Starting phenix.real_space_refine on Thu May 15 04:29:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwv_29520/05_2025/8fwv_29520.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwv_29520/05_2025/8fwv_29520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fwv_29520/05_2025/8fwv_29520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwv_29520/05_2025/8fwv_29520.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwv_29520/05_2025/8fwv_29520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwv_29520/05_2025/8fwv_29520.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 8004 2.51 5 N 2100 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12584 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.00, per 1000 atoms: 0.64 Number of scatterers: 12584 At special positions: 0 Unit cell: (104, 160.576, 85.696, 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 2412 8.00 N 2100 7.00 C 8004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1001 " - " ASN A 275 " " NAG A1002 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG C1001 " - " ASN C 275 " " NAG C1002 " - " ASN C 412 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN A 67 " " NAG G 1 " - " ASN B 378 " " NAG H 1 " - " ASN B 67 " " NAG I 1 " - " ASN C 378 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN D 378 " " NAG L 1 " - " ASN D 67 " Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.7 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 20 sheets defined 39.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.957A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.525A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.664A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.630A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.957A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.525A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.631A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.958A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 161 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.597A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.526A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.630A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.747A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.958A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.526A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.631A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY A 40 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS A 129 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 149 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN A 131 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG A 384 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER A 148 " --> pdb=" O ARG A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.813A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 395 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY B 40 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS B 129 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU B 149 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N GLN B 131 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.813A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 395 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY C 40 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU C 149 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN C 131 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG C 384 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N SER C 148 " --> pdb=" O ARG C 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.812A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 392 through 395 Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY D 40 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS D 129 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU D 149 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN D 131 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.812A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 392 through 395 428 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3741 1.33 - 1.45: 2114 1.45 - 1.57: 6882 1.57 - 1.69: 7 1.69 - 1.81: 120 Bond restraints: 12864 Sorted by residual: bond pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " ideal model delta sigma weight residual 1.406 1.558 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.659 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.647 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.645 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.530 -0.124 2.00e-02 2.50e+03 3.81e+01 ... (remaining 12859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 16711 2.38 - 4.75: 610 4.75 - 7.13: 81 7.13 - 9.50: 9 9.50 - 11.88: 9 Bond angle restraints: 17420 Sorted by residual: angle pdb=" N THR B 414 " pdb=" CA THR B 414 " pdb=" C THR B 414 " ideal model delta sigma weight residual 112.88 107.59 5.29 1.29e+00 6.01e-01 1.68e+01 angle pdb=" N THR C 414 " pdb=" CA THR C 414 " pdb=" C THR C 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" N THR A 414 " pdb=" CA THR A 414 " pdb=" C THR A 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" N THR D 414 " pdb=" CA THR D 414 " pdb=" C THR D 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " pdb=" C5 NAG D1002 " ideal model delta sigma weight residual 113.21 125.09 -11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 17415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 7718 23.14 - 46.27: 238 46.27 - 69.41: 48 69.41 - 92.54: 31 92.54 - 115.68: 25 Dihedral angle restraints: 8060 sinusoidal: 3592 harmonic: 4468 Sorted by residual: dihedral pdb=" CA GLY C 310 " pdb=" C GLY C 310 " pdb=" N LEU C 311 " pdb=" CA LEU C 311 " ideal model delta harmonic sigma weight residual -180.00 -119.43 -60.57 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLY A 310 " pdb=" C GLY A 310 " pdb=" N LEU A 311 " pdb=" CA LEU A 311 " ideal model delta harmonic sigma weight residual -180.00 -119.44 -60.56 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLY B 310 " pdb=" C GLY B 310 " pdb=" N LEU B 311 " pdb=" CA LEU B 311 " ideal model delta harmonic sigma weight residual 180.00 -119.49 -60.51 0 5.00e+00 4.00e-02 1.46e+02 ... (remaining 8057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.373: 2018 0.373 - 0.747: 2 0.747 - 1.120: 0 1.120 - 1.493: 0 1.493 - 1.866: 4 Chirality restraints: 2024 Sorted by residual: chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 275 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.53 -1.87 2.00e-01 2.50e+01 8.71e+01 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 275 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.60 -1.80 2.00e-01 2.50e+01 8.14e+01 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 275 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.16e+01 ... (remaining 2021 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 191 " -0.066 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO B 192 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 191 " 0.066 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO D 192 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 191 " -0.066 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO A 192 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.055 5.00e-02 4.00e+02 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4072 2.85 - 3.36: 10859 3.36 - 3.87: 20453 3.87 - 4.39: 23789 4.39 - 4.90: 41544 Nonbonded interactions: 100717 Sorted by model distance: nonbonded pdb=" OG1 THR A 173 " pdb=" OE1 GLU A 223 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLU B 223 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR D 173 " pdb=" OE1 GLU D 223 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR C 173 " pdb=" OE1 GLU C 223 " model vdw 2.335 3.040 nonbonded pdb=" OE1 GLU D 46 " pdb=" OG SER D 47 " model vdw 2.350 3.040 ... (remaining 100712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' 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: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.820 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.152 12896 Z= 0.329 Angle : 1.238 29.065 17512 Z= 0.624 Chirality : 0.095 1.866 2024 Planarity : 0.008 0.100 2180 Dihedral : 14.818 115.681 5160 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.35 % Favored : 92.39 % Rotamer: Outliers : 1.19 % Allowed : 4.78 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.16), residues: 1524 helix: -4.16 (0.10), residues: 568 sheet: -2.50 (0.27), residues: 328 loop : -3.06 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP A 353 HIS 0.010 0.002 HIS A 253 PHE 0.024 0.003 PHE A 107 TYR 0.016 0.002 TYR D 252 ARG 0.008 0.001 ARG D 158 Details of bonding type rmsd link_NAG-ASN : bond 0.01481 ( 16) link_NAG-ASN : angle 10.18381 ( 48) link_BETA1-4 : bond 0.02842 ( 12) link_BETA1-4 : angle 7.57409 ( 36) hydrogen bonds : bond 0.28591 ( 428) hydrogen bonds : angle 9.69215 ( 1236) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.48138 ( 8) covalent geometry : bond 0.00717 (12864) covalent geometry : angle 1.06588 (17420) *********************** 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 327 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 311 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8632 (m) cc_final: 0.8192 (p) REVERT: A 156 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 222 LYS cc_start: 0.7945 (mttm) cc_final: 0.7691 (mmtm) REVERT: A 262 PHE cc_start: 0.7324 (t80) cc_final: 0.7036 (p90) REVERT: A 291 SER cc_start: 0.7469 (t) cc_final: 0.7240 (m) REVERT: A 360 MET cc_start: 0.7834 (tpt) cc_final: 0.7147 (tpt) REVERT: B 262 PHE cc_start: 0.7190 (t80) cc_final: 0.6935 (p90) REVERT: B 267 GLU cc_start: 0.7154 (tp30) cc_final: 0.6951 (tp30) REVERT: B 351 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7860 (mppt) REVERT: B 360 MET cc_start: 0.8370 (tpt) cc_final: 0.8166 (tpt) REVERT: C 113 SER cc_start: 0.8636 (m) cc_final: 0.8201 (p) REVERT: C 156 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8297 (tp) REVERT: C 222 LYS cc_start: 0.7938 (mttm) cc_final: 0.7684 (mmtm) REVERT: C 262 PHE cc_start: 0.7303 (t80) cc_final: 0.7048 (p90) REVERT: C 291 SER cc_start: 0.7465 (t) cc_final: 0.7236 (m) REVERT: C 360 MET cc_start: 0.7832 (tpt) cc_final: 0.7148 (tpt) REVERT: D 152 ASP cc_start: 0.7924 (t0) cc_final: 0.7626 (t0) REVERT: D 198 ARG cc_start: 0.7350 (tmt-80) cc_final: 0.7052 (tpt90) REVERT: D 200 LYS cc_start: 0.7856 (mttp) cc_final: 0.7610 (mtpt) REVERT: D 247 MET cc_start: 0.9125 (mtp) cc_final: 0.8886 (mtp) REVERT: D 262 PHE cc_start: 0.7139 (t80) cc_final: 0.6876 (p90) REVERT: D 351 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7823 (mppt) outliers start: 16 outliers final: 4 residues processed: 325 average time/residue: 0.3025 time to fit residues: 131.6021 Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 286 ASN A 335 GLN A 336 GLN A 346 GLN A 350 HIS ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 335 GLN B 336 GLN B 350 HIS C 196 ASN C 286 ASN C 335 GLN C 336 GLN C 346 GLN C 350 HIS D 288 GLN D 335 GLN D 336 GLN D 350 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135966 restraints weight = 13425.024| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.22 r_work: 0.3317 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12896 Z= 0.172 Angle : 0.850 23.369 17512 Z= 0.385 Chirality : 0.060 1.100 2024 Planarity : 0.006 0.084 2180 Dihedral : 12.755 83.646 2244 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.88 % Allowed : 9.70 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.18), residues: 1524 helix: -2.26 (0.17), residues: 568 sheet: -2.46 (0.27), residues: 328 loop : -2.73 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 353 HIS 0.007 0.001 HIS D 253 PHE 0.015 0.002 PHE B 107 TYR 0.008 0.001 TYR B 252 ARG 0.005 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.01102 ( 16) link_NAG-ASN : angle 6.97393 ( 48) link_BETA1-4 : bond 0.02510 ( 12) link_BETA1-4 : angle 5.01330 ( 36) hydrogen bonds : bond 0.04423 ( 428) hydrogen bonds : angle 4.93148 ( 1236) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.43455 ( 8) covalent geometry : bond 0.00387 (12864) covalent geometry : angle 0.73519 (17420) *********************** 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 223 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7036 (mm) REVERT: A 113 SER cc_start: 0.8843 (m) cc_final: 0.8489 (p) REVERT: A 156 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8013 (mt) REVERT: A 177 ASP cc_start: 0.8327 (t70) cc_final: 0.8083 (t0) REVERT: A 222 LYS cc_start: 0.8089 (mttm) cc_final: 0.7668 (mmtm) REVERT: A 262 PHE cc_start: 0.7794 (t80) cc_final: 0.7140 (p90) REVERT: A 291 SER cc_start: 0.7653 (t) cc_final: 0.7364 (m) REVERT: A 360 MET cc_start: 0.7950 (tpt) cc_final: 0.7434 (tpt) REVERT: B 262 PHE cc_start: 0.7981 (t80) cc_final: 0.7111 (p90) REVERT: B 288 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7624 (mm110) REVERT: B 351 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7939 (mppt) REVERT: C 55 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7052 (mm) REVERT: C 113 SER cc_start: 0.8833 (m) cc_final: 0.8479 (p) REVERT: C 156 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8008 (mt) REVERT: C 177 ASP cc_start: 0.8350 (t70) cc_final: 0.8109 (t0) REVERT: C 222 LYS cc_start: 0.8080 (mttm) cc_final: 0.7654 (mmtm) REVERT: C 262 PHE cc_start: 0.7786 (t80) cc_final: 0.7112 (p90) REVERT: C 291 SER cc_start: 0.7655 (t) cc_final: 0.7371 (m) REVERT: C 360 MET cc_start: 0.7913 (tpt) cc_final: 0.7404 (tpt) REVERT: D 81 GLN cc_start: 0.8558 (mt0) cc_final: 0.8304 (mt0) REVERT: D 198 ARG cc_start: 0.7940 (tmt-80) cc_final: 0.7477 (tpt90) REVERT: D 218 MET cc_start: 0.8967 (mtp) cc_final: 0.8704 (mtm) REVERT: D 247 MET cc_start: 0.9220 (mtp) cc_final: 0.8979 (mtp) REVERT: D 262 PHE cc_start: 0.7971 (t80) cc_final: 0.7101 (p90) REVERT: D 351 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7709 (mppt) outliers start: 52 outliers final: 25 residues processed: 204 average time/residue: 0.2557 time to fit residues: 74.1134 Evaluate side-chains 179 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 346 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 346 GLN D 98 GLN D 165 GLN D 288 GLN D 346 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.172926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133612 restraints weight = 13575.821| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.35 r_work: 0.3281 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12896 Z= 0.178 Angle : 0.793 22.280 17512 Z= 0.355 Chirality : 0.060 1.063 2024 Planarity : 0.006 0.079 2180 Dihedral : 9.814 59.436 2244 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.03 % Allowed : 9.40 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.19), residues: 1524 helix: -0.59 (0.19), residues: 576 sheet: -2.34 (0.27), residues: 332 loop : -2.76 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 296 HIS 0.008 0.001 HIS D 253 PHE 0.016 0.002 PHE B 107 TYR 0.017 0.002 TYR C 195 ARG 0.003 0.000 ARG B 384 Details of bonding type rmsd link_NAG-ASN : bond 0.01499 ( 16) link_NAG-ASN : angle 6.12757 ( 48) link_BETA1-4 : bond 0.02074 ( 12) link_BETA1-4 : angle 4.65077 ( 36) hydrogen bonds : bond 0.03860 ( 428) hydrogen bonds : angle 4.28272 ( 1236) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.16612 ( 8) covalent geometry : bond 0.00415 (12864) covalent geometry : angle 0.69531 (17420) *********************** 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 229 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6688 (t) cc_final: 0.6487 (p) REVERT: A 55 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7096 (mm) REVERT: A 113 SER cc_start: 0.8791 (m) cc_final: 0.8405 (p) REVERT: A 156 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7866 (mm) REVERT: A 160 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8352 (mp) REVERT: A 220 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7623 (mtm110) REVERT: A 222 LYS cc_start: 0.8082 (mttm) cc_final: 0.7647 (mmtm) REVERT: A 262 PHE cc_start: 0.7855 (t80) cc_final: 0.7049 (p90) REVERT: A 291 SER cc_start: 0.7719 (t) cc_final: 0.7399 (m) REVERT: A 298 MET cc_start: 0.6572 (tmm) cc_final: 0.6335 (tmm) REVERT: A 400 GLU cc_start: 0.7641 (tt0) cc_final: 0.6930 (mm-30) REVERT: B 50 MET cc_start: 0.7473 (ptp) cc_final: 0.7232 (ptt) REVERT: B 262 PHE cc_start: 0.8181 (t80) cc_final: 0.7144 (p90) REVERT: B 288 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7611 (mm110) REVERT: B 351 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7996 (mptt) REVERT: C 45 VAL cc_start: 0.6706 (t) cc_final: 0.6498 (p) REVERT: C 55 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7090 (mm) REVERT: C 113 SER cc_start: 0.8772 (m) cc_final: 0.8355 (p) REVERT: C 156 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7866 (mm) REVERT: C 160 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8364 (mp) REVERT: C 220 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7643 (mtm110) REVERT: C 222 LYS cc_start: 0.8085 (mttm) cc_final: 0.7662 (mmtm) REVERT: C 262 PHE cc_start: 0.7877 (t80) cc_final: 0.7042 (p90) REVERT: C 291 SER cc_start: 0.7750 (t) cc_final: 0.7438 (m) REVERT: C 298 MET cc_start: 0.6558 (tmm) cc_final: 0.6325 (tmm) REVERT: C 400 GLU cc_start: 0.7635 (tt0) cc_final: 0.6927 (mm-30) REVERT: D 50 MET cc_start: 0.7543 (ptp) cc_final: 0.7287 (ptt) REVERT: D 198 ARG cc_start: 0.7880 (tmt-80) cc_final: 0.7452 (tpt90) REVERT: D 218 MET cc_start: 0.9032 (mtp) cc_final: 0.8783 (mtm) REVERT: D 247 MET cc_start: 0.9240 (mtp) cc_final: 0.9037 (mtp) REVERT: D 262 PHE cc_start: 0.8172 (t80) cc_final: 0.7144 (p90) REVERT: D 288 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7570 (mm-40) REVERT: D 351 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7853 (mppt) outliers start: 54 outliers final: 28 residues processed: 212 average time/residue: 0.2484 time to fit residues: 74.5859 Evaluate side-chains 191 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 93 optimal weight: 0.3980 chunk 31 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 137 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 98 GLN C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.173975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134862 restraints weight = 13559.686| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.44 r_work: 0.3303 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12896 Z= 0.134 Angle : 0.759 21.685 17512 Z= 0.334 Chirality : 0.057 1.021 2024 Planarity : 0.005 0.076 2180 Dihedral : 8.441 57.496 2244 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.58 % Allowed : 10.82 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.20), residues: 1524 helix: 0.31 (0.21), residues: 568 sheet: -2.15 (0.28), residues: 312 loop : -2.67 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 296 HIS 0.005 0.001 HIS D 253 PHE 0.012 0.002 PHE B 107 TYR 0.011 0.001 TYR C 195 ARG 0.006 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00990 ( 16) link_NAG-ASN : angle 6.62864 ( 48) link_BETA1-4 : bond 0.02056 ( 12) link_BETA1-4 : angle 4.50042 ( 36) hydrogen bonds : bond 0.03268 ( 428) hydrogen bonds : angle 4.03144 ( 1236) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.78787 ( 8) covalent geometry : bond 0.00303 (12864) covalent geometry : angle 0.64479 (17420) *********************** 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 214 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7028 (mm) REVERT: A 113 SER cc_start: 0.8781 (m) cc_final: 0.8364 (p) REVERT: A 160 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8211 (mp) REVERT: A 220 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7772 (mtm110) REVERT: A 222 LYS cc_start: 0.8049 (mttm) cc_final: 0.7505 (mtmt) REVERT: A 262 PHE cc_start: 0.8015 (t80) cc_final: 0.7035 (p90) REVERT: A 400 GLU cc_start: 0.7625 (tt0) cc_final: 0.6882 (mm-30) REVERT: B 262 PHE cc_start: 0.8182 (t80) cc_final: 0.7104 (p90) REVERT: B 288 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7586 (mm110) REVERT: B 351 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7989 (mptt) REVERT: C 55 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7025 (mm) REVERT: C 113 SER cc_start: 0.8761 (m) cc_final: 0.8332 (p) REVERT: C 160 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8221 (mp) REVERT: C 220 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7782 (mtm110) REVERT: C 222 LYS cc_start: 0.8067 (mttm) cc_final: 0.7525 (mtmt) REVERT: C 262 PHE cc_start: 0.8014 (t80) cc_final: 0.7016 (p90) REVERT: C 400 GLU cc_start: 0.7631 (tt0) cc_final: 0.6890 (mm-30) REVERT: D 198 ARG cc_start: 0.7869 (tmt-80) cc_final: 0.7436 (tpt90) REVERT: D 218 MET cc_start: 0.9024 (mtp) cc_final: 0.8790 (mtm) REVERT: D 247 MET cc_start: 0.9215 (mtp) cc_final: 0.8999 (mtp) REVERT: D 262 PHE cc_start: 0.8174 (t80) cc_final: 0.7134 (p90) REVERT: D 288 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7462 (mm-40) REVERT: D 351 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7841 (mppt) outliers start: 48 outliers final: 26 residues processed: 197 average time/residue: 0.2469 time to fit residues: 70.2320 Evaluate side-chains 181 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 150 optimal weight: 0.0030 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.172900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133487 restraints weight = 13601.542| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.44 r_work: 0.3278 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12896 Z= 0.150 Angle : 0.732 20.509 17512 Z= 0.326 Chirality : 0.056 0.969 2024 Planarity : 0.005 0.074 2180 Dihedral : 7.484 49.801 2240 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.88 % Allowed : 11.34 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1524 helix: 0.76 (0.22), residues: 564 sheet: -2.06 (0.29), residues: 292 loop : -2.48 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 296 HIS 0.004 0.001 HIS B 232 PHE 0.015 0.002 PHE D 107 TYR 0.011 0.001 TYR A 195 ARG 0.004 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.01040 ( 16) link_NAG-ASN : angle 5.85041 ( 48) link_BETA1-4 : bond 0.01853 ( 12) link_BETA1-4 : angle 4.42745 ( 36) hydrogen bonds : bond 0.03201 ( 428) hydrogen bonds : angle 3.94556 ( 1236) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.24289 ( 8) covalent geometry : bond 0.00349 (12864) covalent geometry : angle 0.63543 (17420) *********************** 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 210 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7142 (mm) REVERT: A 113 SER cc_start: 0.8788 (m) cc_final: 0.8341 (p) REVERT: A 160 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 222 LYS cc_start: 0.8127 (mttm) cc_final: 0.7576 (mtmt) REVERT: A 262 PHE cc_start: 0.8116 (t80) cc_final: 0.7078 (p90) REVERT: A 335 GLN cc_start: 0.6843 (tp40) cc_final: 0.6555 (tt0) REVERT: A 351 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7838 (mptt) REVERT: A 400 GLU cc_start: 0.7702 (tt0) cc_final: 0.6975 (mm-30) REVERT: B 262 PHE cc_start: 0.8307 (t80) cc_final: 0.7201 (p90) REVERT: B 288 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7624 (mm110) REVERT: B 351 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7967 (mppt) REVERT: C 55 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7145 (mm) REVERT: C 160 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8346 (mp) REVERT: C 222 LYS cc_start: 0.8123 (mttm) cc_final: 0.7579 (mtmt) REVERT: C 262 PHE cc_start: 0.8106 (t80) cc_final: 0.7058 (p90) REVERT: C 335 GLN cc_start: 0.6849 (tp40) cc_final: 0.6542 (tt0) REVERT: C 351 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7884 (mptt) REVERT: C 400 GLU cc_start: 0.7714 (tt0) cc_final: 0.6990 (mm-30) REVERT: D 198 ARG cc_start: 0.7930 (tmt-80) cc_final: 0.7504 (tpt90) REVERT: D 218 MET cc_start: 0.9043 (mtp) cc_final: 0.8800 (mtm) REVERT: D 262 PHE cc_start: 0.8292 (t80) cc_final: 0.7194 (p90) REVERT: D 288 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7450 (mm-40) REVERT: D 351 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7845 (mppt) outliers start: 52 outliers final: 34 residues processed: 196 average time/residue: 0.2535 time to fit residues: 71.0945 Evaluate side-chains 187 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 42 optimal weight: 1.9990 chunk 141 optimal weight: 0.0270 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.174007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134803 restraints weight = 13662.593| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.35 r_work: 0.3296 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12896 Z= 0.129 Angle : 0.736 21.345 17512 Z= 0.322 Chirality : 0.053 0.941 2024 Planarity : 0.005 0.073 2180 Dihedral : 7.158 50.087 2240 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.06 % Allowed : 12.01 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1524 helix: 1.18 (0.22), residues: 564 sheet: -1.97 (0.29), residues: 292 loop : -2.40 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 296 HIS 0.003 0.000 HIS D 253 PHE 0.013 0.001 PHE C 107 TYR 0.006 0.001 TYR D 269 ARG 0.007 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00966 ( 16) link_NAG-ASN : angle 6.80188 ( 48) link_BETA1-4 : bond 0.01870 ( 12) link_BETA1-4 : angle 4.34009 ( 36) hydrogen bonds : bond 0.02933 ( 428) hydrogen bonds : angle 3.84119 ( 1236) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.20885 ( 8) covalent geometry : bond 0.00293 (12864) covalent geometry : angle 0.61465 (17420) *********************** 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 194 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7216 (mm) REVERT: A 160 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8302 (mp) REVERT: A 222 LYS cc_start: 0.8100 (mttm) cc_final: 0.7560 (mtmt) REVERT: A 262 PHE cc_start: 0.8143 (t80) cc_final: 0.7106 (p90) REVERT: A 335 GLN cc_start: 0.6784 (tp40) cc_final: 0.6516 (tt0) REVERT: B 200 LYS cc_start: 0.8451 (mttp) cc_final: 0.8239 (mttt) REVERT: B 262 PHE cc_start: 0.8339 (t80) cc_final: 0.7210 (p90) REVERT: B 288 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7610 (mm110) REVERT: B 351 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7981 (mppt) REVERT: C 55 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7216 (mm) REVERT: C 160 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 222 LYS cc_start: 0.8099 (mttm) cc_final: 0.7568 (mtmt) REVERT: C 262 PHE cc_start: 0.8080 (t80) cc_final: 0.7053 (p90) REVERT: C 335 GLN cc_start: 0.6862 (tp40) cc_final: 0.6578 (tt0) REVERT: D 198 ARG cc_start: 0.7903 (tmt-80) cc_final: 0.7495 (tpt90) REVERT: D 218 MET cc_start: 0.9015 (mtp) cc_final: 0.8783 (mtm) REVERT: D 262 PHE cc_start: 0.8326 (t80) cc_final: 0.7202 (p90) REVERT: D 288 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7441 (mm-40) REVERT: D 351 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7746 (mppt) outliers start: 41 outliers final: 32 residues processed: 181 average time/residue: 0.2623 time to fit residues: 68.6619 Evaluate side-chains 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135998 restraints weight = 13541.741| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.46 r_work: 0.3315 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12896 Z= 0.138 Angle : 0.693 19.204 17512 Z= 0.311 Chirality : 0.052 0.857 2024 Planarity : 0.005 0.072 2180 Dihedral : 6.873 49.676 2240 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.13 % Allowed : 11.79 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1524 helix: 1.37 (0.22), residues: 564 sheet: -1.96 (0.28), residues: 312 loop : -2.33 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 296 HIS 0.003 0.001 HIS D 253 PHE 0.013 0.002 PHE D 107 TYR 0.012 0.001 TYR A 195 ARG 0.009 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00932 ( 16) link_NAG-ASN : angle 5.54699 ( 48) link_BETA1-4 : bond 0.01774 ( 12) link_BETA1-4 : angle 4.23999 ( 36) hydrogen bonds : bond 0.02890 ( 428) hydrogen bonds : angle 3.83466 ( 1236) SS BOND : bond 0.00036 ( 4) SS BOND : angle 0.13953 ( 8) covalent geometry : bond 0.00322 (12864) covalent geometry : angle 0.60103 (17420) *********************** 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 199 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7184 (mm) REVERT: A 160 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 222 LYS cc_start: 0.8124 (mttm) cc_final: 0.7588 (mtmt) REVERT: A 262 PHE cc_start: 0.8178 (t80) cc_final: 0.7156 (p90) REVERT: A 335 GLN cc_start: 0.6798 (tp40) cc_final: 0.6546 (tt0) REVERT: A 351 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7862 (mptt) REVERT: A 360 MET cc_start: 0.7909 (tpt) cc_final: 0.7519 (tpt) REVERT: B 50 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7228 (ptt) REVERT: B 200 LYS cc_start: 0.8460 (mttp) cc_final: 0.8190 (mttt) REVERT: B 262 PHE cc_start: 0.8413 (t80) cc_final: 0.7246 (p90) REVERT: B 288 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7630 (mm110) REVERT: B 351 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7872 (mppt) REVERT: C 55 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7193 (mm) REVERT: C 160 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8309 (mp) REVERT: C 222 LYS cc_start: 0.8129 (mttm) cc_final: 0.7604 (mtmt) REVERT: C 262 PHE cc_start: 0.8174 (t80) cc_final: 0.7140 (p90) REVERT: C 335 GLN cc_start: 0.6799 (tp40) cc_final: 0.6544 (tt0) REVERT: C 351 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7902 (mptt) REVERT: D 198 ARG cc_start: 0.7911 (tmt-80) cc_final: 0.7475 (tpt90) REVERT: D 200 LYS cc_start: 0.8538 (mttp) cc_final: 0.8281 (mttt) REVERT: D 218 MET cc_start: 0.9031 (mtp) cc_final: 0.8787 (mtm) REVERT: D 262 PHE cc_start: 0.8425 (t80) cc_final: 0.7240 (p90) REVERT: D 288 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7467 (mm-40) REVERT: D 351 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7748 (mppt) outliers start: 42 outliers final: 35 residues processed: 187 average time/residue: 0.2541 time to fit residues: 68.0176 Evaluate side-chains 191 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 0.0770 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.174616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135549 restraints weight = 13613.010| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.47 r_work: 0.3309 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12896 Z= 0.144 Angle : 0.727 23.386 17512 Z= 0.322 Chirality : 0.055 0.933 2024 Planarity : 0.005 0.071 2180 Dihedral : 6.841 50.696 2240 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.43 % Allowed : 11.87 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.21), residues: 1524 helix: 1.43 (0.22), residues: 564 sheet: -1.93 (0.28), residues: 312 loop : -2.32 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 296 HIS 0.003 0.001 HIS D 253 PHE 0.013 0.002 PHE B 107 TYR 0.011 0.001 TYR C 195 ARG 0.013 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00830 ( 16) link_NAG-ASN : angle 6.52315 ( 48) link_BETA1-4 : bond 0.01725 ( 12) link_BETA1-4 : angle 4.15421 ( 36) hydrogen bonds : bond 0.02992 ( 428) hydrogen bonds : angle 3.82882 ( 1236) SS BOND : bond 0.00047 ( 4) SS BOND : angle 0.17238 ( 8) covalent geometry : bond 0.00340 (12864) covalent geometry : angle 0.61490 (17420) *********************** 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 201 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7435 (mt) REVERT: A 160 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 222 LYS cc_start: 0.8123 (mttm) cc_final: 0.7810 (mmtt) REVERT: A 262 PHE cc_start: 0.8232 (t80) cc_final: 0.7183 (p90) REVERT: A 335 GLN cc_start: 0.6819 (tp40) cc_final: 0.6558 (tt0) REVERT: A 351 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7790 (mptt) REVERT: B 50 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7213 (ptt) REVERT: B 200 LYS cc_start: 0.8455 (mttp) cc_final: 0.8178 (mttt) REVERT: B 234 MET cc_start: 0.8999 (ttm) cc_final: 0.8786 (mtp) REVERT: B 262 PHE cc_start: 0.8478 (t80) cc_final: 0.7272 (p90) REVERT: B 288 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7636 (mm110) REVERT: B 351 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7849 (mppt) REVERT: C 55 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7450 (mt) REVERT: C 160 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8316 (mp) REVERT: C 222 LYS cc_start: 0.8129 (mttm) cc_final: 0.7604 (mtmt) REVERT: C 262 PHE cc_start: 0.8209 (t80) cc_final: 0.7174 (p90) REVERT: C 335 GLN cc_start: 0.6820 (tp40) cc_final: 0.6553 (tt0) REVERT: C 351 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7819 (mptt) REVERT: D 50 MET cc_start: 0.7514 (ptt) cc_final: 0.7299 (ptt) REVERT: D 198 ARG cc_start: 0.7950 (tmt-80) cc_final: 0.7509 (tpt90) REVERT: D 200 LYS cc_start: 0.8573 (mttp) cc_final: 0.8314 (mttt) REVERT: D 218 MET cc_start: 0.9040 (mtp) cc_final: 0.8788 (mtm) REVERT: D 262 PHE cc_start: 0.8494 (t80) cc_final: 0.7270 (p90) REVERT: D 288 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7494 (mm-40) REVERT: D 351 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7737 (mptt) outliers start: 46 outliers final: 39 residues processed: 186 average time/residue: 0.2672 time to fit residues: 72.5639 Evaluate side-chains 193 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 104 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.174660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135762 restraints weight = 13478.551| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.47 r_work: 0.3311 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12896 Z= 0.138 Angle : 0.693 18.694 17512 Z= 0.312 Chirality : 0.052 0.953 2024 Planarity : 0.005 0.074 2180 Dihedral : 7.342 78.309 2240 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.43 % Allowed : 11.87 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1524 helix: 1.58 (0.22), residues: 572 sheet: -1.91 (0.28), residues: 312 loop : -2.28 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 296 HIS 0.020 0.001 HIS A 253 PHE 0.013 0.001 PHE D 107 TYR 0.011 0.001 TYR A 195 ARG 0.011 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.01038 ( 16) link_NAG-ASN : angle 5.19821 ( 48) link_BETA1-4 : bond 0.01701 ( 12) link_BETA1-4 : angle 4.08106 ( 36) hydrogen bonds : bond 0.02869 ( 428) hydrogen bonds : angle 3.83523 ( 1236) SS BOND : bond 0.00042 ( 4) SS BOND : angle 0.14300 ( 8) covalent geometry : bond 0.00321 (12864) covalent geometry : angle 0.61160 (17420) *********************** 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 200 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7402 (mt) REVERT: A 160 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 222 LYS cc_start: 0.8201 (mttm) cc_final: 0.7669 (mtmt) REVERT: A 262 PHE cc_start: 0.8248 (t80) cc_final: 0.7260 (p90) REVERT: A 283 ASN cc_start: 0.7106 (t0) cc_final: 0.6786 (t0) REVERT: A 335 GLN cc_start: 0.6805 (tp40) cc_final: 0.6543 (tt0) REVERT: A 351 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7807 (mptt) REVERT: B 50 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7187 (ptt) REVERT: B 200 LYS cc_start: 0.8450 (mttp) cc_final: 0.8171 (mttt) REVERT: B 234 MET cc_start: 0.9007 (ttm) cc_final: 0.8798 (mtp) REVERT: B 262 PHE cc_start: 0.8482 (t80) cc_final: 0.7261 (p90) REVERT: B 288 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7651 (mm110) REVERT: B 351 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7831 (mppt) REVERT: C 55 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7408 (mt) REVERT: C 160 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8310 (mp) REVERT: C 222 LYS cc_start: 0.8122 (mttm) cc_final: 0.7605 (mtmt) REVERT: C 262 PHE cc_start: 0.8238 (t80) cc_final: 0.7242 (p90) REVERT: C 335 GLN cc_start: 0.6806 (tp40) cc_final: 0.6542 (tt0) REVERT: C 351 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7842 (mptt) REVERT: D 198 ARG cc_start: 0.7954 (tmt-80) cc_final: 0.7520 (tpt90) REVERT: D 200 LYS cc_start: 0.8574 (mttp) cc_final: 0.8319 (mttt) REVERT: D 218 MET cc_start: 0.9032 (mtp) cc_final: 0.8790 (mtm) REVERT: D 262 PHE cc_start: 0.8511 (t80) cc_final: 0.7276 (p90) REVERT: D 288 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7483 (mm-40) REVERT: D 351 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7767 (mptt) outliers start: 46 outliers final: 40 residues processed: 187 average time/residue: 0.2418 time to fit residues: 65.4230 Evaluate side-chains 192 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 92 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 57 optimal weight: 0.0060 chunk 52 optimal weight: 0.5980 chunk 150 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN D 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.176200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137398 restraints weight = 13457.073| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.42 r_work: 0.3336 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12896 Z= 0.113 Angle : 0.653 17.827 17512 Z= 0.297 Chirality : 0.049 0.881 2024 Planarity : 0.005 0.073 2180 Dihedral : 6.724 53.076 2240 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.99 % Allowed : 12.84 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1524 helix: 1.76 (0.22), residues: 572 sheet: -1.74 (0.29), residues: 292 loop : -2.25 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 296 HIS 0.014 0.001 HIS A 253 PHE 0.010 0.001 PHE B 107 TYR 0.012 0.001 TYR B 86 ARG 0.011 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00793 ( 16) link_NAG-ASN : angle 5.06606 ( 48) link_BETA1-4 : bond 0.01682 ( 12) link_BETA1-4 : angle 3.88988 ( 36) hydrogen bonds : bond 0.02703 ( 428) hydrogen bonds : angle 3.76741 ( 1236) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.12738 ( 8) covalent geometry : bond 0.00252 (12864) covalent geometry : angle 0.57133 (17420) ********************** 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 197 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7441 (mt) REVERT: A 160 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8297 (mp) REVERT: A 222 LYS cc_start: 0.8122 (mttm) cc_final: 0.7611 (mtmt) REVERT: A 262 PHE cc_start: 0.8314 (t80) cc_final: 0.7249 (p90) REVERT: A 283 ASN cc_start: 0.7029 (t0) cc_final: 0.6684 (m-40) REVERT: A 335 GLN cc_start: 0.6746 (tp40) cc_final: 0.6503 (tt0) REVERT: A 351 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7843 (mptt) REVERT: B 50 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7064 (ptt) REVERT: B 133 ARG cc_start: 0.8851 (ttt-90) cc_final: 0.8391 (mtp85) REVERT: B 200 LYS cc_start: 0.8435 (mttp) cc_final: 0.8175 (mttt) REVERT: B 234 MET cc_start: 0.8988 (ttm) cc_final: 0.8765 (mtp) REVERT: B 262 PHE cc_start: 0.8481 (t80) cc_final: 0.7265 (p90) REVERT: B 288 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7637 (mm110) REVERT: B 351 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7836 (mppt) REVERT: C 55 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7450 (mt) REVERT: C 160 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8282 (mp) REVERT: C 222 LYS cc_start: 0.8088 (mttm) cc_final: 0.7571 (mtmt) REVERT: C 262 PHE cc_start: 0.8285 (t80) cc_final: 0.7230 (p90) REVERT: C 283 ASN cc_start: 0.7086 (t0) cc_final: 0.6698 (m-40) REVERT: C 335 GLN cc_start: 0.6766 (tp40) cc_final: 0.6527 (tt0) REVERT: C 351 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7856 (mptt) REVERT: C 360 MET cc_start: 0.7901 (tpt) cc_final: 0.7582 (tpt) REVERT: D 198 ARG cc_start: 0.7886 (tmt-80) cc_final: 0.7427 (tpt90) REVERT: D 200 LYS cc_start: 0.8579 (mttp) cc_final: 0.8318 (mttt) REVERT: D 218 MET cc_start: 0.9008 (mtp) cc_final: 0.8806 (mtm) REVERT: D 262 PHE cc_start: 0.8526 (t80) cc_final: 0.7265 (p90) REVERT: D 288 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7461 (mm-40) REVERT: D 351 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7739 (mptt) outliers start: 40 outliers final: 32 residues processed: 184 average time/residue: 0.2416 time to fit residues: 64.0990 Evaluate side-chains 187 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 chunk 137 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.174582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135104 restraints weight = 13572.598| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.43 r_work: 0.3302 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12896 Z= 0.145 Angle : 0.674 17.753 17512 Z= 0.309 Chirality : 0.050 0.852 2024 Planarity : 0.005 0.074 2180 Dihedral : 6.618 49.566 2240 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.06 % Allowed : 13.06 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1524 helix: 1.62 (0.22), residues: 576 sheet: -1.79 (0.28), residues: 312 loop : -2.16 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 296 HIS 0.015 0.001 HIS A 253 PHE 0.015 0.002 PHE B 107 TYR 0.019 0.001 TYR D 86 ARG 0.010 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00760 ( 16) link_NAG-ASN : angle 5.01198 ( 48) link_BETA1-4 : bond 0.01608 ( 12) link_BETA1-4 : angle 3.86627 ( 36) hydrogen bonds : bond 0.02858 ( 428) hydrogen bonds : angle 3.81259 ( 1236) SS BOND : bond 0.00015 ( 4) SS BOND : angle 0.11549 ( 8) covalent geometry : bond 0.00343 (12864) covalent geometry : angle 0.59677 (17420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7134.72 seconds wall clock time: 124 minutes 20.38 seconds (7460.38 seconds total)