Starting phenix.real_space_refine on Fri Jul 3 07:00:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fwr_29516/07_2026/8fwr_29516.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwr_29516/07_2026/8fwr_29516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fwr_29516/07_2026/8fwr_29516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwr_29516/07_2026/8fwr_29516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fwr_29516/07_2026/8fwr_29516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwr_29516/07_2026/8fwr_29516.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fwr_29516/07_2026/8fwr_29516.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fwr_29516/07_2026/8fwr_29516.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8028 2.51 5 N 2100 2.21 5 O 2432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12628 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 3.16, per 1000 atoms: 0.25 Number of scatterers: 12628 At special positions: 0 Unit cell: (165.575, 102.675, 84.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2432 8.00 N 2100 7.00 C 8028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.04 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.04 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A1001 " - " ASN A 275 " " NAG A1002 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG C1001 " - " ASN C 275 " " NAG C1002 " - " ASN C 412 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN A 67 " " NAG G 1 " - " ASN B 378 " " NAG H 1 " - " ASN B 67 " " NAG I 1 " - " ASN C 378 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN D 378 " " NAG L 1 " - " ASN D 67 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 597.9 milliseconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 20 sheets defined 40.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.951A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.918A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 removed outlier: 3.594A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.580A pdb=" N SER A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.952A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.919A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 removed outlier: 3.594A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU B 264 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.579A pdb=" N SER B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.951A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.919A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.593A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU C 264 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.580A pdb=" N SER C 297 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 364 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.951A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.919A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.594A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU D 264 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.579A pdb=" N SER D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 43 removed outlier: 6.398A pdb=" N HIS A 34 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 77 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 203 removed outlier: 7.865A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.562A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA6, first strand: chain 'B' and resid 34 through 43 removed outlier: 6.398A pdb=" N HIS B 34 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR B 77 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 removed outlier: 7.866A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.563A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AB2, first strand: chain 'C' and resid 34 through 43 removed outlier: 6.398A pdb=" N HIS C 34 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR C 77 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.866A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.562A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 373 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AB7, first strand: chain 'D' and resid 34 through 43 removed outlier: 6.399A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AB9, first strand: chain 'D' and resid 202 through 203 removed outlier: 7.866A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.563A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D 373 " --> pdb=" O GLY D 370 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 392 through 394 404 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.41 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 - 14.44: 6993 14.44 - 28.89: 387 28.89 - 43.33: 80 43.33 - 57.78: 8 57.78 - 72.22: 12 Dihedral angle restraints: 7480 sinusoidal: 3012 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 7477 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.150 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 10.143 72.222 4580 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.74 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.62 (0.14), residues: 1524 helix: -4.07 (0.09), residues: 580 sheet: -3.43 (0.25), residues: 304 loop : -3.33 (0.18), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 58 TYR 0.014 0.002 TYR B 146 PHE 0.023 0.003 PHE B 359 TRP 0.031 0.004 TRP D 353 HIS 0.009 0.002 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.35 (12908) covalent geometry : angle 1.09996 / 0.61 (17480) SS BOND : bond 0.00685 / 0.32 ( 4) SS BOND : angle 1.23300 / 0.67 ( 8) hydrogen bonds : bond 0.28813 / 19.45 ( 404) hydrogen bonds : angle 9.12031 / 6.48 ( 1188) link_BETA1-4 : bond 0.02464 / 1.80 ( 16) link_BETA1-4 : angle 7.23841 / 5.69 ( 48) link_NAG-ASN : bond 0.01770 / 1.27 ( 16) link_NAG-ASN : angle 8.36398 / 5.69 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.522 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: 0.6885 (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: 0.7592 (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: 0.7653 (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: 0.6902 (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: 0.1325 time to fit residues: 59.0829 Evaluate side-chains 182 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3892 r_free = 0.3892 target = 0.174450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133253 restraints weight = 13152.920| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.45 r_work: 0.3321 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12944 Z= 0.160 Angle : 0.819 15.927 17584 Z= 0.371 Chirality : 0.051 0.581 2044 Planarity : 0.006 0.061 2180 Dihedral : 5.809 37.336 1656 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.72 % Allowed : 8.06 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.18), residues: 1524 helix: -1.71 (0.17), residues: 604 sheet: -3.16 (0.25), residues: 316 loop : -3.00 (0.21), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 66 TYR 0.017 0.001 TYR A 252 PHE 0.017 0.002 PHE C 228 TRP 0.018 0.002 TRP A 353 HIS 0.009 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (12908) covalent geometry : angle 0.73075 / 0.35 (17480) SS BOND : bond 0.00073 / 0.03 ( 4) SS BOND : angle 0.38027 / 0.19 ( 8) hydrogen bonds : bond 0.04674 / 3.21 ( 404) hydrogen bonds : angle 4.24066 / 2.97 ( 1188) link_BETA1-4 : bond 0.01326 / 0.96 ( 16) link_BETA1-4 : angle 4.59150 / 3.64 ( 48) link_NAG-ASN : bond 0.01171 / 0.80 ( 16) link_NAG-ASN : angle 5.51336 / 3.92 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8095 (mttp) cc_final: 0.7512 (mtmt) REVERT: A 234 MET cc_start: 0.6159 (mtp) cc_final: 0.5758 (mtt) REVERT: A 270 ARG cc_start: 0.6751 (ttm170) cc_final: 0.6527 (ttm110) REVERT: A 294 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6412 (mm-30) REVERT: A 312 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6041 (mp) REVERT: A 360 MET cc_start: 0.7927 (tpt) cc_final: 0.7613 (tpt) REVERT: B 82 LYS cc_start: 0.8537 (mmtp) cc_final: 0.7884 (mmtm) REVERT: B 84 ASN cc_start: 0.7727 (t0) cc_final: 0.7442 (t0) REVERT: B 240 LYS cc_start: 0.7352 (mttm) cc_final: 0.7114 (mtpp) REVERT: B 262 PHE cc_start: 0.7055 (t80) cc_final: 0.6285 (p90) REVERT: B 271 TYR cc_start: 0.7562 (m-80) cc_final: 0.6832 (m-80) REVERT: B 288 GLN cc_start: 0.6890 (tp-100) cc_final: 0.6335 (mp10) REVERT: B 312 LEU cc_start: 0.7798 (mt) cc_final: 0.7486 (mt) REVERT: B 361 SER cc_start: 0.7793 (t) cc_final: 0.7445 (p) REVERT: C 78 TYR cc_start: 0.6996 (p90) cc_final: 0.6570 (p90) REVERT: C 170 LYS cc_start: 0.8050 (mttp) cc_final: 0.7465 (mtmt) REVERT: C 234 MET cc_start: 0.6168 (mtp) cc_final: 0.5743 (mtt) REVERT: C 250 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: C 294 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6493 (mm-30) REVERT: C 312 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6227 (mp) REVERT: D 35 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8201 (p) REVERT: D 82 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8440 (mmtm) REVERT: D 137 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6803 (mp-120) REVERT: D 240 LYS cc_start: 0.7239 (mttm) cc_final: 0.6981 (mtpp) REVERT: D 248 MET cc_start: 0.8791 (mmm) cc_final: 0.8507 (mmm) REVERT: D 262 PHE cc_start: 0.7210 (t80) cc_final: 0.6260 (p90) REVERT: D 271 TYR cc_start: 0.7665 (m-80) cc_final: 0.7403 (m-80) REVERT: D 286 ASN cc_start: 0.7068 (t0) cc_final: 0.6691 (t0) REVERT: D 288 GLN cc_start: 0.6940 (tp-100) cc_final: 0.6363 (mp10) REVERT: D 296 TRP cc_start: 0.7520 (t-100) cc_final: 0.7137 (t-100) REVERT: D 312 LEU cc_start: 0.7778 (mt) cc_final: 0.7471 (mt) outliers start: 23 outliers final: 8 residues processed: 212 average time/residue: 0.1232 time to fit residues: 36.9418 Evaluate side-chains 179 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 357 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 120 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3877 r_free = 0.3877 target = 0.173008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132027 restraints weight = 13211.050| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.42 r_work: 0.3233 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2751 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= 0.142 Angle : 0.698 14.040 17584 Z= 0.320 Chirality : 0.048 0.408 2044 Planarity : 0.005 0.056 2180 Dihedral : 5.254 36.740 1656 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 2.16 % Allowed : 8.73 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.20), residues: 1524 helix: -0.16 (0.20), residues: 600 sheet: -2.92 (0.26), residues: 312 loop : -2.42 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 66 TYR 0.014 0.001 TYR A 146 PHE 0.014 0.001 PHE C 337 TRP 0.015 0.001 TRP A 353 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (12908) covalent geometry : angle 0.64286 / 0.31 (17480) SS BOND : bond 0.00113 / 0.06 ( 4) SS BOND : angle 0.24283 / 0.13 ( 8) hydrogen bonds : bond 0.03769 / 2.58 ( 404) hydrogen bonds : angle 3.74410 / 2.62 ( 1188) link_BETA1-4 : bond 0.01192 / 0.87 ( 16) link_BETA1-4 : angle 3.83321 / 3.11 ( 48) link_NAG-ASN : bond 0.01118 / 0.79 ( 16) link_NAG-ASN : angle 3.64700 / 2.97 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8118 (mttp) cc_final: 0.7525 (mtmt) REVERT: A 234 MET cc_start: 0.6136 (mtp) cc_final: 0.5750 (mtt) REVERT: A 270 ARG cc_start: 0.6717 (ttm170) cc_final: 0.6478 (ttm110) REVERT: A 294 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6345 (mm-30) REVERT: A 360 MET cc_start: 0.7613 (tpt) cc_final: 0.7387 (tpt) REVERT: B 82 LYS cc_start: 0.8484 (mmtp) cc_final: 0.7813 (mmtm) REVERT: B 84 ASN cc_start: 0.7679 (t0) cc_final: 0.7478 (t0) REVERT: B 240 LYS cc_start: 0.7256 (mttm) cc_final: 0.7004 (mtpp) REVERT: B 248 MET cc_start: 0.9022 (mmm) cc_final: 0.8612 (mmm) REVERT: B 262 PHE cc_start: 0.7324 (t80) cc_final: 0.6252 (p90) REVERT: B 288 GLN cc_start: 0.6777 (tp-100) cc_final: 0.6395 (mp10) REVERT: B 335 GLN cc_start: 0.6857 (tt0) cc_final: 0.6637 (tt0) REVERT: B 361 SER cc_start: 0.7664 (t) cc_final: 0.7282 (p) REVERT: C 170 LYS cc_start: 0.8149 (mttp) cc_final: 0.7583 (mtmt) REVERT: C 234 MET cc_start: 0.6126 (mtp) cc_final: 0.5724 (mtt) REVERT: C 245 MET cc_start: 0.7171 (mtp) cc_final: 0.6852 (ttm) REVERT: C 250 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: C 251 TYR cc_start: 0.6894 (m-80) cc_final: 0.6359 (m-80) REVERT: C 294 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6457 (mm-30) REVERT: D 35 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8202 (p) REVERT: D 82 LYS cc_start: 0.8656 (mmtp) cc_final: 0.7998 (mmtm) REVERT: D 84 ASN cc_start: 0.7254 (t0) cc_final: 0.6971 (t0) REVERT: D 240 LYS cc_start: 0.7166 (mttm) cc_final: 0.6932 (mtpp) REVERT: D 248 MET cc_start: 0.8940 (mmm) cc_final: 0.8548 (mmm) REVERT: D 262 PHE cc_start: 0.7395 (t80) cc_final: 0.6310 (p90) REVERT: D 271 TYR cc_start: 0.7686 (m-80) cc_final: 0.7362 (m-80) REVERT: D 286 ASN cc_start: 0.7005 (t0) cc_final: 0.6651 (t0) REVERT: D 288 GLN cc_start: 0.6712 (tp-100) cc_final: 0.6288 (mp10) outliers start: 29 outliers final: 13 residues processed: 198 average time/residue: 0.1168 time to fit residues: 33.2126 Evaluate side-chains 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain D residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 80 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 136 HIS D 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.171682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129931 restraints weight = 13141.649| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.41 r_work: 0.3347 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3131 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= 0.139 Angle : 0.671 15.117 17584 Z= 0.304 Chirality : 0.045 0.299 2044 Planarity : 0.005 0.059 2180 Dihedral : 5.006 36.672 1656 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 2.24 % Allowed : 9.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.21), residues: 1524 helix: 0.61 (0.21), residues: 600 sheet: -2.67 (0.26), residues: 304 loop : -2.18 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.020 0.002 TYR A 44 PHE 0.016 0.001 PHE C 337 TRP 0.013 0.001 TRP A 353 HIS 0.005 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (12908) covalent geometry : angle 0.61609 / 0.29 (17480) SS BOND : bond 0.00113 / 0.05 ( 4) SS BOND : angle 0.22298 / 0.13 ( 8) hydrogen bonds : bond 0.03415 / 2.32 ( 404) hydrogen bonds : angle 3.61588 / 2.53 ( 1188) link_BETA1-4 : bond 0.01057 / 0.77 ( 16) link_BETA1-4 : angle 3.46619 / 2.80 ( 48) link_NAG-ASN : bond 0.01011 / 0.72 ( 16) link_NAG-ASN : angle 3.81911 / 3.45 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7051 (mptt) cc_final: 0.6798 (mtmm) REVERT: A 170 LYS cc_start: 0.8198 (mttp) cc_final: 0.7676 (mtmt) REVERT: A 234 MET cc_start: 0.6290 (mtp) cc_final: 0.5931 (mtt) REVERT: A 248 MET cc_start: 0.7992 (mmm) cc_final: 0.7771 (mmm) REVERT: A 294 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6435 (mm-30) REVERT: A 316 MET cc_start: 0.8404 (ttm) cc_final: 0.8175 (ttm) REVERT: B 82 LYS cc_start: 0.8566 (mmtp) cc_final: 0.7959 (mmtm) REVERT: B 84 ASN cc_start: 0.7796 (t0) cc_final: 0.7544 (t0) REVERT: B 85 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6684 (mp) REVERT: B 240 LYS cc_start: 0.7473 (mttm) cc_final: 0.7239 (mtpp) REVERT: B 262 PHE cc_start: 0.7447 (t80) cc_final: 0.6387 (p90) REVERT: B 271 TYR cc_start: 0.7997 (m-80) cc_final: 0.7409 (m-80) REVERT: B 288 GLN cc_start: 0.6806 (tp-100) cc_final: 0.6530 (mp10) REVERT: B 361 SER cc_start: 0.7800 (t) cc_final: 0.7451 (p) REVERT: C 168 LYS cc_start: 0.7109 (mptt) cc_final: 0.6775 (mtmm) REVERT: C 170 LYS cc_start: 0.8235 (mttp) cc_final: 0.7743 (mtmt) REVERT: C 234 MET cc_start: 0.6260 (mtp) cc_final: 0.5865 (mtt) REVERT: C 251 TYR cc_start: 0.6982 (m-80) cc_final: 0.6438 (m-80) REVERT: C 294 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6567 (mm-30) REVERT: D 35 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8235 (m) REVERT: D 82 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8136 (mmtm) REVERT: D 137 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: D 197 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7673 (tp) REVERT: D 240 LYS cc_start: 0.7449 (mttm) cc_final: 0.7225 (mtpp) REVERT: D 248 MET cc_start: 0.8953 (mmm) cc_final: 0.8571 (mmm) REVERT: D 262 PHE cc_start: 0.7530 (t80) cc_final: 0.6485 (p90) REVERT: D 271 TYR cc_start: 0.7953 (m-80) cc_final: 0.7689 (m-80) REVERT: D 288 GLN cc_start: 0.6725 (tp-100) cc_final: 0.6442 (mp10) REVERT: D 365 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7220 (mm-30) outliers start: 30 outliers final: 14 residues processed: 190 average time/residue: 0.1069 time to fit residues: 29.2110 Evaluate side-chains 175 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 B residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain 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 144 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 350 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.170067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128551 restraints weight = 13284.725| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.41 r_work: 0.3265 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12944 Z= 0.155 Angle : 0.661 13.449 17584 Z= 0.302 Chirality : 0.045 0.291 2044 Planarity : 0.005 0.062 2180 Dihedral : 4.967 37.029 1656 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 1.49 % Allowed : 10.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.22), residues: 1524 helix: 0.94 (0.22), residues: 600 sheet: -2.67 (0.26), residues: 312 loop : -2.04 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.015 0.001 TYR C 44 PHE 0.014 0.001 PHE C 337 TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (12908) covalent geometry : angle 0.60854 / 0.29 (17480) SS BOND : bond 0.00084 / 0.04 ( 4) SS BOND : angle 0.18211 / 0.10 ( 8) hydrogen bonds : bond 0.03372 / 2.28 ( 404) hydrogen bonds : angle 3.60956 / 2.52 ( 1188) link_BETA1-4 : bond 0.01011 / 0.75 ( 16) link_BETA1-4 : angle 3.40921 / 2.70 ( 48) link_NAG-ASN : bond 0.01052 / 0.73 ( 16) link_NAG-ASN : angle 3.66591 / 3.30 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7064 (mptt) cc_final: 0.6772 (mtmm) REVERT: A 170 LYS cc_start: 0.8147 (mttp) cc_final: 0.7595 (mtmt) REVERT: A 198 ARG cc_start: 0.7115 (ttt-90) cc_final: 0.6861 (tpt170) REVERT: A 234 MET cc_start: 0.6291 (mtp) cc_final: 0.5868 (mtt) REVERT: A 267 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6850 (mm-30) REVERT: A 294 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6416 (mm-30) REVERT: A 316 MET cc_start: 0.8355 (ttm) cc_final: 0.8118 (ttm) REVERT: B 82 LYS cc_start: 0.8526 (mmtp) cc_final: 0.7922 (mmtm) REVERT: B 84 ASN cc_start: 0.7769 (t0) cc_final: 0.7511 (t0) REVERT: B 85 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6681 (mp) REVERT: B 240 LYS cc_start: 0.7255 (mttm) cc_final: 0.7020 (mtpp) REVERT: B 248 MET cc_start: 0.8977 (mmm) cc_final: 0.8603 (mmm) REVERT: B 262 PHE cc_start: 0.7626 (t80) cc_final: 0.6442 (p90) REVERT: B 271 TYR cc_start: 0.7930 (m-80) cc_final: 0.7440 (m-80) REVERT: B 335 GLN cc_start: 0.6849 (tt0) cc_final: 0.6620 (tt0) REVERT: B 361 SER cc_start: 0.7692 (t) cc_final: 0.7293 (p) REVERT: C 168 LYS cc_start: 0.7097 (mptt) cc_final: 0.6770 (mtmm) REVERT: C 170 LYS cc_start: 0.8227 (mttp) cc_final: 0.7683 (mtmt) REVERT: C 234 MET cc_start: 0.6244 (mtp) cc_final: 0.5809 (mtt) REVERT: C 251 TYR cc_start: 0.6961 (m-80) cc_final: 0.6373 (m-80) REVERT: C 294 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6598 (mm-30) REVERT: D 35 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8299 (m) REVERT: D 82 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8032 (mmtm) REVERT: D 137 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6915 (mp10) REVERT: D 197 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7601 (tp) REVERT: D 240 LYS cc_start: 0.7283 (mttm) cc_final: 0.7070 (mtpp) REVERT: D 248 MET cc_start: 0.9074 (mmm) cc_final: 0.8581 (mmm) REVERT: D 262 PHE cc_start: 0.7649 (t80) cc_final: 0.6391 (p90) REVERT: D 288 GLN cc_start: 0.6591 (tp-100) cc_final: 0.6383 (mp10) REVERT: D 315 PHE cc_start: 0.6773 (p90) cc_final: 0.4965 (m-80) REVERT: D 348 ASN cc_start: 0.7741 (p0) cc_final: 0.7513 (p0) REVERT: D 365 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7195 (mm-30) outliers start: 20 outliers final: 11 residues processed: 175 average time/residue: 0.1174 time to fit residues: 29.4463 Evaluate side-chains 170 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain 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 197 LEU 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 47 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.169039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127207 restraints weight = 13213.958| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.48 r_work: 0.3302 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12944 Z= 0.158 Angle : 0.650 13.333 17584 Z= 0.299 Chirality : 0.045 0.276 2044 Planarity : 0.005 0.064 2180 Dihedral : 4.920 36.606 1656 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 2.01 % Allowed : 10.45 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.22), residues: 1524 helix: 1.11 (0.22), residues: 600 sheet: -2.58 (0.26), residues: 312 loop : -1.99 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.015 0.001 TYR A 44 PHE 0.011 0.001 PHE C 337 TRP 0.011 0.001 TRP C 353 HIS 0.004 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (12908) covalent geometry : angle 0.60279 / 0.29 (17480) SS BOND : bond 0.00045 / 0.02 ( 4) SS BOND : angle 0.13672 / 0.07 ( 8) hydrogen bonds : bond 0.03313 / 2.24 ( 404) hydrogen bonds : angle 3.61537 / 2.53 ( 1188) link_BETA1-4 : bond 0.00963 / 0.71 ( 16) link_BETA1-4 : angle 3.31086 / 2.61 ( 48) link_NAG-ASN : bond 0.01026 / 0.71 ( 16) link_NAG-ASN : angle 3.39093 / 3.06 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7190 (mptt) cc_final: 0.6877 (mtmm) REVERT: A 170 LYS cc_start: 0.8200 (mttp) cc_final: 0.7697 (mtmt) REVERT: A 234 MET cc_start: 0.6467 (mtp) cc_final: 0.6050 (mtt) REVERT: A 248 MET cc_start: 0.8061 (mmm) cc_final: 0.7724 (mmm) REVERT: A 267 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6876 (mm-30) REVERT: A 294 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6494 (mm-30) REVERT: A 316 MET cc_start: 0.8402 (ttm) cc_final: 0.8147 (ttm) REVERT: B 82 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8037 (mmtm) REVERT: B 84 ASN cc_start: 0.7823 (t0) cc_final: 0.7576 (t0) REVERT: B 85 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6842 (mp) REVERT: B 240 LYS cc_start: 0.7446 (mttm) cc_final: 0.7174 (mtpp) REVERT: B 248 MET cc_start: 0.8965 (mmm) cc_final: 0.8570 (mmm) REVERT: B 262 PHE cc_start: 0.7733 (t80) cc_final: 0.6523 (p90) REVERT: B 271 TYR cc_start: 0.8112 (m-80) cc_final: 0.7759 (m-80) REVERT: B 335 GLN cc_start: 0.6938 (tt0) cc_final: 0.6700 (tt0) REVERT: B 361 SER cc_start: 0.7789 (t) cc_final: 0.7382 (p) REVERT: C 168 LYS cc_start: 0.7228 (mptt) cc_final: 0.6926 (mtmm) REVERT: C 170 LYS cc_start: 0.8237 (mttp) cc_final: 0.7723 (mtmt) REVERT: C 234 MET cc_start: 0.6415 (mtp) cc_final: 0.5989 (mtt) REVERT: C 251 TYR cc_start: 0.7018 (m-80) cc_final: 0.6493 (m-80) REVERT: C 294 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6600 (mm-30) REVERT: D 35 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8345 (m) REVERT: D 82 LYS cc_start: 0.8760 (mmtp) cc_final: 0.8136 (mmtm) REVERT: D 137 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6808 (mm-40) REVERT: D 171 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7420 (m) REVERT: D 240 LYS cc_start: 0.7438 (mttm) cc_final: 0.7216 (mtpp) REVERT: D 262 PHE cc_start: 0.7780 (t80) cc_final: 0.6516 (p90) REVERT: D 348 ASN cc_start: 0.7778 (p0) cc_final: 0.7531 (p0) REVERT: D 365 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7257 (mm-30) outliers start: 27 outliers final: 19 residues processed: 170 average time/residue: 0.1030 time to fit residues: 25.6005 Evaluate side-chains 173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 146 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 145 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.170238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127787 restraints weight = 13261.349| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.47 r_work: 0.3346 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3729 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= 0.126 Angle : 0.624 13.254 17584 Z= 0.286 Chirality : 0.044 0.255 2044 Planarity : 0.005 0.063 2180 Dihedral : 4.811 35.938 1656 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 2.16 % Allowed : 10.82 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.22), residues: 1524 helix: 1.36 (0.22), residues: 600 sheet: -2.34 (0.27), residues: 304 loop : -1.94 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 270 TYR 0.015 0.001 TYR A 44 PHE 0.010 0.001 PHE C 337 TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (12908) covalent geometry : angle 0.57914 / 0.28 (17480) SS BOND : bond 0.00055 / 0.03 ( 4) SS BOND : angle 0.17607 / 0.10 ( 8) hydrogen bonds : bond 0.03110 / 2.10 ( 404) hydrogen bonds : angle 3.53884 / 2.48 ( 1188) link_BETA1-4 : bond 0.00944 / 0.69 ( 16) link_BETA1-4 : angle 3.22609 / 2.54 ( 48) link_NAG-ASN : bond 0.00976 / 0.68 ( 16) link_NAG-ASN : angle 3.20150 / 2.95 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7245 (mptt) cc_final: 0.6967 (mtmm) REVERT: A 170 LYS cc_start: 0.8224 (mttp) cc_final: 0.7769 (mtmt) REVERT: A 234 MET cc_start: 0.6534 (mtp) cc_final: 0.6125 (mtt) REVERT: A 248 MET cc_start: 0.8002 (mmm) cc_final: 0.7636 (mmm) REVERT: A 294 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6530 (mm-30) REVERT: B 82 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8062 (mmtm) REVERT: B 84 ASN cc_start: 0.7755 (t0) cc_final: 0.7550 (t0) REVERT: B 85 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6910 (mp) REVERT: B 240 LYS cc_start: 0.7537 (mttm) cc_final: 0.7271 (mtpp) REVERT: B 248 MET cc_start: 0.8969 (mmm) cc_final: 0.8561 (mmm) REVERT: B 262 PHE cc_start: 0.7838 (t80) cc_final: 0.6613 (p90) REVERT: B 271 TYR cc_start: 0.8155 (m-80) cc_final: 0.7811 (m-80) REVERT: B 335 GLN cc_start: 0.6992 (tt0) cc_final: 0.6759 (tt0) REVERT: B 361 SER cc_start: 0.7809 (t) cc_final: 0.7395 (p) REVERT: C 168 LYS cc_start: 0.7329 (mptt) cc_final: 0.6932 (mtmm) REVERT: C 170 LYS cc_start: 0.8272 (mttp) cc_final: 0.7774 (mtmt) REVERT: C 234 MET cc_start: 0.6520 (mtp) cc_final: 0.6089 (mtt) REVERT: C 251 TYR cc_start: 0.7051 (m-80) cc_final: 0.6530 (m-80) REVERT: C 294 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6603 (mm-30) REVERT: D 35 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8319 (m) REVERT: D 82 LYS cc_start: 0.8739 (mmtp) cc_final: 0.8148 (mmtm) REVERT: D 240 LYS cc_start: 0.7499 (mttm) cc_final: 0.7280 (mtpp) REVERT: D 262 PHE cc_start: 0.7869 (t80) cc_final: 0.6592 (p90) REVERT: D 315 PHE cc_start: 0.6913 (p90) cc_final: 0.5065 (m-80) REVERT: D 365 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7263 (mm-30) outliers start: 29 outliers final: 24 residues processed: 172 average time/residue: 0.0927 time to fit residues: 23.6505 Evaluate side-chains 177 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 121 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.169074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126549 restraints weight = 13095.473| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.44 r_work: 0.3328 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3884 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= 0.149 Angle : 0.636 13.192 17584 Z= 0.292 Chirality : 0.044 0.245 2044 Planarity : 0.005 0.065 2180 Dihedral : 4.793 36.229 1656 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.30 % Favored : 93.57 % Rotamer: Outliers : 2.24 % Allowed : 11.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.22), residues: 1524 helix: 1.38 (0.22), residues: 600 sheet: -2.38 (0.27), residues: 312 loop : -1.88 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 349 TYR 0.016 0.001 TYR A 44 PHE 0.010 0.001 PHE C 337 TRP 0.011 0.001 TRP C 353 HIS 0.004 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (12908) covalent geometry : angle 0.59421 / 0.28 (17480) SS BOND : bond 0.00062 / 0.03 ( 4) SS BOND : angle 0.21452 / 0.11 ( 8) hydrogen bonds : bond 0.03167 / 2.14 ( 404) hydrogen bonds : angle 3.57343 / 2.50 ( 1188) link_BETA1-4 : bond 0.00894 / 0.65 ( 16) link_BETA1-4 : angle 3.09758 / 2.43 ( 48) link_NAG-ASN : bond 0.01006 / 0.68 ( 16) link_NAG-ASN : angle 3.18030 / 2.91 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7447 (mptt) cc_final: 0.7070 (mtmm) REVERT: A 170 LYS cc_start: 0.8220 (mttp) cc_final: 0.7773 (mtmt) REVERT: A 234 MET cc_start: 0.6618 (mtp) cc_final: 0.6168 (mtt) REVERT: A 248 MET cc_start: 0.8001 (mmm) cc_final: 0.7647 (mmm) REVERT: A 294 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6619 (mm-30) REVERT: B 82 LYS cc_start: 0.8633 (mmtp) cc_final: 0.8092 (mmtm) REVERT: B 85 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7081 (mp) REVERT: B 240 LYS cc_start: 0.7521 (mttm) cc_final: 0.7283 (mtpp) REVERT: B 262 PHE cc_start: 0.7940 (t80) cc_final: 0.6648 (p90) REVERT: B 335 GLN cc_start: 0.6997 (tt0) cc_final: 0.6765 (tt0) REVERT: B 361 SER cc_start: 0.7831 (t) cc_final: 0.7395 (p) REVERT: C 168 LYS cc_start: 0.7412 (mptt) cc_final: 0.7001 (mtmm) REVERT: C 170 LYS cc_start: 0.8283 (mttp) cc_final: 0.7775 (mtmt) REVERT: C 234 MET cc_start: 0.6642 (mtp) cc_final: 0.6176 (mtt) REVERT: C 251 TYR cc_start: 0.6936 (m-80) cc_final: 0.6356 (m-80) REVERT: C 294 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6675 (mm-30) REVERT: D 35 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8370 (m) REVERT: D 82 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8178 (mmtm) REVERT: D 137 GLN cc_start: 0.7008 (mp10) cc_final: 0.6807 (mp10) REVERT: D 240 LYS cc_start: 0.7474 (mttm) cc_final: 0.7261 (mtpp) REVERT: D 262 PHE cc_start: 0.7961 (t80) cc_final: 0.6614 (p90) REVERT: D 315 PHE cc_start: 0.6929 (p90) cc_final: 0.5105 (m-80) REVERT: D 365 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7228 (mm-30) outliers start: 30 outliers final: 19 residues processed: 181 average time/residue: 0.1031 time to fit residues: 27.1323 Evaluate side-chains 173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 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 357 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.169284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126066 restraints weight = 13147.778| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.53 r_work: 0.3153 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12944 Z= 0.139 Angle : 0.625 13.179 17584 Z= 0.289 Chirality : 0.044 0.232 2044 Planarity : 0.005 0.063 2180 Dihedral : 4.782 36.767 1656 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 1.79 % Allowed : 12.24 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.22), residues: 1524 helix: 1.45 (0.22), residues: 600 sheet: -2.18 (0.27), residues: 304 loop : -1.86 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 358 TYR 0.016 0.001 TYR A 44 PHE 0.016 0.001 PHE A 337 TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (12908) covalent geometry : angle 0.58465 / 0.28 (17480) SS BOND : bond 0.00029 / 0.01 ( 4) SS BOND : angle 0.19952 / 0.10 ( 8) hydrogen bonds : bond 0.03104 / 2.10 ( 404) hydrogen bonds : angle 3.57796 / 2.51 ( 1188) link_BETA1-4 : bond 0.00884 / 0.64 ( 16) link_BETA1-4 : angle 3.03216 / 2.38 ( 48) link_NAG-ASN : bond 0.00941 / 0.65 ( 16) link_NAG-ASN : angle 3.06928 / 2.83 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 SER cc_start: 0.7413 (m) cc_final: 0.7123 (p) REVERT: A 168 LYS cc_start: 0.7259 (mptt) cc_final: 0.6849 (mtmm) REVERT: A 170 LYS cc_start: 0.8154 (mttp) cc_final: 0.7651 (mtmt) REVERT: A 234 MET cc_start: 0.6471 (mtp) cc_final: 0.5998 (mtt) REVERT: A 248 MET cc_start: 0.8094 (mmm) cc_final: 0.7701 (mmm) REVERT: A 294 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6542 (mm-30) REVERT: B 82 LYS cc_start: 0.8569 (mmtp) cc_final: 0.7983 (mmtm) REVERT: B 85 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6906 (mp) REVERT: B 171 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7301 (m) REVERT: B 240 LYS cc_start: 0.7334 (mttm) cc_final: 0.7091 (mtpp) REVERT: B 248 MET cc_start: 0.9003 (mmm) cc_final: 0.8661 (mmm) REVERT: B 262 PHE cc_start: 0.7970 (t80) cc_final: 0.6511 (p90) REVERT: B 294 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6962 (mm-30) REVERT: B 335 GLN cc_start: 0.6836 (tt0) cc_final: 0.6618 (tt0) REVERT: B 361 SER cc_start: 0.7721 (t) cc_final: 0.7253 (p) REVERT: C 168 LYS cc_start: 0.7298 (mptt) cc_final: 0.6861 (mtmm) REVERT: C 170 LYS cc_start: 0.8201 (mttp) cc_final: 0.7661 (mtmt) REVERT: C 234 MET cc_start: 0.6494 (mtp) cc_final: 0.6020 (mtt) REVERT: C 251 TYR cc_start: 0.6849 (m-80) cc_final: 0.6308 (m-80) REVERT: C 294 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6645 (mm-30) REVERT: D 35 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8407 (m) REVERT: D 82 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8051 (mmtm) REVERT: D 262 PHE cc_start: 0.8040 (t80) cc_final: 0.6474 (p90) REVERT: D 294 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6941 (mm-30) REVERT: D 315 PHE cc_start: 0.6858 (p90) cc_final: 0.5004 (m-80) REVERT: D 365 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7195 (mm-30) outliers start: 24 outliers final: 19 residues processed: 174 average time/residue: 0.0999 time to fit residues: 25.3943 Evaluate side-chains 173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 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 357 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 147 optimal weight: 0.0060 chunk 99 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.169562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125955 restraints weight = 13132.733| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.35 r_work: 0.3316 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12944 Z= 0.132 Angle : 0.614 13.059 17584 Z= 0.284 Chirality : 0.044 0.216 2044 Planarity : 0.005 0.063 2180 Dihedral : 4.707 35.668 1656 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.77 % Favored : 94.09 % Rotamer: Outliers : 1.79 % Allowed : 12.24 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.22), residues: 1524 helix: 1.55 (0.22), residues: 600 sheet: -2.09 (0.27), residues: 304 loop : -1.81 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 349 TYR 0.016 0.001 TYR A 44 PHE 0.013 0.001 PHE A 337 TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (12908) covalent geometry : angle 0.57700 / 0.28 (17480) SS BOND : bond 0.00072 / 0.03 ( 4) SS BOND : angle 0.23410 / 0.13 ( 8) hydrogen bonds : bond 0.03034 / 2.05 ( 404) hydrogen bonds : angle 3.55446 / 2.49 ( 1188) link_BETA1-4 : bond 0.00873 / 0.62 ( 16) link_BETA1-4 : angle 2.89692 / 2.28 ( 48) link_NAG-ASN : bond 0.00937 / 0.63 ( 16) link_NAG-ASN : angle 2.91417 / 2.71 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 SER cc_start: 0.7546 (m) cc_final: 0.7301 (p) REVERT: A 168 LYS cc_start: 0.7415 (mptt) cc_final: 0.6995 (mtmm) REVERT: A 170 LYS cc_start: 0.8210 (mttp) cc_final: 0.7786 (mtmt) REVERT: A 294 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6636 (mm-30) REVERT: A 337 PHE cc_start: 0.7489 (t80) cc_final: 0.6925 (t80) REVERT: B 82 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8139 (mmtm) REVERT: B 85 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7151 (mp) REVERT: B 171 THR cc_start: 0.7651 (OUTLIER) cc_final: 0.7442 (m) REVERT: B 240 LYS cc_start: 0.7519 (mttm) cc_final: 0.7287 (mtpp) REVERT: B 248 MET cc_start: 0.8877 (mmm) cc_final: 0.8451 (mmm) REVERT: B 262 PHE cc_start: 0.8094 (t80) cc_final: 0.6626 (p90) REVERT: B 271 TYR cc_start: 0.8169 (m-80) cc_final: 0.7882 (m-80) REVERT: B 315 PHE cc_start: 0.6972 (p90) cc_final: 0.5155 (m-80) REVERT: B 335 GLN cc_start: 0.7095 (tt0) cc_final: 0.6814 (tt0) REVERT: B 361 SER cc_start: 0.7714 (t) cc_final: 0.7287 (p) REVERT: C 168 LYS cc_start: 0.7474 (mptt) cc_final: 0.6944 (mtmm) REVERT: C 170 LYS cc_start: 0.8273 (mttp) cc_final: 0.7793 (mtmt) REVERT: C 234 MET cc_start: 0.6688 (mtp) cc_final: 0.6245 (mtt) REVERT: C 251 TYR cc_start: 0.6869 (m-80) cc_final: 0.6308 (m-80) REVERT: C 294 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6756 (mm-30) REVERT: C 349 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7200 (mpp-170) REVERT: D 82 LYS cc_start: 0.8655 (mmtp) cc_final: 0.8145 (mmtm) REVERT: D 262 PHE cc_start: 0.8091 (t80) cc_final: 0.6645 (p90) REVERT: D 315 PHE cc_start: 0.6985 (p90) cc_final: 0.5170 (m-80) REVERT: D 365 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7247 (mm-30) outliers start: 24 outliers final: 20 residues processed: 177 average time/residue: 0.0999 time to fit residues: 26.0901 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 : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain 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 245 MET Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 17 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.168779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125112 restraints weight = 13159.484| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.54 r_work: 0.3313 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12944 Z= 0.150 Angle : 0.628 13.014 17584 Z= 0.292 Chirality : 0.044 0.213 2044 Planarity : 0.005 0.064 2180 Dihedral : 4.741 36.715 1656 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 1.64 % Allowed : 12.31 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.22), residues: 1524 helix: 1.48 (0.22), residues: 600 sheet: -2.04 (0.27), residues: 304 loop : -1.77 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 349 TYR 0.016 0.001 TYR A 44 PHE 0.015 0.001 PHE A 337 TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (12908) covalent geometry : angle 0.59287 / 0.28 (17480) SS BOND : bond 0.00046 / 0.02 ( 4) SS BOND : angle 0.26535 / 0.13 ( 8) hydrogen bonds : bond 0.03117 / 2.11 ( 404) hydrogen bonds : angle 3.59341 / 2.52 ( 1188) link_BETA1-4 : bond 0.00832 / 0.59 ( 16) link_BETA1-4 : angle 2.80917 / 2.21 ( 48) link_NAG-ASN : bond 0.00904 / 0.61 ( 16) link_NAG-ASN : angle 2.91620 / 2.69 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2670.36 seconds wall clock time: 46 minutes 38.10 seconds (2798.10 seconds total)