Starting phenix.real_space_refine on Wed Jun 11 10:54:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwr_29516/06_2025/8fwr_29516.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwr_29516/06_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_29516/06_2025/8fwr_29516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwr_29516/06_2025/8fwr_29516.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwr_29516/06_2025/8fwr_29516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwr_29516/06_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-5710/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: 8.55, per 1000 atoms: 0.68 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: 3.21 Conformation dependent library (CDL) restraints added in 1.5 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 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: 1.24 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: 3.29 Time building geometry restraints manager: 3.73 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.330 Find NCS groups from input model: 0.490 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- 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 : 1.547 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: 0.3062 time to fit residues: 134.1759 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 : 1.372 ------------------------------------------------------------------------------- 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: 0.7323 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 : 1.519 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8178 (mttp) cc_final: 0.7652 (mtmt) REVERT: A 234 MET cc_start: 0.6318 (mtp) cc_final: 0.5939 (mtt) REVERT: A 294 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6415 (mm-30) REVERT: A 312 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6337 (mp) REVERT: A 360 MET cc_start: 0.8160 (tpt) cc_final: 0.7875 (tpt) REVERT: B 35 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8128 (m) REVERT: B 82 LYS cc_start: 0.8637 (mmtp) cc_final: 0.8046 (mmtm) REVERT: B 84 ASN cc_start: 0.7843 (t0) cc_final: 0.7594 (t0) REVERT: B 240 LYS cc_start: 0.7599 (mttm) cc_final: 0.7339 (mtpp) REVERT: B 262 PHE cc_start: 0.7103 (t80) cc_final: 0.6433 (p90) REVERT: B 288 GLN cc_start: 0.6964 (tp-100) cc_final: 0.6449 (mp10) REVERT: B 312 LEU cc_start: 0.8006 (mt) cc_final: 0.7719 (mt) REVERT: B 361 SER cc_start: 0.7949 (t) cc_final: 0.7632 (p) REVERT: C 78 TYR cc_start: 0.7062 (p90) cc_final: 0.6653 (p90) REVERT: C 170 LYS cc_start: 0.8161 (mttp) cc_final: 0.7651 (mtmt) REVERT: C 234 MET cc_start: 0.6338 (mtp) cc_final: 0.5937 (mtt) REVERT: C 250 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: C 294 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6522 (mm-30) REVERT: C 312 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6332 (mp) REVERT: D 35 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8186 (p) REVERT: D 82 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8567 (mmtm) REVERT: D 137 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.7108 (mm-40) REVERT: D 240 LYS cc_start: 0.7575 (mttm) cc_final: 0.7287 (mtpp) REVERT: D 248 MET cc_start: 0.8728 (mmm) cc_final: 0.8479 (mmm) REVERT: D 262 PHE cc_start: 0.7269 (t80) cc_final: 0.6420 (p90) REVERT: D 271 TYR cc_start: 0.7865 (m-80) cc_final: 0.7617 (m-80) REVERT: D 286 ASN cc_start: 0.7267 (t0) cc_final: 0.6936 (t0) REVERT: D 288 GLN cc_start: 0.7023 (tp-100) cc_final: 0.6460 (mp10) REVERT: D 296 TRP cc_start: 0.7690 (t-100) cc_final: 0.7319 (t-100) REVERT: D 312 LEU cc_start: 0.7990 (mt) cc_final: 0.7702 (mt) outliers start: 23 outliers final: 8 residues processed: 214 average time/residue: 0.2743 time to fit residues: 82.4313 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 : 1.498 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.9990 chunk 128 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.173598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131793 restraints weight = 13253.323| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.42 r_work: 0.3380 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12944 Z= 0.134 Angle : 0.743 13.984 17584 Z= 0.331 Chirality : 0.048 0.306 2044 Planarity : 0.005 0.056 2180 Dihedral : 13.691 81.119 2312 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.09 % Allowed : 8.96 % Favored : 88.96 % 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: -2.53 (0.20), residues: 1524 helix: -0.20 (0.20), residues: 600 sheet: -2.92 (0.26), residues: 312 loop : -2.40 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.005 0.001 HIS C 253 PHE 0.016 0.001 PHE C 337 TYR 0.013 0.001 TYR A 146 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01091 ( 16) link_NAG-ASN : angle 3.64647 ( 48) link_BETA1-4 : bond 0.01282 ( 16) link_BETA1-4 : angle 4.50559 ( 48) hydrogen bonds : bond 0.03703 ( 404) hydrogen bonds : angle 3.72750 ( 1188) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.23209 ( 8) covalent geometry : bond 0.00295 (12908) covalent geometry : angle 0.68037 (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 202 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8240 (mttp) cc_final: 0.7746 (mtmt) REVERT: A 234 MET cc_start: 0.6324 (mtp) cc_final: 0.5972 (mtt) REVERT: A 360 MET cc_start: 0.7930 (tpt) cc_final: 0.7696 (tpt) REVERT: B 82 LYS cc_start: 0.8598 (mmtp) cc_final: 0.7992 (mmtm) REVERT: B 240 LYS cc_start: 0.7489 (mttm) cc_final: 0.7228 (mtpp) REVERT: B 248 MET cc_start: 0.8938 (mmm) cc_final: 0.8638 (mmm) REVERT: B 262 PHE cc_start: 0.7346 (t80) cc_final: 0.6401 (p90) REVERT: B 288 GLN cc_start: 0.6897 (tp-100) cc_final: 0.6517 (mp10) REVERT: B 335 GLN cc_start: 0.7015 (tt0) cc_final: 0.6799 (tt0) REVERT: B 361 SER cc_start: 0.7787 (t) cc_final: 0.7484 (p) REVERT: C 170 LYS cc_start: 0.8197 (mttp) cc_final: 0.7702 (mtmt) REVERT: C 234 MET cc_start: 0.6317 (mtp) cc_final: 0.5945 (mtt) REVERT: C 245 MET cc_start: 0.7193 (mtp) cc_final: 0.6898 (ttm) REVERT: C 250 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: C 251 TYR cc_start: 0.6980 (m-80) cc_final: 0.6475 (m-80) REVERT: C 294 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6469 (mm-30) REVERT: D 35 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8198 (p) REVERT: D 82 LYS cc_start: 0.8784 (mmtp) cc_final: 0.8176 (mmtm) REVERT: D 84 ASN cc_start: 0.7459 (t0) cc_final: 0.7208 (t0) REVERT: D 240 LYS cc_start: 0.7469 (mttm) cc_final: 0.7222 (mtpp) REVERT: D 248 MET cc_start: 0.8840 (mmm) cc_final: 0.8494 (mmm) REVERT: D 262 PHE cc_start: 0.7421 (t80) cc_final: 0.6455 (p90) REVERT: D 271 TYR cc_start: 0.7892 (m-80) cc_final: 0.7576 (m-80) REVERT: D 286 ASN cc_start: 0.7224 (t0) cc_final: 0.6858 (t0) REVERT: D 288 GLN cc_start: 0.6834 (tp-100) cc_final: 0.6399 (mp10) outliers start: 28 outliers final: 13 residues processed: 196 average time/residue: 0.2619 time to fit residues: 73.3659 Evaluate side-chains 176 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 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: 0.0010 chunk 137 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.171696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.130415 restraints weight = 13125.784| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.43 r_work: 0.3352 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3217 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= 0.141 Angle : 0.706 15.258 17584 Z= 0.313 Chirality : 0.045 0.260 2044 Planarity : 0.005 0.059 2180 Dihedral : 12.225 131.521 2312 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 2.31 % Allowed : 9.18 % Favored : 88.51 % 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: -1.81 (0.21), residues: 1524 helix: 0.60 (0.21), residues: 600 sheet: -2.68 (0.26), residues: 304 loop : -2.17 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 353 HIS 0.005 0.001 HIS C 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 0.01013 ( 16) link_NAG-ASN : angle 3.83361 ( 48) link_BETA1-4 : bond 0.01295 ( 16) link_BETA1-4 : angle 4.29753 ( 48) hydrogen bonds : bond 0.03371 ( 404) hydrogen bonds : angle 3.61114 ( 1188) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.22227 ( 8) covalent geometry : bond 0.00327 (12908) covalent geometry : angle 0.64017 (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 199 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7038 (mptt) cc_final: 0.6773 (mtmm) REVERT: A 170 LYS cc_start: 0.8217 (mttp) cc_final: 0.7699 (mtmt) REVERT: A 234 MET cc_start: 0.6275 (mtp) cc_final: 0.5922 (mtt) REVERT: A 248 MET cc_start: 0.8037 (mmm) cc_final: 0.7754 (mmm) REVERT: B 82 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8045 (mmtm) REVERT: B 85 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6694 (mp) REVERT: B 240 LYS cc_start: 0.7451 (mttm) cc_final: 0.7219 (mtpp) REVERT: B 262 PHE cc_start: 0.7423 (t80) cc_final: 0.6365 (p90) REVERT: B 271 TYR cc_start: 0.7979 (m-80) cc_final: 0.7392 (m-80) REVERT: B 288 GLN cc_start: 0.6797 (tp-100) cc_final: 0.6541 (mp10) REVERT: B 335 GLN cc_start: 0.6975 (tt0) cc_final: 0.6744 (tt0) REVERT: B 361 SER cc_start: 0.7793 (t) cc_final: 0.7454 (p) REVERT: C 168 LYS cc_start: 0.7102 (mptt) cc_final: 0.6767 (mtmm) REVERT: C 170 LYS cc_start: 0.8241 (mttp) cc_final: 0.7752 (mtmt) REVERT: C 234 MET cc_start: 0.6215 (mtp) cc_final: 0.5825 (mtt) REVERT: C 251 TYR cc_start: 0.6976 (m-80) cc_final: 0.6434 (m-80) REVERT: C 294 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6564 (mm-30) REVERT: D 35 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8232 (m) REVERT: D 82 LYS cc_start: 0.8775 (mmtp) cc_final: 0.8180 (mmtm) REVERT: D 137 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: D 240 LYS cc_start: 0.7429 (mttm) cc_final: 0.7216 (mtpp) REVERT: D 248 MET cc_start: 0.8935 (mmm) cc_final: 0.8574 (mmm) REVERT: D 262 PHE cc_start: 0.7512 (t80) cc_final: 0.6471 (p90) REVERT: D 271 TYR cc_start: 0.7930 (m-80) cc_final: 0.7638 (m-80) REVERT: D 288 GLN cc_start: 0.6714 (tp-100) cc_final: 0.6439 (mp10) REVERT: D 365 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7172 (mm-30) outliers start: 31 outliers final: 14 residues processed: 188 average time/residue: 0.2595 time to fit residues: 70.3298 Evaluate side-chains 173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 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 199 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 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: 1.9990 chunk 38 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 86 optimal weight: 0.0570 chunk 139 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.170500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128513 restraints weight = 13131.567| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.43 r_work: 0.3320 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3464 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= 0.151 Angle : 0.700 14.988 17584 Z= 0.312 Chirality : 0.045 0.252 2044 Planarity : 0.005 0.062 2180 Dihedral : 11.321 126.896 2312 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 1.64 % Allowed : 9.78 % Favored : 88.58 % 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: -1.49 (0.22), residues: 1524 helix: 0.99 (0.22), residues: 600 sheet: -2.65 (0.26), residues: 312 loop : -2.05 (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 0.014 0.001 PHE C 337 TYR 0.015 0.001 TYR C 44 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01002 ( 16) link_NAG-ASN : angle 3.99443 ( 48) link_BETA1-4 : bond 0.01194 ( 16) link_BETA1-4 : angle 4.26617 ( 48) hydrogen bonds : bond 0.03342 ( 404) hydrogen bonds : angle 3.59003 ( 1188) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.19048 ( 8) covalent geometry : bond 0.00361 (12908) covalent geometry : angle 0.63212 (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 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7134 (mptt) cc_final: 0.6859 (mtmm) REVERT: A 170 LYS cc_start: 0.8290 (mttp) cc_final: 0.7766 (mtmt) REVERT: A 198 ARG cc_start: 0.7217 (ttt-90) cc_final: 0.6970 (tpt170) REVERT: A 234 MET cc_start: 0.6410 (mtp) cc_final: 0.6021 (mtt) REVERT: A 294 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6448 (mm-30) REVERT: A 340 MET cc_start: 0.7868 (tpp) cc_final: 0.7634 (mmt) REVERT: B 82 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8041 (mmtm) REVERT: B 85 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6857 (mp) REVERT: B 240 LYS cc_start: 0.7429 (mttm) cc_final: 0.7178 (mtpp) REVERT: B 248 MET cc_start: 0.8935 (mmm) cc_final: 0.8564 (mmm) REVERT: B 262 PHE cc_start: 0.7608 (t80) cc_final: 0.6471 (p90) REVERT: B 271 TYR cc_start: 0.8013 (m-80) cc_final: 0.7533 (m-80) REVERT: B 335 GLN cc_start: 0.6929 (tt0) cc_final: 0.6701 (tt0) REVERT: B 361 SER cc_start: 0.7796 (t) cc_final: 0.7449 (p) REVERT: C 168 LYS cc_start: 0.7161 (mptt) cc_final: 0.6858 (mtmm) REVERT: C 170 LYS cc_start: 0.8264 (mttp) cc_final: 0.7754 (mtmt) REVERT: C 234 MET cc_start: 0.6366 (mtp) cc_final: 0.5969 (mtt) REVERT: C 251 TYR cc_start: 0.6969 (m-80) cc_final: 0.6401 (m-80) REVERT: C 294 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6536 (mm-30) REVERT: D 35 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8283 (m) REVERT: D 82 LYS cc_start: 0.8743 (mmtp) cc_final: 0.8090 (mmtm) REVERT: D 240 LYS cc_start: 0.7364 (mttm) cc_final: 0.7152 (mtpp) REVERT: D 248 MET cc_start: 0.9007 (mmm) cc_final: 0.8545 (mmm) REVERT: D 262 PHE cc_start: 0.7645 (t80) cc_final: 0.6462 (p90) REVERT: D 271 TYR cc_start: 0.7964 (m-80) cc_final: 0.7716 (m-80) REVERT: D 315 PHE cc_start: 0.6849 (p90) cc_final: 0.5046 (m-80) REVERT: D 348 ASN cc_start: 0.7778 (p0) cc_final: 0.7531 (p0) REVERT: D 365 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7258 (mm-30) outliers start: 22 outliers final: 15 residues processed: 175 average time/residue: 0.2636 time to fit residues: 65.7761 Evaluate side-chains 168 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 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: 0.0270 chunk 41 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.170854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128468 restraints weight = 13186.405| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.51 r_work: 0.3174 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12944 Z= 0.133 Angle : 0.669 14.166 17584 Z= 0.298 Chirality : 0.044 0.240 2044 Planarity : 0.005 0.063 2180 Dihedral : 10.473 126.713 2312 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.45 % Favored : 94.42 % Rotamer: Outliers : 1.64 % Allowed : 10.45 % Favored : 87.91 % 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: -1.19 (0.22), residues: 1524 helix: 1.26 (0.22), residues: 600 sheet: -2.39 (0.26), residues: 304 loop : -1.98 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS A 253 PHE 0.010 0.001 PHE C 337 TYR 0.015 0.001 TYR A 44 ARG 0.003 0.000 ARG A 300 Details of bonding type rmsd link_NAG-ASN : bond 0.00931 ( 16) link_NAG-ASN : angle 3.67486 ( 48) link_BETA1-4 : bond 0.01165 ( 16) link_BETA1-4 : angle 4.22678 ( 48) hydrogen bonds : bond 0.03130 ( 404) hydrogen bonds : angle 3.53631 ( 1188) SS BOND : bond 0.00066 ( 4) SS BOND : angle 0.15292 ( 8) covalent geometry : bond 0.00311 (12908) covalent geometry : angle 0.60384 (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 176 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7054 (mptt) cc_final: 0.6730 (mtmm) REVERT: A 170 LYS cc_start: 0.8176 (mttp) cc_final: 0.7599 (mtmt) REVERT: A 198 ARG cc_start: 0.7104 (ttt-90) cc_final: 0.5465 (ttp-170) REVERT: A 234 MET cc_start: 0.6307 (mtp) cc_final: 0.5904 (mtt) REVERT: A 248 MET cc_start: 0.8096 (mmm) cc_final: 0.7766 (mmm) REVERT: A 294 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6448 (mm-30) REVERT: A 340 MET cc_start: 0.7849 (tpp) cc_final: 0.7640 (mmt) REVERT: B 82 LYS cc_start: 0.8510 (mmtp) cc_final: 0.7885 (mmtm) REVERT: B 85 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6737 (mp) REVERT: B 240 LYS cc_start: 0.7247 (mttm) cc_final: 0.7016 (mtpp) REVERT: B 248 MET cc_start: 0.9019 (mmm) cc_final: 0.8632 (mmm) REVERT: B 262 PHE cc_start: 0.7657 (t80) cc_final: 0.6350 (p90) REVERT: B 271 TYR cc_start: 0.7869 (m-80) cc_final: 0.7452 (m-80) REVERT: B 335 GLN cc_start: 0.6735 (tt0) cc_final: 0.6525 (tt0) REVERT: B 361 SER cc_start: 0.7672 (t) cc_final: 0.7225 (p) REVERT: C 168 LYS cc_start: 0.7117 (mptt) cc_final: 0.6752 (mtmm) REVERT: C 170 LYS cc_start: 0.8164 (mttp) cc_final: 0.7598 (mtmt) REVERT: C 234 MET cc_start: 0.6285 (mtp) cc_final: 0.5864 (mtt) REVERT: C 251 TYR cc_start: 0.6989 (m-80) cc_final: 0.6477 (m-80) REVERT: C 294 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6555 (mm-30) REVERT: D 35 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8325 (m) REVERT: D 82 LYS cc_start: 0.8603 (mmtp) cc_final: 0.7942 (mmtm) REVERT: D 240 LYS cc_start: 0.7189 (mttm) cc_final: 0.6984 (mtpp) REVERT: D 262 PHE cc_start: 0.7779 (t80) cc_final: 0.6367 (p90) REVERT: D 271 TYR cc_start: 0.7845 (m-80) cc_final: 0.7625 (m-80) REVERT: D 348 ASN cc_start: 0.7690 (p0) cc_final: 0.7453 (p0) REVERT: D 365 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7184 (mm-30) outliers start: 22 outliers final: 13 residues processed: 166 average time/residue: 0.2550 time to fit residues: 61.2288 Evaluate side-chains 163 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 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 70 LEU Chi-restraints excluded: chain C residue 77 THR 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 350 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 143 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.170005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127616 restraints weight = 13105.972| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.56 r_work: 0.3169 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12944 Z= 0.144 Angle : 0.672 13.455 17584 Z= 0.300 Chirality : 0.045 0.246 2044 Planarity : 0.005 0.064 2180 Dihedral : 9.968 126.155 2312 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.63 % Favored : 93.24 % Rotamer: Outliers : 1.72 % Allowed : 11.19 % Favored : 87.09 % 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: -1.08 (0.22), residues: 1524 helix: 1.36 (0.22), residues: 600 sheet: -2.39 (0.26), residues: 312 loop : -1.88 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS D 232 PHE 0.010 0.001 PHE A 359 TYR 0.015 0.001 TYR A 44 ARG 0.003 0.000 ARG C 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00886 ( 16) link_NAG-ASN : angle 3.55611 ( 48) link_BETA1-4 : bond 0.01108 ( 16) link_BETA1-4 : angle 4.15557 ( 48) hydrogen bonds : bond 0.03136 ( 404) hydrogen bonds : angle 3.55451 ( 1188) SS BOND : bond 0.00052 ( 4) SS BOND : angle 0.23118 ( 8) covalent geometry : bond 0.00345 (12908) covalent geometry : angle 0.61041 (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 176 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7125 (mptt) cc_final: 0.6815 (mtmm) REVERT: A 170 LYS cc_start: 0.8230 (mttp) cc_final: 0.7690 (mtmt) REVERT: A 234 MET cc_start: 0.6475 (mtp) cc_final: 0.6041 (mtt) REVERT: A 248 MET cc_start: 0.8075 (mmm) cc_final: 0.7688 (mmm) REVERT: A 294 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6506 (mm-30) REVERT: A 340 MET cc_start: 0.7895 (tpp) cc_final: 0.7627 (mmt) REVERT: B 82 LYS cc_start: 0.8554 (mmtp) cc_final: 0.7959 (mmtm) REVERT: B 85 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6922 (mp) REVERT: B 240 LYS cc_start: 0.7358 (mttm) cc_final: 0.7111 (mtpp) REVERT: B 248 MET cc_start: 0.9033 (mmm) cc_final: 0.8629 (mmm) REVERT: B 262 PHE cc_start: 0.7831 (t80) cc_final: 0.6480 (p90) REVERT: B 271 TYR cc_start: 0.7997 (m-80) cc_final: 0.7619 (m-80) REVERT: B 335 GLN cc_start: 0.6817 (tt0) cc_final: 0.6604 (tt0) REVERT: B 361 SER cc_start: 0.7786 (t) cc_final: 0.7352 (p) REVERT: C 168 LYS cc_start: 0.7320 (mptt) cc_final: 0.6915 (mtmm) REVERT: C 170 LYS cc_start: 0.8210 (mttp) cc_final: 0.7666 (mtmt) REVERT: C 234 MET cc_start: 0.6423 (mtp) cc_final: 0.5986 (mtt) REVERT: C 251 TYR cc_start: 0.6991 (m-80) cc_final: 0.6441 (m-80) REVERT: C 294 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6584 (mm-30) REVERT: D 35 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8319 (m) REVERT: D 82 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8032 (mmtm) REVERT: D 240 LYS cc_start: 0.7354 (mttm) cc_final: 0.7142 (mtpp) REVERT: D 262 PHE cc_start: 0.7917 (t80) cc_final: 0.6456 (p90) REVERT: D 315 PHE cc_start: 0.6835 (p90) cc_final: 0.4946 (m-80) REVERT: D 348 ASN cc_start: 0.7675 (p0) cc_final: 0.7468 (p0) REVERT: D 365 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7185 (mm-30) outliers start: 23 outliers final: 17 residues processed: 170 average time/residue: 0.3195 time to fit residues: 78.9285 Evaluate side-chains 169 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 2.668 ------------------------------------------------------------------------------- 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 101 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 61 optimal weight: 0.0000 chunk 71 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.170659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.128281 restraints weight = 13175.610| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.56 r_work: 0.3182 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12944 Z= 0.128 Angle : 0.659 13.054 17584 Z= 0.295 Chirality : 0.044 0.237 2044 Planarity : 0.005 0.061 2180 Dihedral : 9.523 125.669 2312 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.51 % Favored : 94.36 % Rotamer: Outliers : 2.24 % Allowed : 11.49 % 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: -0.90 (0.22), residues: 1524 helix: 1.49 (0.22), residues: 600 sheet: -2.17 (0.27), residues: 304 loop : -1.86 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS A 253 PHE 0.008 0.001 PHE A 359 TYR 0.016 0.001 TYR A 44 ARG 0.012 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00908 ( 16) link_NAG-ASN : angle 3.44416 ( 48) link_BETA1-4 : bond 0.01102 ( 16) link_BETA1-4 : angle 4.11962 ( 48) hydrogen bonds : bond 0.03023 ( 404) hydrogen bonds : angle 3.52114 ( 1188) SS BOND : bond 0.00043 ( 4) SS BOND : angle 0.16447 ( 8) covalent geometry : bond 0.00298 (12908) covalent geometry : angle 0.59849 (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 190 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7266 (mptt) cc_final: 0.6854 (mtmm) REVERT: A 170 LYS cc_start: 0.8193 (mttp) cc_final: 0.7611 (mtmt) REVERT: A 234 MET cc_start: 0.6396 (mtp) cc_final: 0.5959 (mtt) REVERT: A 248 MET cc_start: 0.8056 (mmm) cc_final: 0.7669 (mmm) REVERT: A 294 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6504 (mm-30) REVERT: B 82 LYS cc_start: 0.8479 (mmtp) cc_final: 0.7882 (mmtm) REVERT: B 85 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6784 (mp) REVERT: B 240 LYS cc_start: 0.7278 (mttm) cc_final: 0.7043 (mtpp) REVERT: B 248 MET cc_start: 0.9037 (mmm) cc_final: 0.8637 (mmm) REVERT: B 262 PHE cc_start: 0.7895 (t80) cc_final: 0.6453 (p90) REVERT: B 271 TYR cc_start: 0.7887 (m-80) cc_final: 0.7494 (m-80) REVERT: B 335 GLN cc_start: 0.6777 (tt0) cc_final: 0.6571 (tt0) REVERT: B 361 SER cc_start: 0.7566 (t) cc_final: 0.7105 (p) REVERT: C 168 LYS cc_start: 0.7223 (mptt) cc_final: 0.6801 (mtmm) REVERT: C 170 LYS cc_start: 0.8164 (mttp) cc_final: 0.7611 (mtmt) REVERT: C 234 MET cc_start: 0.6366 (mtp) cc_final: 0.5912 (mtt) REVERT: C 251 TYR cc_start: 0.6861 (m-80) cc_final: 0.6283 (m-80) REVERT: C 294 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6629 (mm-30) REVERT: D 35 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8369 (m) REVERT: D 82 LYS cc_start: 0.8592 (mmtp) cc_final: 0.7956 (mmtm) REVERT: D 240 LYS cc_start: 0.7190 (mttm) cc_final: 0.6985 (mtpp) REVERT: D 262 PHE cc_start: 0.7953 (t80) cc_final: 0.6424 (p90) REVERT: D 315 PHE cc_start: 0.6802 (p90) cc_final: 0.4960 (m-80) REVERT: D 365 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7154 (mm-30) outliers start: 30 outliers final: 19 residues processed: 181 average time/residue: 0.2467 time to fit residues: 64.4769 Evaluate side-chains 175 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 101 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 0.0170 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.169913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.128267 restraints weight = 13093.842| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.52 r_work: 0.3170 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12944 Z= 0.134 Angle : 0.655 12.883 17584 Z= 0.295 Chirality : 0.044 0.238 2044 Planarity : 0.005 0.063 2180 Dihedral : 9.154 125.355 2312 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 2.01 % Allowed : 11.49 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (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: -0.84 (0.22), residues: 1524 helix: 1.52 (0.22), residues: 600 sheet: -2.11 (0.27), residues: 304 loop : -1.81 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.003 0.001 HIS D 232 PHE 0.012 0.001 PHE C 337 TYR 0.022 0.001 TYR D 269 ARG 0.012 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 16) link_NAG-ASN : angle 3.35893 ( 48) link_BETA1-4 : bond 0.01050 ( 16) link_BETA1-4 : angle 4.06326 ( 48) hydrogen bonds : bond 0.03043 ( 404) hydrogen bonds : angle 3.54507 ( 1188) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.22475 ( 8) covalent geometry : bond 0.00317 (12908) covalent geometry : angle 0.59635 (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 186 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7267 (mptt) cc_final: 0.6843 (mtmm) REVERT: A 170 LYS cc_start: 0.8187 (mttp) cc_final: 0.7647 (mtmt) REVERT: A 234 MET cc_start: 0.6526 (mtp) cc_final: 0.6066 (mtt) REVERT: A 248 MET cc_start: 0.8060 (mmm) cc_final: 0.7678 (mmm) REVERT: A 294 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6596 (mm-30) REVERT: B 82 LYS cc_start: 0.8452 (mmtp) cc_final: 0.7827 (mmtm) REVERT: B 85 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6940 (mp) REVERT: B 240 LYS cc_start: 0.7368 (mttm) cc_final: 0.7149 (mtpp) REVERT: B 262 PHE cc_start: 0.8015 (t80) cc_final: 0.6480 (p90) REVERT: B 271 TYR cc_start: 0.7953 (m-80) cc_final: 0.7559 (m-80) REVERT: B 294 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7037 (mm-30) REVERT: B 315 PHE cc_start: 0.6881 (p90) cc_final: 0.5044 (m-80) REVERT: B 335 GLN cc_start: 0.6834 (tt0) cc_final: 0.6619 (tt0) REVERT: B 361 SER cc_start: 0.7636 (t) cc_final: 0.7178 (p) REVERT: C 168 LYS cc_start: 0.7304 (mptt) cc_final: 0.6869 (mtmm) REVERT: C 170 LYS cc_start: 0.8201 (mttp) cc_final: 0.7636 (mtmt) REVERT: C 234 MET cc_start: 0.6531 (mtp) cc_final: 0.6062 (mtt) REVERT: C 251 TYR cc_start: 0.6867 (m-80) cc_final: 0.6317 (m-80) REVERT: C 294 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6678 (mm-30) REVERT: D 35 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8400 (m) REVERT: D 82 LYS cc_start: 0.8586 (mmtp) cc_final: 0.7997 (mmtm) REVERT: D 262 PHE cc_start: 0.8037 (t80) cc_final: 0.6487 (p90) REVERT: D 271 TYR cc_start: 0.7959 (m-80) cc_final: 0.7738 (m-80) REVERT: D 294 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6938 (mm-30) REVERT: D 315 PHE cc_start: 0.6842 (p90) cc_final: 0.5016 (m-80) REVERT: D 365 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7223 (mm-30) outliers start: 27 outliers final: 22 residues processed: 177 average time/residue: 0.3035 time to fit residues: 78.0787 Evaluate side-chains 178 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 312 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.172030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128919 restraints weight = 13155.383| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.63 r_work: 0.3113 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12944 Z= 0.155 Angle : 0.671 12.712 17584 Z= 0.304 Chirality : 0.045 0.243 2044 Planarity : 0.005 0.065 2180 Dihedral : 8.891 125.016 2312 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.58 % Favored : 94.29 % Rotamer: Outliers : 1.72 % Allowed : 12.09 % 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: -0.91 (0.22), residues: 1524 helix: 1.44 (0.22), residues: 600 sheet: -2.21 (0.27), residues: 312 loop : -1.76 (0.25), 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 0.015 0.001 PHE A 337 TYR 0.016 0.001 TYR A 44 ARG 0.011 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00880 ( 16) link_NAG-ASN : angle 3.27641 ( 48) link_BETA1-4 : bond 0.00986 ( 16) link_BETA1-4 : angle 4.02110 ( 48) hydrogen bonds : bond 0.03169 ( 404) hydrogen bonds : angle 3.60261 ( 1188) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.33445 ( 8) covalent geometry : bond 0.00376 (12908) covalent geometry : angle 0.61526 (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 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7309 (mptt) cc_final: 0.6856 (mtmm) REVERT: A 170 LYS cc_start: 0.8244 (mttp) cc_final: 0.7663 (mtmt) REVERT: A 234 MET cc_start: 0.6620 (mtp) cc_final: 0.6407 (tpp) REVERT: A 248 MET cc_start: 0.8086 (mmm) cc_final: 0.7732 (mmm) REVERT: A 294 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6660 (mm-30) REVERT: A 396 GLU cc_start: 0.6493 (tt0) cc_final: 0.6247 (tp30) REVERT: B 82 LYS cc_start: 0.8561 (mmtp) cc_final: 0.7937 (mmtm) REVERT: B 85 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6998 (mp) REVERT: B 240 LYS cc_start: 0.7369 (mttm) cc_final: 0.7138 (mtpp) REVERT: B 248 MET cc_start: 0.8949 (mmm) cc_final: 0.8684 (mmm) REVERT: B 262 PHE cc_start: 0.8148 (t80) cc_final: 0.6528 (p90) REVERT: B 271 TYR cc_start: 0.8062 (m-80) cc_final: 0.7747 (m-80) REVERT: B 294 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7066 (mm-30) REVERT: B 315 PHE cc_start: 0.6906 (p90) cc_final: 0.5050 (m-80) REVERT: B 335 GLN cc_start: 0.6831 (tt0) cc_final: 0.6625 (tt0) REVERT: B 361 SER cc_start: 0.7672 (t) cc_final: 0.7199 (p) REVERT: C 168 LYS cc_start: 0.7371 (mptt) cc_final: 0.6821 (mtmm) REVERT: C 170 LYS cc_start: 0.8196 (mttp) cc_final: 0.7693 (mtmt) REVERT: C 234 MET cc_start: 0.6594 (mtp) cc_final: 0.6118 (mtt) REVERT: C 247 MET cc_start: 0.7917 (mmm) cc_final: 0.7712 (mmt) REVERT: C 251 TYR cc_start: 0.6842 (m-80) cc_final: 0.6296 (m-80) REVERT: C 294 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6774 (mm-30) REVERT: D 82 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8057 (mmtm) REVERT: D 262 PHE cc_start: 0.8150 (t80) cc_final: 0.6534 (p90) REVERT: D 294 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7016 (mm-30) REVERT: D 315 PHE cc_start: 0.6868 (p90) cc_final: 0.5048 (m-80) REVERT: D 365 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7232 (mm-30) REVERT: D 400 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7553 (mt-10) outliers start: 23 outliers final: 19 residues processed: 178 average time/residue: 0.3157 time to fit residues: 83.6333 Evaluate side-chains 176 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 101 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 257 THR 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 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 357 THR Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 97 optimal weight: 0.0060 chunk 90 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 124 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.0050 chunk 130 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.3768 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.170934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129194 restraints weight = 13085.330| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.40 r_work: 0.3321 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12944 Z= 0.113 Angle : 0.639 12.624 17584 Z= 0.290 Chirality : 0.043 0.233 2044 Planarity : 0.005 0.062 2180 Dihedral : 8.488 124.590 2312 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer: Outliers : 1.57 % Allowed : 12.24 % 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: -0.65 (0.22), residues: 1524 helix: 1.65 (0.22), residues: 600 sheet: -1.92 (0.27), residues: 304 loop : -1.73 (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 B 253 PHE 0.017 0.001 PHE A 337 TYR 0.016 0.001 TYR A 44 ARG 0.011 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00851 ( 16) link_NAG-ASN : angle 3.15302 ( 48) link_BETA1-4 : bond 0.01006 ( 16) link_BETA1-4 : angle 3.97481 ( 48) hydrogen bonds : bond 0.02900 ( 404) hydrogen bonds : angle 3.51435 ( 1188) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.16703 ( 8) covalent geometry : bond 0.00256 (12908) covalent geometry : angle 0.58282 (17480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6565.52 seconds wall clock time: 118 minutes 27.12 seconds (7107.12 seconds total)