle 5.39425 ( 48) link_BETA1-4 : bond 0.01422 ( 16) link_BETA1-4 : angle 4.86409 ( 48) hydrogen bonds : bond 0.04518 ( 404) hydrogen bonds : angle 4.27847 ( 1188) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.43483 ( 8) covalent geometry : bond 0.00372 (12908) covalent geometry : angle 0.76064 (17480) *********************** 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 221 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8181 (mttp) cc_final: 0.7659 (mtmt) REVERT: A 234 MET cc_start: 0.6326 (mtp) cc_final: 0.5949 (mtt) REVERT: A 294 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6413 (mm-30) REVERT: A 312 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6353 (mp) REVERT: A 360 MET cc_start: 0.8171 (tpt) cc_final: 0.7888 (tpt) REVERT: B 35 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8128 (m) REVERT: B 82 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8051 (mmtm) REVERT: B 84 ASN cc_start: 0.7847 (t0) cc_final: 0.7600 (t0) REVERT: B 240 LYS cc_start: 0.7608 (mttm) cc_final: 0.7349 (mtpp) REVERT: B 262 PHE cc_start: 0.7110 (t80) cc_final: 0.6440 (p90) REVERT: B 288 GLN cc_start: 0.6975 (tp-100) cc_final: 0.6457 (mp10) REVERT: B 312 LEU cc_start: 0.8011 (mt) cc_final: 0.7723 (mt) REVERT: B 361 SER cc_start: 0.7955 (t) cc_final: 0.7642 (p) REVERT: C 78 TYR cc_start: 0.7065 (p90) cc_final: 0.6657 (p90) REVERT: C 170 LYS cc_start: 0.8165 (mttp) cc_final: 0.7657 (mtmt) REVERT: C 234 MET cc_start: 0.6349 (mtp) cc_final: 0.5949 (mtt) REVERT: C 250 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: C 294 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6523 (mm-30) REVERT: C 312 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6350 (mp) REVERT: D 35 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8185 (p) REVERT: D 82 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8572 (mmtm) REVERT: D 137 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7111 (mm-40) REVERT: D 240 LYS cc_start: 0.7586 (mttm) cc_final: 0.7298 (mtpp) REVERT: D 248 MET cc_start: 0.8727 (mmm) cc_final: 0.8479 (mmm) REVERT: D 262 PHE cc_start: 0.7273 (t80) cc_final: 0.6425 (p90) REVERT: D 271 TYR cc_start: 0.7869 (m-80) cc_final: 0.7621 (m-80) REVERT: D 286 ASN cc_start: 0.7279 (t0) cc_final: 0.6952 (t0) REVERT: D 288 GLN cc_start: 0.7033 (tp-100) cc_final: 0.6468 (mp10) REVERT: D 296 TRP cc_start: 0.7697 (t-100) cc_final: 0.7327 (t-100) REVERT: D 312 LEU cc_start: 0.7994 (mt) cc_final: 0.7707 (mt) outliers start: 23 outliers final: 8 residues processed: 214 average time/residue: 0.2663 time to fit residues: 80.4448 Evaluate side-chains 179 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 35 VAL 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 34 optimal weight: 0.3980 chunk 81 optimal weight: 0.0970 chunk 60 optimal weight: 0.1980 chunk 148 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 87 optimal weight: 0.2980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.174629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133110 restraints weight = 13271.749| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.40 r_work: 0.3400 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12944 Z= 0.124 Angle : 0.738 14.057 17584 Z= 0.327 Chirality : 0.048 0.303 2044 Planarity : 0.005 0.054 2180 Dihedral : 13.726 82.380 2312 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.94 % Allowed : 9.03 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.20), residues: 1524 helix: -0.12 (0.20), residues: 600 sheet: -2.90 (0.26), residues: 312 loop : -2.41 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.006 0.001 HIS C 253 PHE 0.016 0.001 PHE C 337 TYR 0.014 0.001 TYR B 86 ARG 0.005 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01108 ( 16) link_NAG-ASN : angle 3.64797 ( 48) link_BETA1-4 : bond 0.01307 ( 16) link_BETA1-4 : angle 4.46436 ( 48) hydrogen bonds : bond 0.03651 ( 404) hydrogen bonds : angle 3.69675 ( 1188) SS BOND : bond 0.00115 ( 4) SS BOND : angle 0.22628 ( 8) covalent geometry : bond 0.00264 (12908) covalent geometry : angle 0.67568 (17480) *********************** 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: 26 poor density : 174 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8201 (mttp) cc_final: 0.7677 (mtmt) REVERT: A 234 MET cc_start: 0.6230 (mtp) cc_final: 0.5889 (mtt) REVERT: A 283 ASN cc_start: 0.6770 (t0) cc_final: 0.5623 (p0) REVERT: A 360 MET cc_start: 0.7884 (tpt) cc_final: 0.7664 (tpt) REVERT: B 82 LYS cc_start: 0.8564 (mmtp) cc_final: 0.7940 (mmtm) REVERT: B 240 LYS cc_start: 0.7420 (mttm) cc_final: 0.7163 (mtpp) REVERT: B 248 MET cc_start: 0.8918 (mmm) cc_final: 0.8612 (mmm) REVERT: B 262 PHE cc_start: 0.7304 (t80) cc_final: 0.6360 (p90) REVERT: B 288 GLN cc_start: 0.6876 (tp-100) cc_final: 0.6499 (mp10) REVERT: B 335 GLN cc_start: 0.6975 (tt0) cc_final: 0.6759 (tt0) REVERT: B 361 SER cc_start: 0.7719 (t) cc_final: 0.7407 (p) REVERT: C 170 LYS cc_start: 0.8182 (mttp) cc_final: 0.7683 (mtmt) REVERT: C 234 MET cc_start: 0.6238 (mtp) cc_final: 0.5882 (mtt) REVERT: C 245 MET cc_start: 0.7151 (mtp) cc_final: 0.6867 (ttm) REVERT: C 250 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: C 251 TYR cc_start: 0.6926 (m-80) cc_final: 0.6415 (m-80) REVERT: D 35 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8206 (p) REVERT: D 82 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8094 (mmtm) REVERT: D 84 ASN cc_start: 0.7417 (t0) cc_final: 0.7143 (t0) REVERT: D 240 LYS cc_start: 0.7387 (mttm) cc_final: 0.7152 (mtpp) REVERT: D 248 MET cc_start: 0.8819 (mmm) cc_final: 0.8495 (mmm) REVERT: D 262 PHE cc_start: 0.7366 (t80) cc_final: 0.6398 (p90) REVERT: D 271 TYR cc_start: 0.7836 (m-80) cc_final: 0.7574 (m-80) REVERT: D 286 ASN cc_start: 0.7169 (t0) cc_final: 0.6801 (t0) REVERT: D 288 GLN cc_start: 0.6811 (tp-100) cc_final: 0.6379 (mp10) outliers start: 26 outliers final: 12 residues processed: 193 average time/residue: 0.2477 time to fit residues: 68.8283 Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 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 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 30 optimal weight: 0.3980 chunk 137 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 145 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.171564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129984 restraints weight = 13115.622| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.40 r_work: 0.3346 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12944 Z= 0.154 Angle : 0.717 14.615 17584 Z= 0.319 Chirality : 0.046 0.265 2044 Planarity : 0.005 0.059 2180 Dihedral : 12.461 132.641 2312 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 2.54 % Allowed : 9.25 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.21), residues: 1524 helix: 0.59 (0.21), residues: 600 sheet: -2.70 (0.26), residues: 304 loop : -2.16 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 353 HIS 0.004 0.001 HIS B 253 PHE 0.016 0.001 PHE C 337 TYR 0.019 0.001 TYR A 44 ARG 0.004 0.000 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01111 ( 16) link_NAG-ASN : angle 3.83729 ( 48) link_BETA1-4 : bond 0.01233 ( 16) link_BETA1-4 : angle 4.28234 ( 48) hydrogen bonds : bond 0.03465 ( 404) hydrogen bonds : angle 3.63382 ( 1188) SS BOND : bond 0.00101 ( 4) SS BOND : angle 0.21762 ( 8) covalent geometry : bond 0.00365 (12908) covalent geometry : angle 0.65260 (17480) *********************** 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 201 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7044 (mptt) cc_final: 0.6785 (mtmm) REVERT: A 170 LYS cc_start: 0.8229 (mttp) cc_final: 0.7702 (mtmt) REVERT: A 198 ARG cc_start: 0.7141 (ttt-90) cc_final: 0.6896 (tpt170) REVERT: A 234 MET cc_start: 0.6291 (mtp) cc_final: 0.5930 (mtt) REVERT: A 248 MET cc_start: 0.7961 (mmm) cc_final: 0.7761 (mmm) REVERT: B 82 LYS cc_start: 0.8584 (mmtp) cc_final: 0.8000 (mmtm) REVERT: B 85 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6756 (mp) REVERT: B 240 LYS cc_start: 0.7468 (mttm) cc_final: 0.7239 (mtpp) REVERT: B 262 PHE cc_start: 0.7453 (t80) cc_final: 0.6399 (p90) REVERT: B 271 TYR cc_start: 0.7979 (m-80) cc_final: 0.7386 (m-80) REVERT: B 288 GLN cc_start: 0.6818 (tp-100) cc_final: 0.6540 (mp10) REVERT: B 335 GLN cc_start: 0.7031 (tt0) cc_final: 0.6776 (tt0) REVERT: B 361 SER cc_start: 0.7814 (t) cc_final: 0.7476 (p) REVERT: C 170 LYS cc_start: 0.8259 (mttp) cc_final: 0.7746 (mtmt) REVERT: C 234 MET cc_start: 0.6261 (mtp) cc_final: 0.5863 (mtt) REVERT: C 250 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: C 251 TYR cc_start: 0.6961 (m-80) cc_final: 0.6454 (m-80) REVERT: C 294 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6541 (mm-30) REVERT: D 35 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8224 (m) REVERT: D 82 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8202 (mmtm) REVERT: D 137 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: D 240 LYS cc_start: 0.7457 (mttm) cc_final: 0.7240 (mtpp) REVERT: D 248 MET cc_start: 0.8941 (mmm) cc_final: 0.8566 (mmm) REVERT: D 262 PHE cc_start: 0.7490 (t80) cc_final: 0.6473 (p90) REVERT: D 271 TYR cc_start: 0.7968 (m-80) cc_final: 0.7672 (m-80) REVERT: D 288 GLN cc_start: 0.6745 (tp-100) cc_final: 0.6452 (mp10) REVERT: D 365 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7200 (mm-30) outliers start: 34 outliers final: 16 residues processed: 189 average time/residue: 0.2556 time to fit residues: 69.9706 Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 199 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL 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 113 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.170033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.127479 restraints weight = 13103.946| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.51 r_work: 0.3321 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12944 Z= 0.162 Angle : 0.710 15.258 17584 Z= 0.317 Chirality : 0.046 0.260 2044 Planarity : 0.005 0.063 2180 Dihedral : 11.403 126.803 2312 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.44 % Rotamer: Outliers : 1.87 % Allowed : 9.93 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1524 helix: 0.95 (0.22), residues: 600 sheet: -2.67 (0.26), residues: 312 loop : -2.04 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.004 0.001 HIS D 232 PHE 0.015 0.001 PHE C 337 TYR 0.014 0.001 TYR C 44 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01003 ( 16) link_NAG-ASN : angle 4.03446 ( 48) link_BETA1-4 : bond 0.01233 ( 16) link_BETA1-4 : angle 4.27294 ( 48) hydrogen bonds : bond 0.03400 ( 404) hydrogen bonds : angle 3.61793 ( 1188) SS BOND : bond 0.00085 ( 4) SS BOND : angle 0.19977 ( 8) covalent geometry : bond 0.00390 (12908) covalent geometry : angle 0.64165 (17480) *********************** 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 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7156 (mptt) cc_final: 0.6859 (mtmm) REVERT: A 170 LYS cc_start: 0.8281 (mttp) cc_final: 0.7747 (mtmt) REVERT: A 234 MET cc_start: 0.6428 (mtp) cc_final: 0.6019 (mtt) REVERT: A 294 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6452 (mm-30) REVERT: B 82 LYS cc_start: 0.8577 (mmtp) cc_final: 0.7948 (mmtm) REVERT: B 85 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6899 (mp) REVERT: B 240 LYS cc_start: 0.7392 (mttm) cc_final: 0.7138 (mtpp) REVERT: B 248 MET cc_start: 0.8933 (mmm) cc_final: 0.8621 (mmm) REVERT: B 262 PHE cc_start: 0.7645 (t80) cc_final: 0.6489 (p90) REVERT: B 271 TYR cc_start: 0.8018 (m-80) cc_final: 0.7554 (m-80) REVERT: B 335 GLN cc_start: 0.6953 (tt0) cc_final: 0.6712 (tt0) REVERT: B 361 SER cc_start: 0.7830 (t) cc_final: 0.7464 (p) REVERT: C 168 LYS cc_start: 0.7159 (mptt) cc_final: 0.6854 (mtmm) REVERT: C 170 LYS cc_start: 0.8249 (mttp) cc_final: 0.7731 (mtmt) REVERT: C 234 MET cc_start: 0.6385 (mtp) cc_final: 0.5970 (mtt) REVERT: C 251 TYR cc_start: 0.6977 (m-80) cc_final: 0.6402 (m-80) REVERT: C 294 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6542 (mm-30) REVERT: D 35 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8292 (m) REVERT: D 82 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8122 (mmtm) REVERT: D 240 LYS cc_start: 0.7368 (mttm) cc_final: 0.7147 (mtpp) REVERT: D 248 MET cc_start: 0.9074 (mmm) cc_final: 0.8467 (mmm) REVERT: D 262 PHE cc_start: 0.7675 (t80) cc_final: 0.6487 (p90) REVERT: D 348 ASN cc_start: 0.7770 (p0) cc_final: 0.7529 (p0) REVERT: D 365 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7245 (mm-30) outliers start: 25 outliers final: 16 residues processed: 172 average time/residue: 0.2439 time to fit residues: 60.5055 Evaluate side-chains 167 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 138 VAL 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 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 172 VAL Chi-restraints excluded: chain D residue 350 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 22 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 126 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.169419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127241 restraints weight = 13289.642| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.64 r_work: 0.3151 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12944 Z= 0.153 Angle : 0.685 13.915 17584 Z= 0.307 Chirality : 0.045 0.247 2044 Planarity : 0.005 0.066 2180 Dihedral : 10.443 126.709 2312 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 1.87 % Allowed : 10.82 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.22), residues: 1524 helix: 1.18 (0.22), residues: 600 sheet: -2.40 (0.27), residues: 304 loop : -1.98 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.004 0.001 HIS D 232 PHE 0.013 0.001 PHE C 337 TYR 0.022 0.001 TYR A 44 ARG 0.004 0.001 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00951 ( 16) link_NAG-ASN : angle 3.61897 ( 48) link_BETA1-4 : bond 0.01144 ( 16) link_BETA1-4 : angle 4.23204 ( 48) hydrogen bonds : bond 0.03223 ( 404) hydrogen bonds : angle 3.59076 ( 1188) SS BOND : bond 0.00044 ( 4) SS BOND : angle 0.11674 ( 8) covalent geometry : bond 0.00366 (12908) covalent geometry : angle 0.62182 (17480) *********************** 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 180 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7159 (mptt) cc_final: 0.6897 (mtmm) REVERT: A 170 LYS cc_start: 0.8200 (mttp) cc_final: 0.7646 (mtmt) REVERT: A 234 MET cc_start: 0.6473 (mtp) cc_final: 0.6037 (mtt) REVERT: A 248 MET cc_start: 0.8024 (mmm) cc_final: 0.7738 (mmm) REVERT: A 294 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6501 (mm-30) REVERT: B 82 LYS cc_start: 0.8533 (mmtp) cc_final: 0.7939 (mmtm) REVERT: B 85 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6769 (mp) REVERT: B 240 LYS cc_start: 0.7396 (mttm) cc_final: 0.7132 (mtpp) REVERT: B 248 MET cc_start: 0.9012 (mmm) cc_final: 0.8660 (mmm) REVERT: B 262 PHE cc_start: 0.7824 (t80) cc_final: 0.6459 (p90) REVERT: B 335 GLN cc_start: 0.6830 (tt0) cc_final: 0.6602 (tt0) REVERT: B 361 SER cc_start: 0.7753 (t) cc_final: 0.7344 (p) REVERT: C 168 LYS cc_start: 0.7299 (mptt) cc_final: 0.6890 (mtmm) REVERT: C 170 LYS cc_start: 0.8175 (mttp) cc_final: 0.7644 (mtmt) REVERT: C 234 MET cc_start: 0.6403 (mtp) cc_final: 0.5961 (mtt) REVERT: C 251 TYR cc_start: 0.6999 (m-80) cc_final: 0.6479 (m-80) REVERT: C 294 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6596 (mm-30) REVERT: D 35 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8348 (m) REVERT: D 82 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8052 (mmtm) REVERT: D 240 LYS cc_start: 0.7411 (mttm) cc_final: 0.7188 (mtpp) REVERT: D 262 PHE cc_start: 0.7843 (t80) cc_final: 0.6438 (p90) REVERT: D 315 PHE cc_start: 0.6756 (p90) cc_final: 0.4922 (m-80) REVERT: D 348 ASN cc_start: 0.7700 (p0) cc_final: 0.7490 (p0) REVERT: D 365 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7195 (mm-30) outliers start: 25 outliers final: 16 residues processed: 168 average time/residue: 0.2518 time to fit residues: 61.3066 Evaluate side-chains 168 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 B residue 85 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 234 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 D residue 35 VAL Chi-restraints excluded: chain D residue 85 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 378 ASN Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 143 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.167520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125679 restraints weight = 13114.289| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.46 r_work: 0.3209 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12944 Z= 0.172 Angle : 0.690 13.187 17584 Z= 0.310 Chirality : 0.046 0.254 2044 Planarity : 0.005 0.068 2180 Dihedral : 10.086 126.064 2312 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 2.01 % Allowed : 11.04 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1524 helix: 1.17 (0.22), residues: 600 sheet: -2.46 (0.26), residues: 312 loop : -1.90 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.004 0.001 HIS D 232 PHE 0.011 0.001 PHE B 359 TYR 0.017 0.001 TYR A 44 ARG 0.008 0.000 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00921 ( 16) link_NAG-ASN : angle 3.54383 ( 48) link_BETA1-4 : bond 0.01091 ( 16) link_BETA1-4 : angle 4.19524 ( 48) hydrogen bonds : bond 0.03303 ( 404) hydrogen bonds : angle 3.63437 ( 1188) SS BOND : bond 0.00030 ( 4) SS BOND : angle 0.19476 ( 8) covalent geometry : bond 0.00422 (12908) covalent geometry : angle 0.62938 (17480) *********************** 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 179 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7264 (mptt) cc_final: 0.6865 (mtmm) REVERT: A 170 LYS cc_start: 0.8213 (mttp) cc_final: 0.7689 (mtmt) REVERT: A 234 MET cc_start: 0.6586 (mtp) cc_final: 0.6124 (mtt) REVERT: A 248 MET cc_start: 0.7983 (mmm) cc_final: 0.7625 (mmm) REVERT: A 294 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6557 (mm-30) REVERT: B 82 LYS cc_start: 0.8510 (mmtp) cc_final: 0.7873 (mmtm) REVERT: B 85 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6929 (mp) REVERT: B 240 LYS cc_start: 0.7288 (mttm) cc_final: 0.7025 (mtpp) REVERT: B 248 MET cc_start: 0.9006 (mmm) cc_final: 0.8591 (mmm) REVERT: B 262 PHE cc_start: 0.7933 (t80) cc_final: 0.6497 (p90) REVERT: B 335 GLN cc_start: 0.6792 (tt0) cc_final: 0.6583 (tt0) REVERT: B 361 SER cc_start: 0.7710 (t) cc_final: 0.7266 (p) REVERT: C 168 LYS cc_start: 0.7279 (mptt) cc_final: 0.6849 (mtmm) REVERT: C 170 LYS cc_start: 0.8186 (mttp) cc_final: 0.7614 (mtmt) REVERT: C 234 MET cc_start: 0.6531 (mtp) cc_final: 0.6045 (mtt) REVERT: C 251 TYR cc_start: 0.6950 (m-80) cc_final: 0.6341 (m-80) REVERT: C 294 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6637 (mm-30) REVERT: D 82 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8045 (mmtm) REVERT: D 240 LYS cc_start: 0.7268 (mttm) cc_final: 0.7039 (mtpp) REVERT: D 262 PHE cc_start: 0.7963 (t80) cc_final: 0.6457 (p90) REVERT: D 315 PHE cc_start: 0.6695 (p90) cc_final: 0.4859 (m-80) REVERT: D 365 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7122 (mm-30) outliers start: 27 outliers final: 20 residues processed: 171 average time/residue: 0.2405 time to fit residues: 59.8329 Evaluate side-chains 167 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 245 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 340 MET Chi-restraints excluded: chain D residue 85 LEU 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 257 THR Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 0.4980 chunk 122 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 61 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 141 optimal weight: 0.0470 chunk 139 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.170169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128777 restraints weight = 13099.331| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.45 r_work: 0.3181 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12944 Z= 0.118 Angle : 0.657 13.100 17584 Z= 0.295 Chirality : 0.044 0.239 2044 Planarity : 0.005 0.063 2180 Dihedral : 9.565 125.669 2312 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer: Outliers : 1.79 % Allowed : 11.64 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1524 helix: 1.49 (0.22), residues: 600 sheet: -2.21 (0.27), residues: 304 loop : -1.87 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.004 0.001 HIS A 253 PHE 0.010 0.001 PHE A 337 TYR 0.022 0.001 TYR D 269 ARG 0.004 0.000 ARG C 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00879 ( 16) link_NAG-ASN : angle 3.40371 ( 48) link_BETA1-4 : bond 0.01098 ( 16) link_BETA1-4 : angle 4.15348 ( 48) hydrogen bonds : bond 0.02995 ( 404) hydrogen bonds : angle 3.54507 ( 1188) SS BOND : bond 0.00076 ( 4) SS BOND : angle 0.20244 ( 8) covalent geometry : bond 0.00269 (12908) covalent geometry : angle 0.59599 (17480) *********************** 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 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7323 (mptt) cc_final: 0.6905 (mtmm) REVERT: A 170 LYS cc_start: 0.8190 (mttp) cc_final: 0.7630 (mtmt) REVERT: A 234 MET cc_start: 0.6461 (mtp) cc_final: 0.6006 (mtt) REVERT: A 248 MET cc_start: 0.7945 (mmm) cc_final: 0.7617 (mmm) REVERT: A 294 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6595 (mm-30) REVERT: A 337 PHE cc_start: 0.7383 (t80) cc_final: 0.7177 (t80) REVERT: B 82 LYS cc_start: 0.8429 (mmtp) cc_final: 0.7857 (mmtm) REVERT: B 171 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7268 (m) REVERT: B 240 LYS cc_start: 0.7316 (mttm) cc_final: 0.7065 (mtpp) REVERT: B 248 MET cc_start: 0.8997 (mmm) cc_final: 0.8626 (mmm) REVERT: B 262 PHE cc_start: 0.7999 (t80) cc_final: 0.6490 (p90) REVERT: B 294 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6957 (mm-30) REVERT: B 335 GLN cc_start: 0.6855 (tt0) cc_final: 0.6622 (tt0) REVERT: B 361 SER cc_start: 0.7700 (t) cc_final: 0.7240 (p) REVERT: C 168 LYS cc_start: 0.7263 (mptt) cc_final: 0.6824 (mtmm) REVERT: C 170 LYS cc_start: 0.8183 (mttp) cc_final: 0.7626 (mtmt) REVERT: C 234 MET cc_start: 0.6425 (mtp) cc_final: 0.5963 (mtt) REVERT: C 251 TYR cc_start: 0.6881 (m-80) cc_final: 0.6309 (m-80) REVERT: C 267 GLU cc_start: 0.7864 (mp0) cc_final: 0.7379 (mm-30) REVERT: C 294 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6655 (mm-30) REVERT: D 82 LYS cc_start: 0.8617 (mmtp) cc_final: 0.8011 (mmtm) REVERT: D 240 LYS cc_start: 0.7295 (mttm) cc_final: 0.7085 (mtpp) REVERT: D 262 PHE cc_start: 0.8013 (t80) cc_final: 0.6452 (p90) REVERT: D 315 PHE cc_start: 0.6711 (p90) cc_final: 0.4853 (m-80) REVERT: D 365 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7201 (mm-30) outliers start: 24 outliers final: 18 residues processed: 174 average time/residue: 0.2505 time to fit residues: 63.4256 Evaluate side-chains 173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 245 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 340 MET Chi-restraints excluded: chain D residue 85 LEU 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 378 ASN Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 0.7980 chunk 95 optimal weight: 0.0070 chunk 22 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.0010 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.171301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130145 restraints weight = 13112.560| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.41 r_work: 0.3346 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12944 Z= 0.113 Angle : 0.640 12.889 17584 Z= 0.288 Chirality : 0.043 0.233 2044 Planarity : 0.004 0.060 2180 Dihedral : 8.984 125.220 2312 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer: Outliers : 1.42 % Allowed : 12.31 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1524 helix: 1.65 (0.22), residues: 600 sheet: -2.11 (0.27), residues: 312 loop : -1.78 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 353 HIS 0.004 0.001 HIS A 253 PHE 0.009 0.001 PHE A 337 TYR 0.017 0.001 TYR D 269 ARG 0.003 0.000 ARG C 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 16) link_NAG-ASN : angle 3.30171 ( 48) link_BETA1-4 : bond 0.01071 ( 16) link_BETA1-4 : angle 4.06606 ( 48) hydrogen bonds : bond 0.02888 ( 404) hydrogen bonds : angle 3.49374 ( 1188) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.23802 ( 8) covalent geometry : bond 0.00256 (12908) covalent geometry : angle 0.57987 (17480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7349 (mptt) cc_final: 0.6950 (mtmm) REVERT: A 170 LYS cc_start: 0.8268 (mttp) cc_final: 0.7783 (mtmt) REVERT: A 234 MET cc_start: 0.6566 (mtp) cc_final: 0.6136 (mtt) REVERT: A 248 MET cc_start: 0.7880 (mmm) cc_final: 0.7545 (mmm) REVERT: A 294 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6659 (mm-30) REVERT: B 82 LYS cc_start: 0.8443 (mmtp) cc_final: 0.7890 (mmtm) REVERT: B 218 MET cc_start: 0.8899 (mtm) cc_final: 0.8697 (mtp) REVERT: B 240 LYS cc_start: 0.7428 (mttm) cc_final: 0.7222 (mtpp) REVERT: B 241 GLN cc_start: 0.8203 (mt0) cc_final: 0.7812 (mt0) REVERT: B 248 MET cc_start: 0.8914 (mmm) cc_final: 0.8537 (mmm) REVERT: B 262 PHE cc_start: 0.8048 (t80) cc_final: 0.6571 (p90) REVERT: B 271 TYR cc_start: 0.8080 (m-80) cc_final: 0.7706 (m-80) REVERT: B 315 PHE cc_start: 0.6937 (p90) cc_final: 0.5135 (m-80) REVERT: B 335 GLN cc_start: 0.7028 (tt0) cc_final: 0.6780 (tt0) REVERT: B 361 SER cc_start: 0.7690 (t) cc_final: 0.7280 (p) REVERT: C 168 LYS cc_start: 0.7386 (mptt) cc_final: 0.6962 (mtmm) REVERT: C 170 LYS cc_start: 0.8239 (mttp) cc_final: 0.7742 (mtmt) REVERT: C 234 MET cc_start: 0.6578 (mtp) cc_final: 0.6131 (mtt) REVERT: C 251 TYR cc_start: 0.6910 (m-80) cc_final: 0.6340 (m-80) REVERT: C 267 GLU cc_start: 0.7974 (mp0) cc_final: 0.7467 (mm-30) REVERT: C 294 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6686 (mm-30) REVERT: D 82 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8096 (mmtm) REVERT: D 262 PHE cc_start: 0.8067 (t80) cc_final: 0.6579 (p90) REVERT: D 271 TYR cc_start: 0.8071 (m-80) cc_final: 0.7851 (m-80) REVERT: D 294 GLU cc_start: 0.7237 (mt-10) cc_final: 0.7014 (mm-30) REVERT: D 315 PHE cc_start: 0.6833 (p90) cc_final: 0.4999 (m-80) REVERT: D 339 GLN cc_start: 0.7708 (pm20) cc_final: 0.7499 (pm20) REVERT: D 365 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7286 (mm-30) outliers start: 19 outliers final: 17 residues processed: 177 average time/residue: 0.2408 time to fit residues: 61.9024 Evaluate side-chains 175 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 245 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 312 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 143 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.174503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131409 restraints weight = 13095.359| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.59 r_work: 0.3129 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12944 Z= 0.141 Angle : 0.657 12.673 17584 Z= 0.297 Chirality : 0.044 0.236 2044 Planarity : 0.005 0.062 2180 Dihedral : 8.726 124.922 2312 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.77 % Favored : 94.09 % Rotamer: Outliers : 1.87 % Allowed : 11.94 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1524 helix: 1.58 (0.22), residues: 600 sheet: -1.92 (0.27), residues: 304 loop : -1.76 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS A 253 PHE 0.035 0.001 PHE A 337 TYR 0.016 0.001 TYR A 44 ARG 0.004 0.000 ARG C 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00808 ( 16) link_NAG-ASN : angle 3.23802 ( 48) link_BETA1-4 : bond 0.01010 ( 16) link_BETA1-4 : angle 4.01655 ( 48) hydrogen bonds : bond 0.03061 ( 404) hydrogen bonds : angle 3.53292 ( 1188) SS BOND : bond 0.00081 ( 4) SS BOND : angle 0.34746 ( 8) covalent geometry : bond 0.00338 (12908) covalent geometry : angle 0.60124 (17480) ********************** 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 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7410 (mptt) cc_final: 0.6856 (mtmm) REVERT: A 170 LYS cc_start: 0.8244 (mttp) cc_final: 0.7676 (mtmt) REVERT: A 234 MET cc_start: 0.6598 (mtp) cc_final: 0.6350 (tpp) REVERT: A 248 MET cc_start: 0.7934 (mmm) cc_final: 0.7535 (mmm) REVERT: A 294 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6710 (mm-30) REVERT: A 337 PHE cc_start: 0.7252 (t80) cc_final: 0.6997 (t80) REVERT: B 82 LYS cc_start: 0.8440 (mmtp) cc_final: 0.7862 (mmtm) REVERT: B 171 THR cc_start: 0.7724 (OUTLIER) cc_final: 0.7494 (m) REVERT: B 240 LYS cc_start: 0.7436 (mttm) cc_final: 0.7210 (mtpp) REVERT: B 248 MET cc_start: 0.9009 (mmm) cc_final: 0.8673 (mmm) REVERT: B 262 PHE cc_start: 0.8150 (t80) cc_final: 0.6544 (p90) REVERT: B 271 TYR cc_start: 0.8077 (m-80) cc_final: 0.7724 (m-80) REVERT: B 315 PHE cc_start: 0.6940 (p90) cc_final: 0.5087 (m-80) REVERT: B 335 GLN cc_start: 0.6963 (tt0) cc_final: 0.6733 (tt0) REVERT: B 361 SER cc_start: 0.7672 (t) cc_final: 0.7235 (p) REVERT: C 168 LYS cc_start: 0.7427 (mptt) cc_final: 0.6872 (mtmm) REVERT: C 170 LYS cc_start: 0.8236 (mttp) cc_final: 0.7668 (mtmt) REVERT: C 234 MET cc_start: 0.6629 (mtp) cc_final: 0.6155 (mtt) REVERT: C 251 TYR cc_start: 0.6912 (m-80) cc_final: 0.6327 (m-80) REVERT: C 267 GLU cc_start: 0.8016 (mp0) cc_final: 0.7489 (mm-30) REVERT: C 294 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6776 (mm-30) REVERT: D 82 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8086 (mmtm) REVERT: D 262 PHE cc_start: 0.8157 (t80) cc_final: 0.6552 (p90) REVERT: D 294 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7015 (mm-30) REVERT: D 315 PHE cc_start: 0.6819 (p90) cc_final: 0.4920 (m-80) REVERT: D 365 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7266 (mm-30) outliers start: 25 outliers final: 21 residues processed: 174 average time/residue: 0.2442 time to fit residues: 61.7944 Evaluate side-chains 177 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 234 MET 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 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 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 Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 14 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.169636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126335 restraints weight = 13032.977| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.47 r_work: 0.3305 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12944 Z= 0.135 Angle : 0.657 12.507 17584 Z= 0.297 Chirality : 0.044 0.234 2044 Planarity : 0.005 0.062 2180 Dihedral : 8.489 124.547 2312 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.64 % Favored : 94.23 % Rotamer: Outliers : 1.72 % Allowed : 12.01 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1524 helix: 1.60 (0.22), residues: 600 sheet: -1.97 (0.27), residues: 312 loop : -1.74 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS B 253 PHE 0.025 0.001 PHE A 337 TYR 0.018 0.001 TYR B 86 ARG 0.004 0.000 ARG C 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 16) link_NAG-ASN : angle 3.10789 ( 48) link_BETA1-4 : bond 0.00991 ( 16) link_BETA1-4 : angle 4.03076 ( 48) hydrogen bonds : bond 0.02986 ( 404) hydrogen bonds : angle 3.53728 ( 1188) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.38679 ( 8) covalent geometry : bond 0.00321 (12908) covalent geometry : angle 0.60274 (17480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5793.76 seconds wall clock time: 101 minutes 32.33 seconds (6092.33 seconds total)