Starting phenix.real_space_refine on Wed Mar 4 09:55:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwv_29520/03_2026/8fwv_29520.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwv_29520/03_2026/8fwv_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_29520/03_2026/8fwv_29520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwv_29520/03_2026/8fwv_29520.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwv_29520/03_2026/8fwv_29520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwv_29520/03_2026/8fwv_29520.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.05, per 1000 atoms: 0.24 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: 1.18 Conformation dependent library (CDL) restraints added in 570.4 milliseconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 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: 0.41 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: 1.98 Time building geometry restraints manager: 1.52 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain '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: 7.050 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.390 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.20 (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 ARG 0.008 0.001 ARG D 158 TYR 0.016 0.002 TYR D 252 PHE 0.024 0.003 PHE A 107 TRP 0.028 0.004 TRP A 353 HIS 0.010 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00717 (12864) covalent geometry : angle 1.06588 (17420) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.48138 ( 8) hydrogen bonds : bond 0.28591 ( 428) hydrogen bonds : angle 9.69215 ( 1236) link_BETA1-4 : bond 0.02842 ( 12) link_BETA1-4 : angle 7.57409 ( 36) link_NAG-ASN : bond 0.01481 ( 16) link_NAG-ASN : angle 10.18381 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 311 time to evaluate : 0.398 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: 0.7692 (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: 0.7627 (t0) REVERT: D 198 ARG cc_start: 0.7349 (tmt-80) cc_final: 0.7052 (tpt90) REVERT: D 200 LYS cc_start: 0.7855 (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: 0.1386 time to fit residues: 60.4275 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 : 0.415 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.137018 restraints weight = 13489.417| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.24 r_work: 0.3332 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12896 Z= 0.160 Angle : 0.835 23.258 17512 Z= 0.379 Chirality : 0.061 1.088 2024 Planarity : 0.006 0.084 2180 Dihedral : 12.663 83.065 2244 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.88 % Allowed : 9.40 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.18), residues: 1524 helix: -2.31 (0.16), residues: 568 sheet: -2.46 (0.27), residues: 328 loop : -2.73 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 158 TYR 0.007 0.001 TYR B 252 PHE 0.017 0.002 PHE B 166 TRP 0.013 0.002 TRP C 353 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00348 (12864) covalent geometry : angle 0.72196 (17420) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.38002 ( 8) hydrogen bonds : bond 0.04492 ( 428) hydrogen bonds : angle 4.95429 ( 1236) link_BETA1-4 : bond 0.02564 ( 12) link_BETA1-4 : angle 4.99247 ( 36) link_NAG-ASN : bond 0.01115 ( 16) link_NAG-ASN : angle 6.80205 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7034 (mm) REVERT: A 113 SER cc_start: 0.8852 (m) cc_final: 0.8490 (p) REVERT: A 156 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8007 (mt) REVERT: A 177 ASP cc_start: 0.8322 (t70) cc_final: 0.8072 (t0) REVERT: A 222 LYS cc_start: 0.8069 (mttm) cc_final: 0.7650 (mmtm) REVERT: A 262 PHE cc_start: 0.7744 (t80) cc_final: 0.7132 (p90) REVERT: A 291 SER cc_start: 0.7643 (t) cc_final: 0.7346 (m) REVERT: B 262 PHE cc_start: 0.7942 (t80) cc_final: 0.7095 (p90) REVERT: B 288 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7621 (mm110) REVERT: B 351 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7937 (mppt) REVERT: C 55 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7046 (mm) REVERT: C 113 SER cc_start: 0.8843 (m) cc_final: 0.8478 (p) REVERT: C 156 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7997 (mt) REVERT: C 177 ASP cc_start: 0.8339 (t70) cc_final: 0.8092 (t0) REVERT: C 222 LYS cc_start: 0.8061 (mttm) cc_final: 0.7639 (mmtm) REVERT: C 262 PHE cc_start: 0.7751 (t80) cc_final: 0.7099 (p90) REVERT: C 291 SER cc_start: 0.7636 (t) cc_final: 0.7361 (m) REVERT: D 198 ARG cc_start: 0.7927 (tmt-80) cc_final: 0.7475 (tpt90) REVERT: D 218 MET cc_start: 0.8947 (mtp) cc_final: 0.8684 (mtm) REVERT: D 247 MET cc_start: 0.9198 (mtp) cc_final: 0.8966 (mtp) REVERT: D 262 PHE cc_start: 0.7939 (t80) cc_final: 0.7084 (p90) REVERT: D 351 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7696 (mppt) outliers start: 52 outliers final: 25 residues processed: 209 average time/residue: 0.1145 time to fit residues: 34.3916 Evaluate side-chains 182 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 97 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.0070 chunk 74 optimal weight: 0.0470 chunk 56 optimal weight: 1.9990 chunk 113 optimal weight: 0.0870 chunk 151 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.2474 ------------------------------------------------------------------------------- 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 C 196 ASN C 346 GLN D 165 GLN D 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139556 restraints weight = 13715.007| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.26 r_work: 0.3364 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12896 Z= 0.115 Angle : 0.741 20.904 17512 Z= 0.326 Chirality : 0.055 0.912 2024 Planarity : 0.005 0.077 2180 Dihedral : 9.618 57.318 2244 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.58 % Allowed : 9.33 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.19), residues: 1524 helix: -0.44 (0.20), residues: 572 sheet: -2.35 (0.28), residues: 312 loop : -2.74 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 37 TYR 0.016 0.001 TYR C 195 PHE 0.011 0.001 PHE B 359 TRP 0.016 0.002 TRP C 296 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00234 (12864) covalent geometry : angle 0.63641 (17420) SS BOND : bond 0.00175 ( 4) SS BOND : angle 0.13513 ( 8) hydrogen bonds : bond 0.03528 ( 428) hydrogen bonds : angle 4.23253 ( 1236) link_BETA1-4 : bond 0.02112 ( 12) link_BETA1-4 : angle 4.56369 ( 36) link_NAG-ASN : bond 0.01245 ( 16) link_NAG-ASN : angle 6.12390 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6903 (mm) REVERT: A 113 SER cc_start: 0.8618 (m) cc_final: 0.8221 (p) REVERT: A 156 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7662 (mt) REVERT: A 177 ASP cc_start: 0.8062 (t70) cc_final: 0.7845 (t0) REVERT: A 220 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7710 (mtm110) REVERT: A 222 LYS cc_start: 0.7969 (mttm) cc_final: 0.7641 (mmtm) REVERT: A 262 PHE cc_start: 0.7771 (t80) cc_final: 0.7119 (p90) REVERT: A 283 ASN cc_start: 0.7125 (t0) cc_final: 0.6716 (m-40) REVERT: A 360 MET cc_start: 0.7776 (tpt) cc_final: 0.7323 (tpt) REVERT: B 262 PHE cc_start: 0.7804 (t80) cc_final: 0.7096 (p90) REVERT: B 288 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7555 (mm110) REVERT: B 294 GLU cc_start: 0.7697 (tt0) cc_final: 0.7157 (pt0) REVERT: B 351 LYS cc_start: 0.8258 (mtmt) cc_final: 0.8038 (mptt) REVERT: C 55 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6880 (mm) REVERT: C 113 SER cc_start: 0.8596 (m) cc_final: 0.8180 (p) REVERT: C 156 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7654 (mt) REVERT: C 177 ASP cc_start: 0.8063 (t70) cc_final: 0.7848 (t0) REVERT: C 222 LYS cc_start: 0.7987 (mttm) cc_final: 0.7677 (mmtm) REVERT: C 262 PHE cc_start: 0.7791 (t80) cc_final: 0.7111 (p90) REVERT: C 283 ASN cc_start: 0.7141 (t0) cc_final: 0.6738 (m-40) REVERT: C 291 SER cc_start: 0.7649 (t) cc_final: 0.7368 (m) REVERT: D 50 MET cc_start: 0.7411 (ptp) cc_final: 0.7185 (ptt) REVERT: D 198 ARG cc_start: 0.7629 (tmt-80) cc_final: 0.7334 (tpt90) REVERT: D 218 MET cc_start: 0.8883 (mtp) cc_final: 0.8665 (mtm) REVERT: D 247 MET cc_start: 0.9144 (mtp) cc_final: 0.8923 (mtp) REVERT: D 262 PHE cc_start: 0.7779 (t80) cc_final: 0.7159 (p90) REVERT: D 288 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7472 (mm-40) outliers start: 48 outliers final: 20 residues processed: 207 average time/residue: 0.1055 time to fit residues: 31.8834 Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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 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 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 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 139 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 130 optimal weight: 0.0570 chunk 82 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN C 196 ASN D 98 GLN D 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.176092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137047 restraints weight = 13539.045| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.28 r_work: 0.3331 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12896 Z= 0.133 Angle : 0.741 20.551 17512 Z= 0.328 Chirality : 0.056 0.969 2024 Planarity : 0.005 0.079 2180 Dihedral : 7.998 58.087 2244 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.36 % Allowed : 10.60 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.20), residues: 1524 helix: 0.44 (0.21), residues: 572 sheet: -2.23 (0.28), residues: 312 loop : -2.66 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 37 TYR 0.014 0.001 TYR A 195 PHE 0.014 0.002 PHE B 107 TRP 0.014 0.001 TRP C 296 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00296 (12864) covalent geometry : angle 0.64075 (17420) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.21156 ( 8) hydrogen bonds : bond 0.03295 ( 428) hydrogen bonds : angle 4.00981 ( 1236) link_BETA1-4 : bond 0.01954 ( 12) link_BETA1-4 : angle 4.41325 ( 36) link_NAG-ASN : bond 0.01145 ( 16) link_NAG-ASN : angle 6.05913 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7038 (mm) REVERT: A 113 SER cc_start: 0.8782 (m) cc_final: 0.8358 (p) REVERT: A 156 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7784 (mm) REVERT: A 160 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8230 (mp) REVERT: A 220 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7681 (mtm110) REVERT: A 222 LYS cc_start: 0.8037 (mttm) cc_final: 0.7666 (mmtm) REVERT: A 262 PHE cc_start: 0.7926 (t80) cc_final: 0.7065 (p90) REVERT: A 283 ASN cc_start: 0.7186 (t0) cc_final: 0.6788 (m-40) REVERT: A 351 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7808 (mptt) REVERT: B 50 MET cc_start: 0.7607 (ptt) cc_final: 0.7317 (ptt) REVERT: B 262 PHE cc_start: 0.8116 (t80) cc_final: 0.7129 (p90) REVERT: B 288 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7611 (mm110) REVERT: B 351 LYS cc_start: 0.8328 (mtmt) cc_final: 0.8021 (mppt) REVERT: C 55 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7016 (mm) REVERT: C 113 SER cc_start: 0.8776 (m) cc_final: 0.8342 (p) REVERT: C 156 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7804 (mm) REVERT: C 160 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8243 (mp) REVERT: C 222 LYS cc_start: 0.8057 (mttm) cc_final: 0.7723 (mmtm) REVERT: C 262 PHE cc_start: 0.7926 (t80) cc_final: 0.7042 (p90) REVERT: C 283 ASN cc_start: 0.7171 (t0) cc_final: 0.6763 (m-40) REVERT: D 198 ARG cc_start: 0.7861 (tmt-80) cc_final: 0.7413 (tpt90) REVERT: D 218 MET cc_start: 0.9001 (mtp) cc_final: 0.8759 (mtm) REVERT: D 247 MET cc_start: 0.9194 (mtp) cc_final: 0.8987 (mtp) REVERT: D 262 PHE cc_start: 0.8121 (t80) cc_final: 0.7181 (p90) REVERT: D 288 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7435 (mm-40) outliers start: 45 outliers final: 29 residues processed: 195 average time/residue: 0.1105 time to fit residues: 30.9153 Evaluate side-chains 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 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 156 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.172937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133238 restraints weight = 13654.703| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.49 r_work: 0.3276 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12896 Z= 0.183 Angle : 0.744 20.774 17512 Z= 0.334 Chirality : 0.057 0.955 2024 Planarity : 0.005 0.079 2180 Dihedral : 7.688 57.151 2244 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.66 % Allowed : 10.97 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.20), residues: 1524 helix: 0.70 (0.21), residues: 572 sheet: -2.21 (0.27), residues: 312 loop : -2.52 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 37 TYR 0.015 0.002 TYR C 195 PHE 0.019 0.002 PHE A 107 TRP 0.011 0.001 TRP C 296 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00440 (12864) covalent geometry : angle 0.65171 (17420) SS BOND : bond 0.00067 ( 4) SS BOND : angle 0.69713 ( 8) hydrogen bonds : bond 0.03290 ( 428) hydrogen bonds : angle 4.02248 ( 1236) link_BETA1-4 : bond 0.01910 ( 12) link_BETA1-4 : angle 4.47977 ( 36) link_NAG-ASN : bond 0.00884 ( 16) link_NAG-ASN : angle 5.72091 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6543 (t) cc_final: 0.6336 (p) REVERT: A 55 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7156 (mm) REVERT: A 113 SER cc_start: 0.8787 (m) cc_final: 0.8337 (p) REVERT: A 220 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7803 (mtm110) REVERT: A 222 LYS cc_start: 0.8084 (mttm) cc_final: 0.7564 (mtmt) REVERT: A 262 PHE cc_start: 0.8059 (t80) cc_final: 0.7059 (p90) REVERT: A 283 ASN cc_start: 0.7257 (t0) cc_final: 0.6941 (t0) REVERT: B 50 MET cc_start: 0.7621 (ptt) cc_final: 0.7340 (ptt) REVERT: B 262 PHE cc_start: 0.8255 (t80) cc_final: 0.7173 (p90) REVERT: B 288 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7587 (mm110) REVERT: B 351 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7987 (mptt) REVERT: C 45 VAL cc_start: 0.6579 (t) cc_final: 0.6375 (p) REVERT: C 55 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7169 (mm) REVERT: C 222 LYS cc_start: 0.8124 (mttm) cc_final: 0.7772 (mmtm) REVERT: C 262 PHE cc_start: 0.8041 (t80) cc_final: 0.7034 (p90) REVERT: C 283 ASN cc_start: 0.7253 (t0) cc_final: 0.6942 (t0) REVERT: D 198 ARG cc_start: 0.7936 (tmt-80) cc_final: 0.7504 (tpt90) REVERT: D 218 MET cc_start: 0.9063 (mtp) cc_final: 0.8791 (mtm) REVERT: D 247 MET cc_start: 0.9217 (mtp) cc_final: 0.9014 (mtp) REVERT: D 262 PHE cc_start: 0.8239 (t80) cc_final: 0.7177 (p90) REVERT: D 288 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7453 (mm-40) outliers start: 49 outliers final: 33 residues processed: 193 average time/residue: 0.1103 time to fit residues: 30.6605 Evaluate side-chains 188 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 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 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 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 172 VAL Chi-restraints excluded: chain C residue 233 GLU 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 385 THR 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 61 optimal weight: 0.7980 chunk 54 optimal weight: 0.0470 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN C 196 ASN D 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134077 restraints weight = 13538.144| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.45 r_work: 0.3281 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12896 Z= 0.152 Angle : 0.704 20.194 17512 Z= 0.317 Chirality : 0.049 0.910 2024 Planarity : 0.005 0.077 2180 Dihedral : 7.678 58.138 2240 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.51 % Allowed : 11.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.21), residues: 1524 helix: 1.03 (0.21), residues: 572 sheet: -2.03 (0.28), residues: 308 loop : -2.52 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 37 TYR 0.013 0.001 TYR B 86 PHE 0.014 0.002 PHE D 107 TRP 0.013 0.001 TRP D 296 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00355 (12864) covalent geometry : angle 0.63697 (17420) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.19022 ( 8) hydrogen bonds : bond 0.03026 ( 428) hydrogen bonds : angle 3.96558 ( 1236) link_BETA1-4 : bond 0.01891 ( 12) link_BETA1-4 : angle 4.40787 ( 36) link_NAG-ASN : bond 0.00834 ( 16) link_NAG-ASN : angle 4.37798 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6569 (t) cc_final: 0.6355 (p) REVERT: A 55 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7102 (mm) REVERT: A 113 SER cc_start: 0.8753 (m) cc_final: 0.8288 (p) REVERT: A 160 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 222 LYS cc_start: 0.8116 (mttm) cc_final: 0.7564 (mtmt) REVERT: A 262 PHE cc_start: 0.8086 (t80) cc_final: 0.7056 (p90) REVERT: A 335 GLN cc_start: 0.6758 (tp40) cc_final: 0.6475 (tt0) REVERT: A 351 LYS cc_start: 0.8124 (mtmm) cc_final: 0.7787 (mptt) REVERT: B 262 PHE cc_start: 0.8271 (t80) cc_final: 0.7183 (p90) REVERT: B 288 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7604 (mm110) REVERT: B 351 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7969 (mppt) REVERT: C 45 VAL cc_start: 0.6595 (t) cc_final: 0.6382 (p) REVERT: C 55 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7126 (mm) REVERT: C 160 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8261 (mp) REVERT: C 222 LYS cc_start: 0.8119 (mttm) cc_final: 0.7766 (mmtm) REVERT: C 262 PHE cc_start: 0.8055 (t80) cc_final: 0.7029 (p90) REVERT: C 335 GLN cc_start: 0.6800 (tp40) cc_final: 0.6513 (tt0) REVERT: C 351 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7784 (mptt) REVERT: D 198 ARG cc_start: 0.7886 (tmt-80) cc_final: 0.7450 (tpt90) REVERT: D 218 MET cc_start: 0.9048 (mtp) cc_final: 0.8776 (mtm) REVERT: D 262 PHE cc_start: 0.8280 (t80) cc_final: 0.7228 (p90) REVERT: D 288 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7445 (mm-40) outliers start: 47 outliers final: 32 residues processed: 200 average time/residue: 0.1074 time to fit residues: 31.1419 Evaluate side-chains 187 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 0.0060 chunk 100 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN C 196 ASN D 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.175381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137081 restraints weight = 13574.577| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.47 r_work: 0.3324 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12896 Z= 0.126 Angle : 0.676 19.378 17512 Z= 0.306 Chirality : 0.047 0.856 2024 Planarity : 0.005 0.075 2180 Dihedral : 7.157 49.955 2240 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.84 % Allowed : 12.16 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.21), residues: 1524 helix: 1.37 (0.22), residues: 572 sheet: -1.92 (0.29), residues: 288 loop : -2.43 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 37 TYR 0.026 0.001 TYR B 86 PHE 0.012 0.001 PHE D 107 TRP 0.014 0.001 TRP D 296 HIS 0.009 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00288 (12864) covalent geometry : angle 0.60690 (17420) SS BOND : bond 0.00064 ( 4) SS BOND : angle 0.51406 ( 8) hydrogen bonds : bond 0.02854 ( 428) hydrogen bonds : angle 3.88179 ( 1236) link_BETA1-4 : bond 0.01862 ( 12) link_BETA1-4 : angle 4.31013 ( 36) link_NAG-ASN : bond 0.00778 ( 16) link_NAG-ASN : angle 4.35227 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6599 (t) cc_final: 0.6371 (p) REVERT: A 55 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7131 (mm) REVERT: A 160 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 222 LYS cc_start: 0.8074 (mttm) cc_final: 0.7537 (mtmt) REVERT: A 247 MET cc_start: 0.7483 (mtp) cc_final: 0.7259 (mmm) REVERT: A 262 PHE cc_start: 0.8118 (t80) cc_final: 0.7148 (p90) REVERT: A 283 ASN cc_start: 0.7065 (t0) cc_final: 0.6752 (m-40) REVERT: A 335 GLN cc_start: 0.6729 (tp40) cc_final: 0.6469 (tt0) REVERT: A 351 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7768 (mptt) REVERT: B 262 PHE cc_start: 0.8264 (t80) cc_final: 0.7169 (p90) REVERT: B 288 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7637 (mm110) REVERT: B 351 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7942 (mppt) REVERT: C 45 VAL cc_start: 0.6620 (t) cc_final: 0.6392 (p) REVERT: C 55 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7130 (mm) REVERT: C 160 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8173 (mp) REVERT: C 222 LYS cc_start: 0.8109 (mttm) cc_final: 0.7693 (mmtm) REVERT: C 262 PHE cc_start: 0.8101 (t80) cc_final: 0.7098 (p90) REVERT: C 283 ASN cc_start: 0.7111 (t0) cc_final: 0.6770 (m-40) REVERT: C 335 GLN cc_start: 0.6806 (tp40) cc_final: 0.6534 (tt0) REVERT: C 351 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7812 (mptt) REVERT: D 198 ARG cc_start: 0.7927 (tmt-80) cc_final: 0.7504 (tpt90) REVERT: D 218 MET cc_start: 0.9021 (mtp) cc_final: 0.8782 (mtm) REVERT: D 262 PHE cc_start: 0.8282 (t80) cc_final: 0.7203 (p90) REVERT: D 288 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7464 (mm-40) outliers start: 38 outliers final: 28 residues processed: 188 average time/residue: 0.1142 time to fit residues: 30.8805 Evaluate side-chains 189 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 0.0980 chunk 113 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 16 optimal weight: 0.0040 chunk 56 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.177500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139244 restraints weight = 13472.583| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.34 r_work: 0.3359 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12896 Z= 0.106 Angle : 0.624 18.059 17512 Z= 0.285 Chirality : 0.045 0.771 2024 Planarity : 0.005 0.074 2180 Dihedral : 6.527 50.846 2240 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.31 % Allowed : 12.16 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.21), residues: 1524 helix: 1.73 (0.22), residues: 572 sheet: -1.72 (0.29), residues: 288 loop : -2.33 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 37 TYR 0.017 0.001 TYR B 86 PHE 0.012 0.001 PHE A 107 TRP 0.015 0.001 TRP D 296 HIS 0.008 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00232 (12864) covalent geometry : angle 0.55715 (17420) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.20794 ( 8) hydrogen bonds : bond 0.02628 ( 428) hydrogen bonds : angle 3.76876 ( 1236) link_BETA1-4 : bond 0.01776 ( 12) link_BETA1-4 : angle 4.10610 ( 36) link_NAG-ASN : bond 0.00745 ( 16) link_NAG-ASN : angle 4.08875 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6533 (t) cc_final: 0.6302 (p) REVERT: A 160 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8177 (mp) REVERT: A 222 LYS cc_start: 0.8125 (mttm) cc_final: 0.7700 (mmtm) REVERT: A 247 MET cc_start: 0.7449 (mtp) cc_final: 0.7240 (mmm) REVERT: A 262 PHE cc_start: 0.8198 (t80) cc_final: 0.7146 (p90) REVERT: A 283 ASN cc_start: 0.6957 (t0) cc_final: 0.6704 (m-40) REVERT: A 335 GLN cc_start: 0.6760 (tp40) cc_final: 0.6518 (tt0) REVERT: A 351 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7806 (mptt) REVERT: B 133 ARG cc_start: 0.8831 (ttt-90) cc_final: 0.8374 (mtp85) REVERT: B 262 PHE cc_start: 0.8344 (t80) cc_final: 0.7207 (p90) REVERT: B 288 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7632 (mm110) REVERT: B 351 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7943 (mptt) REVERT: C 45 VAL cc_start: 0.6543 (t) cc_final: 0.6309 (p) REVERT: C 160 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8191 (mp) REVERT: C 194 ARG cc_start: 0.8049 (ptm160) cc_final: 0.7845 (ptm160) REVERT: C 222 LYS cc_start: 0.8105 (mttm) cc_final: 0.7696 (mmtm) REVERT: C 262 PHE cc_start: 0.8185 (t80) cc_final: 0.7136 (p90) REVERT: C 283 ASN cc_start: 0.6971 (t0) cc_final: 0.6683 (m-40) REVERT: C 335 GLN cc_start: 0.6781 (tp40) cc_final: 0.6534 (tt0) REVERT: C 351 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7825 (mptt) REVERT: D 37 ARG cc_start: 0.8450 (ttm110) cc_final: 0.8094 (ttp-110) REVERT: D 133 ARG cc_start: 0.8802 (ttt-90) cc_final: 0.8332 (mtp85) REVERT: D 198 ARG cc_start: 0.7899 (tmt-80) cc_final: 0.7482 (tpt90) REVERT: D 262 PHE cc_start: 0.8338 (t80) cc_final: 0.7214 (p90) REVERT: D 288 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7453 (mm-40) outliers start: 31 outliers final: 23 residues processed: 189 average time/residue: 0.1174 time to fit residues: 31.6193 Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 291 SER 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 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 160 ILE Chi-restraints excluded: chain C residue 172 VAL 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.2980 chunk 144 optimal weight: 0.0030 chunk 101 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 165 GLN D 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138376 restraints weight = 13502.515| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.38 r_work: 0.3342 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12896 Z= 0.111 Angle : 0.611 17.596 17512 Z= 0.281 Chirality : 0.045 0.753 2024 Planarity : 0.004 0.072 2180 Dihedral : 6.321 50.473 2240 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.39 % Allowed : 12.61 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.21), residues: 1524 helix: 1.77 (0.22), residues: 576 sheet: -1.63 (0.29), residues: 288 loop : -2.30 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.020 0.001 TYR B 86 PHE 0.013 0.001 PHE C 107 TRP 0.011 0.001 TRP B 296 HIS 0.007 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00248 (12864) covalent geometry : angle 0.54657 (17420) SS BOND : bond 0.00025 ( 4) SS BOND : angle 0.12681 ( 8) hydrogen bonds : bond 0.02628 ( 428) hydrogen bonds : angle 3.73983 ( 1236) link_BETA1-4 : bond 0.01738 ( 12) link_BETA1-4 : angle 4.02931 ( 36) link_NAG-ASN : bond 0.00734 ( 16) link_NAG-ASN : angle 3.92305 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6499 (t) cc_final: 0.6271 (p) REVERT: A 55 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7199 (mm) REVERT: A 160 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8166 (mp) REVERT: A 222 LYS cc_start: 0.8138 (mttm) cc_final: 0.7606 (mtmt) REVERT: A 262 PHE cc_start: 0.8264 (t80) cc_final: 0.7148 (p90) REVERT: A 283 ASN cc_start: 0.6865 (t0) cc_final: 0.6626 (m-40) REVERT: A 335 GLN cc_start: 0.6775 (tp40) cc_final: 0.6523 (tt0) REVERT: A 351 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7798 (mptt) REVERT: B 133 ARG cc_start: 0.8821 (ttt-90) cc_final: 0.8329 (mtp85) REVERT: B 165 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8062 (mt0) REVERT: B 262 PHE cc_start: 0.8359 (t80) cc_final: 0.7209 (p90) REVERT: B 288 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7624 (mm110) REVERT: B 351 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7887 (mppt) REVERT: C 45 VAL cc_start: 0.6537 (t) cc_final: 0.6310 (p) REVERT: C 55 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7195 (mm) REVERT: C 160 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8155 (mp) REVERT: C 222 LYS cc_start: 0.8018 (mttm) cc_final: 0.7590 (mmtm) REVERT: C 262 PHE cc_start: 0.8262 (t80) cc_final: 0.7136 (p90) REVERT: C 283 ASN cc_start: 0.6952 (t0) cc_final: 0.6656 (m-40) REVERT: C 335 GLN cc_start: 0.6811 (tp40) cc_final: 0.6532 (tt0) REVERT: C 351 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7844 (mptt) REVERT: D 37 ARG cc_start: 0.8427 (ttm110) cc_final: 0.8058 (ttp-110) REVERT: D 133 ARG cc_start: 0.8808 (ttt-90) cc_final: 0.8318 (mtp85) REVERT: D 198 ARG cc_start: 0.7928 (tmt-80) cc_final: 0.7443 (tpt90) REVERT: D 200 LYS cc_start: 0.8486 (mttp) cc_final: 0.8238 (mttt) REVERT: D 262 PHE cc_start: 0.8366 (t80) cc_final: 0.7190 (p90) REVERT: D 288 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7457 (mm-40) outliers start: 32 outliers final: 25 residues processed: 181 average time/residue: 0.1218 time to fit residues: 31.3592 Evaluate side-chains 182 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 291 SER 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 160 ILE Chi-restraints excluded: chain C residue 172 VAL 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 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 346 GLN 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 136 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.175884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136642 restraints weight = 13549.543| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.38 r_work: 0.3321 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12896 Z= 0.136 Angle : 0.629 17.510 17512 Z= 0.291 Chirality : 0.046 0.755 2024 Planarity : 0.005 0.073 2180 Dihedral : 6.320 49.958 2240 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.24 % Allowed : 12.69 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1524 helix: 1.72 (0.22), residues: 576 sheet: -1.69 (0.28), residues: 308 loop : -2.25 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.024 0.001 TYR B 86 PHE 0.013 0.001 PHE B 107 TRP 0.011 0.001 TRP A 296 HIS 0.006 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00320 (12864) covalent geometry : angle 0.56811 (17420) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.60663 ( 8) hydrogen bonds : bond 0.02722 ( 428) hydrogen bonds : angle 3.76204 ( 1236) link_BETA1-4 : bond 0.01704 ( 12) link_BETA1-4 : angle 4.00010 ( 36) link_NAG-ASN : bond 0.00717 ( 16) link_NAG-ASN : angle 3.89826 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.6486 (t) cc_final: 0.6254 (p) REVERT: A 55 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7375 (mt) REVERT: A 160 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8207 (mp) REVERT: A 222 LYS cc_start: 0.8149 (mttm) cc_final: 0.7617 (mtmt) REVERT: A 262 PHE cc_start: 0.8296 (t80) cc_final: 0.7174 (p90) REVERT: A 283 ASN cc_start: 0.6908 (t0) cc_final: 0.6624 (m-40) REVERT: A 335 GLN cc_start: 0.6803 (tp40) cc_final: 0.6531 (tt0) REVERT: A 351 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7796 (mptt) REVERT: B 133 ARG cc_start: 0.8855 (ttt-90) cc_final: 0.8374 (mtp85) REVERT: B 165 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8091 (mt0) REVERT: B 262 PHE cc_start: 0.8400 (t80) cc_final: 0.7235 (p90) REVERT: B 288 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7661 (mm110) REVERT: B 351 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7903 (mppt) REVERT: C 45 VAL cc_start: 0.6519 (t) cc_final: 0.6289 (p) REVERT: C 55 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7394 (mt) REVERT: C 160 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 222 LYS cc_start: 0.8050 (mttm) cc_final: 0.7627 (mmtm) REVERT: C 262 PHE cc_start: 0.8296 (t80) cc_final: 0.7164 (p90) REVERT: C 283 ASN cc_start: 0.6975 (t0) cc_final: 0.6666 (m-40) REVERT: C 335 GLN cc_start: 0.6780 (tp40) cc_final: 0.6520 (tt0) REVERT: C 351 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7855 (mptt) REVERT: D 37 ARG cc_start: 0.8439 (ttm110) cc_final: 0.8062 (ttp-110) REVERT: D 133 ARG cc_start: 0.8834 (ttt-90) cc_final: 0.8359 (mtp85) REVERT: D 198 ARG cc_start: 0.7956 (tmt-80) cc_final: 0.7477 (tpt90) REVERT: D 200 LYS cc_start: 0.8478 (mttp) cc_final: 0.8234 (mttt) REVERT: D 262 PHE cc_start: 0.8402 (t80) cc_final: 0.7212 (p90) REVERT: D 288 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7470 (mm-40) outliers start: 30 outliers final: 26 residues processed: 184 average time/residue: 0.1129 time to fit residues: 29.9857 Evaluate side-chains 187 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 291 SER 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 0.0170 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 134 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 165 GLN D 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.176541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137365 restraints weight = 13533.806| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.38 r_work: 0.3332 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12896 Z= 0.119 Angle : 0.610 17.083 17512 Z= 0.284 Chirality : 0.045 0.723 2024 Planarity : 0.005 0.072 2180 Dihedral : 6.185 49.909 2240 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.61 % Allowed : 12.54 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.22), residues: 1524 helix: 1.83 (0.22), residues: 576 sheet: -1.63 (0.28), residues: 308 loop : -2.13 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.023 0.001 TYR B 86 PHE 0.011 0.001 PHE D 107 TRP 0.011 0.001 TRP B 296 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00270 (12864) covalent geometry : angle 0.55262 (17420) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.15287 ( 8) hydrogen bonds : bond 0.02645 ( 428) hydrogen bonds : angle 3.74990 ( 1236) link_BETA1-4 : bond 0.01653 ( 12) link_BETA1-4 : angle 3.84171 ( 36) link_NAG-ASN : bond 0.00714 ( 16) link_NAG-ASN : angle 3.72830 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3512.16 seconds wall clock time: 60 minutes 46.01 seconds (3646.01 seconds total)