Starting phenix.real_space_refine on Wed Mar 4 05:47:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7occ_12803/03_2026/7occ_12803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7occ_12803/03_2026/7occ_12803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7occ_12803/03_2026/7occ_12803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7occ_12803/03_2026/7occ_12803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7occ_12803/03_2026/7occ_12803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7occ_12803/03_2026/7occ_12803.map" } resolution = 3.4 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= 0.000 sd= 0.004 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 36 5.16 5 C 7178 2.51 5 N 1860 2.21 5 O 2128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 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: 11202 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2624 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 404 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 7, 'GLN:plan1': 9, 'ARG:plan': 14, 'GLU:plan': 11, 'ASP:plan': 11, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 215 Chain: "B" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2840 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 364} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 4, 'GLN:plan1': 5, 'ARG:plan': 5, 'ASP:plan': 5, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2624 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 404 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 7, 'GLN:plan1': 9, 'ARG:plan': 14, 'GLU:plan': 11, 'ASP:plan': 11, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 215 Chain: "D" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2840 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 364} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 4, 'GLN:plan1': 5, 'ARG:plan': 5, 'ASP:plan': 5, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 96 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: 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 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: "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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.77, per 1000 atoms: 0.25 Number of scatterers: 11202 At special positions: 0 Unit cell: (144.45, 127.33, 81.32, 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 36 16.00 O 2128 8.00 N 1860 7.00 C 7178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 309 " 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 H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 901 " - " ASN A 231 " " NAG A 902 " - " ASN A 239 " " NAG B 901 " - " ASN B 349 " " NAG C 901 " - " ASN C 231 " " NAG C 902 " - " ASN C 239 " " NAG D 901 " - " ASN D 349 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 345 " " NAG G 1 " - " ASN B 235 " " NAG H 1 " - " ASN C 45 " " NAG I 1 " - " ASN C 345 " " NAG J 1 " - " ASN D 235 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 569.0 milliseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2756 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 16 sheets defined 41.9% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 removed outlier: 3.676A pdb=" N LEU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 Processing helix chain 'A' and resid 72 through 86 removed outlier: 4.779A pdb=" N ASN A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N MET A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.735A pdb=" N ARG A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.657A pdb=" N LYS A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 4.001A pdb=" N ASN A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 242 through 259 Processing helix chain 'A' and resid 269 through 293 removed outlier: 3.555A pdb=" N VAL A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'B' and resid 16 through 31 removed outlier: 4.179A pdb=" N TYR B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.536A pdb=" N GLU B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 151 Processing helix chain 'B' and resid 166 through 181 removed outlier: 3.816A pdb=" N THR B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 removed outlier: 4.107A pdb=" N GLN B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 removed outlier: 3.680A pdb=" N THR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 297 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.676A pdb=" N LEU C 28 " --> pdb=" O PHE C 24 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN C 30 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 63 Processing helix chain 'C' and resid 72 through 86 removed outlier: 4.779A pdb=" N ASN C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N MET C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.735A pdb=" N ARG C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 3.657A pdb=" N LYS C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 201 removed outlier: 4.002A pdb=" N ASN C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C 201 " --> pdb=" O GLN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 242 through 259 Processing helix chain 'C' and resid 269 through 293 removed outlier: 3.555A pdb=" N VAL C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 326 Processing helix chain 'D' and resid 16 through 31 removed outlier: 4.179A pdb=" N TYR D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 Processing helix chain 'D' and resid 75 through 87 Processing helix chain 'D' and resid 111 through 122 removed outlier: 3.536A pdb=" N GLU D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 151 Processing helix chain 'D' and resid 166 through 181 removed outlier: 3.817A pdb=" N THR D 170 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG D 172 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 removed outlier: 4.107A pdb=" N GLN D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 258 removed outlier: 3.681A pdb=" N THR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 297 Processing helix chain 'D' and resid 319 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.062A pdb=" N LYS A 36 " --> pdb=" O ILE A 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.639A pdb=" N ILE A 67 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 158 removed outlier: 7.238A pdb=" N PHE A 127 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL A 157 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR A 129 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR A 126 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL A 183 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 128 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASP A 185 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE A 130 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN A 231 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 235 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 232 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 348 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR A 363 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 350 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 357 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 329 removed outlier: 3.581A pdb=" N PHE A 328 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 44 removed outlier: 3.897A pdb=" N ILE B 6 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N ALA B 66 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN B 7 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N PHE B 68 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY B 9 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 67 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N PHE B 90 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 158 removed outlier: 7.739A pdb=" N LYS B 126 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ILE B 187 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 128 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP B 189 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 130 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE B 239 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL B 236 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B 366 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU B 356 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS B 364 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS B 358 " --> pdb=" O PRO B 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 333 removed outlier: 3.995A pdb=" N LYS B 340 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 8 removed outlier: 6.062A pdb=" N LYS C 36 " --> pdb=" O ILE C 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.639A pdb=" N ILE C 67 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 153 through 158 removed outlier: 7.238A pdb=" N PHE C 127 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL C 157 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR C 129 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR C 126 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL C 183 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 128 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASP C 185 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE C 130 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN C 231 " --> pdb=" O TYR C 208 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE C 235 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 232 " --> pdb=" O MET C 353 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 348 " --> pdb=" O TYR C 363 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR C 363 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL C 350 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 357 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 328 through 329 removed outlier: 3.581A pdb=" N PHE C 328 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 36 through 44 removed outlier: 3.897A pdb=" N ILE D 6 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 10.871A pdb=" N ALA D 66 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN D 7 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N PHE D 68 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY D 9 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE D 67 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE D 90 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 153 through 158 removed outlier: 7.740A pdb=" N LYS D 126 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ILE D 187 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA D 128 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP D 189 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU D 130 " --> pdb=" O ASP D 189 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE D 239 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL D 236 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D 366 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU D 356 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS D 364 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS D 358 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 332 through 333 removed outlier: 3.994A pdb=" N LYS D 340 " --> pdb=" O ILE D 348 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1518 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: 1.80 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3619 1.34 - 1.46: 2776 1.46 - 1.58: 4999 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 11448 Sorted by residual: bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CB VAL D 76 " pdb=" CG2 VAL D 76 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.32e+00 bond pdb=" CB VAL B 76 " pdb=" CG2 VAL B 76 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.26e+00 bond pdb=" CG1 ILE D 187 " pdb=" CD1 ILE D 187 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.35e+00 ... (remaining 11443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.07: 15619 6.07 - 12.15: 5 12.15 - 18.22: 0 18.22 - 24.29: 0 24.29 - 30.36: 2 Bond angle restraints: 15626 Sorted by residual: angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 143.06 -30.36 3.00e+00 1.11e-01 1.02e+02 angle pdb=" CB MET A 52 " pdb=" CG MET A 52 " pdb=" SD MET A 52 " ideal model delta sigma weight residual 112.70 143.05 -30.35 3.00e+00 1.11e-01 1.02e+02 angle pdb=" CA MET C 52 " pdb=" CB MET C 52 " pdb=" CG MET C 52 " ideal model delta sigma weight residual 114.10 108.08 6.02 2.00e+00 2.50e-01 9.07e+00 angle pdb=" CA MET A 52 " pdb=" CB MET A 52 " pdb=" CG MET A 52 " ideal model delta sigma weight residual 114.10 108.10 6.00 2.00e+00 2.50e-01 9.00e+00 angle pdb=" CB ARG B 24 " pdb=" CG ARG B 24 " pdb=" CD ARG B 24 " ideal model delta sigma weight residual 111.30 118.18 -6.88 2.30e+00 1.89e-01 8.94e+00 ... (remaining 15621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.80: 6369 22.80 - 45.60: 385 45.60 - 68.40: 62 68.40 - 91.20: 40 91.20 - 114.00: 46 Dihedral angle restraints: 6902 sinusoidal: 2612 harmonic: 4290 Sorted by residual: dihedral pdb=" CA LYS D 373 " pdb=" C LYS D 373 " pdb=" N MET D 374 " pdb=" CA MET D 374 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LYS B 373 " pdb=" C LYS B 373 " pdb=" N MET B 374 " pdb=" CA MET B 374 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ASN C 151 " pdb=" C ASN C 151 " pdb=" N TRP C 152 " pdb=" CA TRP C 152 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 6899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1383 0.052 - 0.104: 405 0.104 - 0.156: 64 0.156 - 0.208: 0 0.208 - 0.259: 6 Chirality restraints: 1858 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.53e+00 ... (remaining 1855 not shown) Planarity restraints: 2006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 152 " 0.021 2.00e-02 2.50e+03 1.69e-02 7.18e+00 pdb=" CG TRP C 152 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 152 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 152 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 152 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 152 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 152 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 152 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 152 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 152 " -0.021 2.00e-02 2.50e+03 1.69e-02 7.14e+00 pdb=" CG TRP A 152 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 152 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 152 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 152 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 152 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 152 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 82 " -0.011 2.00e-02 2.50e+03 1.52e-02 4.03e+00 pdb=" CG PHE A 82 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 82 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 82 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 82 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 82 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 82 " -0.002 2.00e-02 2.50e+03 ... (remaining 2003 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 276 2.69 - 3.25: 11608 3.25 - 3.80: 17402 3.80 - 4.35: 21818 4.35 - 4.90: 37836 Nonbonded interactions: 88940 Sorted by model distance: nonbonded pdb=" O SER A 58 " pdb=" OG SER A 61 " model vdw 2.143 3.040 nonbonded pdb=" O SER C 58 " pdb=" OG SER C 61 " model vdw 2.144 3.040 nonbonded pdb=" OH TYR D 71 " pdb=" O PHE D 95 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR B 71 " pdb=" O PHE B 95 " model vdw 2.313 3.040 nonbonded pdb=" OE2 GLU B 333 " pdb=" ND2 ASN B 338 " model vdw 2.323 3.120 ... (remaining 88935 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.100 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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: 15.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.010 0.083 11472 Z= 0.394 Angle : 0.773 30.364 15694 Z= 0.383 Chirality : 0.048 0.259 1858 Planarity : 0.004 0.049 1994 Dihedral : 19.503 113.997 4134 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.39 % Allowed : 1.16 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.15 (0.21), residues: 1468 helix: 0.38 (0.21), residues: 576 sheet: -1.31 (0.32), residues: 232 loop : -1.56 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 14 TYR 0.029 0.002 TYR B 71 PHE 0.033 0.002 PHE A 82 TRP 0.046 0.002 TRP C 152 HIS 0.008 0.002 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00992 (11448) covalent geometry : angle 0.76157 (15626) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.42673 ( 8) hydrogen bonds : bond 0.17749 ( 516) hydrogen bonds : angle 6.51865 ( 1518) link_BETA1-4 : bond 0.00801 ( 8) link_BETA1-4 : angle 2.41514 ( 24) link_NAG-ASN : bond 0.00865 ( 12) link_NAG-ASN : angle 2.15646 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.398 Fit side-chains REVERT: C 151 ASN cc_start: 0.6999 (t0) cc_final: 0.6595 (t0) outliers start: 4 outliers final: 2 residues processed: 174 average time/residue: 0.1158 time to fit residues: 27.8018 Evaluate side-chains 152 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain D residue 106 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.169342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136610 restraints weight = 13699.344| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.74 r_work: 0.3114 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11472 Z= 0.135 Angle : 0.611 10.343 15694 Z= 0.298 Chirality : 0.046 0.182 1858 Planarity : 0.004 0.041 1994 Dihedral : 14.853 85.402 2004 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.96 % Allowed : 5.97 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.01 (0.21), residues: 1468 helix: 1.48 (0.21), residues: 578 sheet: -0.69 (0.31), residues: 242 loop : -1.05 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 325 TYR 0.022 0.002 TYR B 367 PHE 0.013 0.002 PHE B 50 TRP 0.034 0.002 TRP A 152 HIS 0.007 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00301 (11448) covalent geometry : angle 0.59492 (15626) SS BOND : bond 0.00778 ( 4) SS BOND : angle 0.52796 ( 8) hydrogen bonds : bond 0.03883 ( 516) hydrogen bonds : angle 4.61220 ( 1518) link_BETA1-4 : bond 0.00501 ( 8) link_BETA1-4 : angle 2.41397 ( 24) link_NAG-ASN : bond 0.00393 ( 12) link_NAG-ASN : angle 2.28341 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.396 Fit side-chains REVERT: A 55 ARG cc_start: 0.8333 (mmt180) cc_final: 0.7789 (mmt180) REVERT: A 120 ASP cc_start: 0.6946 (t0) cc_final: 0.6720 (t70) REVERT: B 121 TYR cc_start: 0.8907 (t80) cc_final: 0.8609 (t80) REVERT: C 359 ARG cc_start: 0.7809 (mtm110) cc_final: 0.7426 (mtt90) REVERT: D 121 TYR cc_start: 0.8837 (t80) cc_final: 0.8579 (t80) outliers start: 10 outliers final: 7 residues processed: 180 average time/residue: 0.1146 time to fit residues: 28.6267 Evaluate side-chains 161 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 86 optimal weight: 0.0470 chunk 89 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN D 59 GLN D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.167020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135531 restraints weight = 13898.661| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.81 r_work: 0.3049 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11472 Z= 0.146 Angle : 0.592 11.016 15694 Z= 0.281 Chirality : 0.044 0.196 1858 Planarity : 0.004 0.039 1994 Dihedral : 10.933 73.797 1998 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.35 % Allowed : 9.25 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.44 (0.22), residues: 1468 helix: 1.86 (0.21), residues: 580 sheet: -0.20 (0.31), residues: 248 loop : -0.97 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 325 TYR 0.020 0.002 TYR D 367 PHE 0.011 0.001 PHE A 127 TRP 0.029 0.002 TRP C 152 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00344 (11448) covalent geometry : angle 0.57354 (15626) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.84612 ( 8) hydrogen bonds : bond 0.03637 ( 516) hydrogen bonds : angle 4.31553 ( 1518) link_BETA1-4 : bond 0.00500 ( 8) link_BETA1-4 : angle 2.12068 ( 24) link_NAG-ASN : bond 0.00493 ( 12) link_NAG-ASN : angle 2.65708 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.394 Fit side-chains REVERT: A 55 ARG cc_start: 0.8407 (mmt180) cc_final: 0.8145 (mmt180) REVERT: A 151 ASN cc_start: 0.7550 (t0) cc_final: 0.7089 (t0) REVERT: C 52 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7920 (mtp) REVERT: C 151 ASN cc_start: 0.7624 (t0) cc_final: 0.7123 (t0) REVERT: C 352 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7067 (tm-30) REVERT: C 359 ARG cc_start: 0.7658 (mtm110) cc_final: 0.7339 (mtt90) REVERT: D 121 TYR cc_start: 0.8986 (t80) cc_final: 0.8773 (t80) outliers start: 14 outliers final: 8 residues processed: 167 average time/residue: 0.1196 time to fit residues: 27.6671 Evaluate side-chains 160 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.165824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133430 restraints weight = 13895.337| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.78 r_work: 0.3030 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11472 Z= 0.150 Angle : 0.566 7.363 15694 Z= 0.273 Chirality : 0.043 0.181 1858 Planarity : 0.004 0.039 1994 Dihedral : 8.974 71.588 1998 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.93 % Allowed : 10.12 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.53 (0.22), residues: 1468 helix: 1.92 (0.21), residues: 580 sheet: -0.19 (0.30), residues: 248 loop : -0.89 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 342 TYR 0.019 0.002 TYR D 367 PHE 0.011 0.001 PHE B 127 TRP 0.023 0.001 TRP A 152 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00353 (11448) covalent geometry : angle 0.54160 (15626) SS BOND : bond 0.00548 ( 4) SS BOND : angle 0.66941 ( 8) hydrogen bonds : bond 0.03346 ( 516) hydrogen bonds : angle 4.20963 ( 1518) link_BETA1-4 : bond 0.00417 ( 8) link_BETA1-4 : angle 2.21979 ( 24) link_NAG-ASN : bond 0.00526 ( 12) link_NAG-ASN : angle 2.97092 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.379 Fit side-chains REVERT: A 55 ARG cc_start: 0.8369 (mmt180) cc_final: 0.8134 (mmt180) REVERT: A 151 ASN cc_start: 0.7551 (t0) cc_final: 0.7124 (t0) REVERT: A 359 ARG cc_start: 0.7568 (mtm110) cc_final: 0.7244 (mtt90) REVERT: C 52 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7883 (mtp) REVERT: C 151 ASN cc_start: 0.7596 (t0) cc_final: 0.7157 (t0) outliers start: 20 outliers final: 8 residues processed: 174 average time/residue: 0.1164 time to fit residues: 28.0658 Evaluate side-chains 159 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 110 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 141 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.166324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133827 restraints weight = 13828.058| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.99 r_work: 0.3020 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11472 Z= 0.117 Angle : 0.529 7.692 15694 Z= 0.255 Chirality : 0.042 0.178 1858 Planarity : 0.003 0.038 1994 Dihedral : 7.969 68.023 1998 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.83 % Allowed : 11.66 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.66 (0.22), residues: 1468 helix: 2.04 (0.21), residues: 586 sheet: -0.08 (0.30), residues: 250 loop : -0.88 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 359 TYR 0.019 0.001 TYR D 367 PHE 0.009 0.001 PHE B 70 TRP 0.021 0.001 TRP C 152 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00270 (11448) covalent geometry : angle 0.50814 (15626) SS BOND : bond 0.00709 ( 4) SS BOND : angle 0.67769 ( 8) hydrogen bonds : bond 0.03026 ( 516) hydrogen bonds : angle 4.04609 ( 1518) link_BETA1-4 : bond 0.00497 ( 8) link_BETA1-4 : angle 2.18873 ( 24) link_NAG-ASN : bond 0.00357 ( 12) link_NAG-ASN : angle 2.60936 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.430 Fit side-chains REVERT: A 151 ASN cc_start: 0.7605 (t0) cc_final: 0.7125 (t0) REVERT: C 52 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7954 (mtp) REVERT: C 151 ASN cc_start: 0.7647 (t0) cc_final: 0.7167 (t0) outliers start: 19 outliers final: 11 residues processed: 168 average time/residue: 0.1167 time to fit residues: 26.9361 Evaluate side-chains 157 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 1 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.164943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130199 restraints weight = 13917.361| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.26 r_work: 0.2991 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11472 Z= 0.164 Angle : 0.563 7.508 15694 Z= 0.275 Chirality : 0.043 0.176 1858 Planarity : 0.004 0.037 1994 Dihedral : 7.479 63.830 1998 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.31 % Allowed : 11.66 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.59 (0.22), residues: 1468 helix: 1.94 (0.21), residues: 586 sheet: -0.10 (0.31), residues: 250 loop : -0.88 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 291 TYR 0.020 0.002 TYR D 367 PHE 0.011 0.001 PHE C 127 TRP 0.019 0.001 TRP C 152 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00393 (11448) covalent geometry : angle 0.54290 (15626) SS BOND : bond 0.00355 ( 4) SS BOND : angle 0.85884 ( 8) hydrogen bonds : bond 0.03343 ( 516) hydrogen bonds : angle 4.11314 ( 1518) link_BETA1-4 : bond 0.00368 ( 8) link_BETA1-4 : angle 2.37271 ( 24) link_NAG-ASN : bond 0.00547 ( 12) link_NAG-ASN : angle 2.54039 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.294 Fit side-chains REVERT: A 151 ASN cc_start: 0.7745 (t0) cc_final: 0.7227 (t0) REVERT: C 52 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7979 (mtp) REVERT: C 151 ASN cc_start: 0.7778 (t0) cc_final: 0.7231 (t0) REVERT: C 359 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7578 (mtt90) outliers start: 24 outliers final: 18 residues processed: 161 average time/residue: 0.1157 time to fit residues: 25.7370 Evaluate side-chains 162 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 132 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.166912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135987 restraints weight = 13951.206| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.02 r_work: 0.3012 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11472 Z= 0.144 Angle : 0.546 7.239 15694 Z= 0.267 Chirality : 0.042 0.157 1858 Planarity : 0.003 0.036 1994 Dihedral : 6.967 61.047 1998 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.02 % Allowed : 12.62 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.65 (0.22), residues: 1468 helix: 2.01 (0.21), residues: 586 sheet: -0.08 (0.31), residues: 250 loop : -0.87 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.018 0.002 TYR D 367 PHE 0.010 0.001 PHE D 127 TRP 0.018 0.001 TRP A 152 HIS 0.003 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00342 (11448) covalent geometry : angle 0.52622 (15626) SS BOND : bond 0.00277 ( 4) SS BOND : angle 0.69431 ( 8) hydrogen bonds : bond 0.03189 ( 516) hydrogen bonds : angle 4.04854 ( 1518) link_BETA1-4 : bond 0.00414 ( 8) link_BETA1-4 : angle 2.33522 ( 24) link_NAG-ASN : bond 0.00444 ( 12) link_NAG-ASN : angle 2.44516 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.364 Fit side-chains REVERT: A 151 ASN cc_start: 0.7667 (t0) cc_final: 0.7209 (t0) REVERT: A 185 ASP cc_start: 0.8437 (t0) cc_final: 0.8131 (t0) REVERT: B 27 MET cc_start: 0.7926 (mmt) cc_final: 0.7481 (mmt) REVERT: C 151 ASN cc_start: 0.7742 (t0) cc_final: 0.7250 (t0) REVERT: C 359 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7672 (mtt90) REVERT: D 27 MET cc_start: 0.7962 (mmt) cc_final: 0.7497 (mmt) outliers start: 21 outliers final: 13 residues processed: 156 average time/residue: 0.1248 time to fit residues: 26.7241 Evaluate side-chains 153 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 140 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.167462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133880 restraints weight = 13946.413| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.95 r_work: 0.3037 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11472 Z= 0.120 Angle : 0.525 7.183 15694 Z= 0.256 Chirality : 0.041 0.146 1858 Planarity : 0.003 0.036 1994 Dihedral : 6.471 58.661 1998 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.54 % Allowed : 13.39 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1468 helix: 2.12 (0.21), residues: 586 sheet: -0.04 (0.32), residues: 250 loop : -0.87 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 291 TYR 0.019 0.001 TYR D 367 PHE 0.014 0.001 PHE C 328 TRP 0.017 0.001 TRP C 152 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00281 (11448) covalent geometry : angle 0.50628 (15626) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.58893 ( 8) hydrogen bonds : bond 0.02997 ( 516) hydrogen bonds : angle 3.99590 ( 1518) link_BETA1-4 : bond 0.00444 ( 8) link_BETA1-4 : angle 2.26154 ( 24) link_NAG-ASN : bond 0.00380 ( 12) link_NAG-ASN : angle 2.35591 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.349 Fit side-chains REVERT: A 151 ASN cc_start: 0.7651 (t0) cc_final: 0.7212 (t0) REVERT: A 185 ASP cc_start: 0.8376 (t0) cc_final: 0.8058 (t0) REVERT: A 277 ASP cc_start: 0.8643 (m-30) cc_final: 0.8441 (m-30) REVERT: A 352 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7128 (tt0) REVERT: C 151 ASN cc_start: 0.7759 (t0) cc_final: 0.7300 (t0) REVERT: C 359 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7644 (mtt90) REVERT: D 27 MET cc_start: 0.7880 (mmt) cc_final: 0.7479 (mmt) outliers start: 16 outliers final: 12 residues processed: 156 average time/residue: 0.1192 time to fit residues: 25.5271 Evaluate side-chains 154 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 24 optimal weight: 0.0770 chunk 123 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.167231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134476 restraints weight = 13827.911| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.75 r_work: 0.3060 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11472 Z= 0.116 Angle : 0.528 7.152 15694 Z= 0.258 Chirality : 0.041 0.145 1858 Planarity : 0.003 0.036 1994 Dihedral : 6.193 57.110 1998 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.73 % Allowed : 13.68 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.78 (0.22), residues: 1468 helix: 2.14 (0.21), residues: 586 sheet: -0.02 (0.32), residues: 250 loop : -0.82 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.019 0.001 TYR D 367 PHE 0.038 0.001 PHE B 23 TRP 0.016 0.001 TRP C 152 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00271 (11448) covalent geometry : angle 0.50927 (15626) SS BOND : bond 0.00243 ( 4) SS BOND : angle 0.58675 ( 8) hydrogen bonds : bond 0.02975 ( 516) hydrogen bonds : angle 3.98311 ( 1518) link_BETA1-4 : bond 0.00446 ( 8) link_BETA1-4 : angle 2.23014 ( 24) link_NAG-ASN : bond 0.00363 ( 12) link_NAG-ASN : angle 2.31154 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.302 Fit side-chains REVERT: A 151 ASN cc_start: 0.7651 (t0) cc_final: 0.7233 (t0) REVERT: A 185 ASP cc_start: 0.8337 (t0) cc_final: 0.8023 (t0) REVERT: A 339 GLU cc_start: 0.7332 (tp30) cc_final: 0.6688 (tm-30) REVERT: C 151 ASN cc_start: 0.7711 (t0) cc_final: 0.7259 (t0) REVERT: C 185 ASP cc_start: 0.8285 (t0) cc_final: 0.8001 (t0) REVERT: C 359 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7665 (mtt90) outliers start: 18 outliers final: 15 residues processed: 158 average time/residue: 0.1127 time to fit residues: 24.5211 Evaluate side-chains 159 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 5 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.167726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134095 restraints weight = 13888.774| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.93 r_work: 0.3068 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11472 Z= 0.120 Angle : 0.528 7.068 15694 Z= 0.259 Chirality : 0.041 0.181 1858 Planarity : 0.003 0.036 1994 Dihedral : 5.935 57.490 1998 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.64 % Allowed : 13.49 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.82 (0.22), residues: 1468 helix: 2.18 (0.21), residues: 586 sheet: -0.07 (0.32), residues: 250 loop : -0.78 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.020 0.001 TYR D 367 PHE 0.036 0.001 PHE D 23 TRP 0.016 0.001 TRP C 152 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00280 (11448) covalent geometry : angle 0.51080 (15626) SS BOND : bond 0.00224 ( 4) SS BOND : angle 0.61491 ( 8) hydrogen bonds : bond 0.02988 ( 516) hydrogen bonds : angle 3.95795 ( 1518) link_BETA1-4 : bond 0.00443 ( 8) link_BETA1-4 : angle 2.17944 ( 24) link_NAG-ASN : bond 0.00357 ( 12) link_NAG-ASN : angle 2.26834 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.335 Fit side-chains REVERT: A 151 ASN cc_start: 0.7673 (t0) cc_final: 0.7251 (t0) REVERT: A 185 ASP cc_start: 0.8351 (t0) cc_final: 0.8040 (t0) REVERT: A 277 ASP cc_start: 0.8643 (m-30) cc_final: 0.8435 (m-30) REVERT: A 339 GLU cc_start: 0.7350 (tp30) cc_final: 0.6695 (tm-30) REVERT: A 352 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7099 (tt0) REVERT: C 151 ASN cc_start: 0.7762 (t0) cc_final: 0.7304 (t0) REVERT: C 352 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7056 (tt0) outliers start: 17 outliers final: 14 residues processed: 163 average time/residue: 0.1179 time to fit residues: 26.5776 Evaluate side-chains 159 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.166480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131898 restraints weight = 14003.862| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.22 r_work: 0.3006 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11472 Z= 0.149 Angle : 0.550 10.155 15694 Z= 0.271 Chirality : 0.042 0.189 1858 Planarity : 0.003 0.036 1994 Dihedral : 5.713 53.718 1998 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.73 % Allowed : 13.78 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.75 (0.22), residues: 1468 helix: 2.09 (0.21), residues: 586 sheet: -0.04 (0.31), residues: 250 loop : -0.80 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.020 0.002 TYR D 367 PHE 0.032 0.002 PHE D 23 TRP 0.017 0.001 TRP C 152 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00358 (11448) covalent geometry : angle 0.53294 (15626) SS BOND : bond 0.00246 ( 4) SS BOND : angle 0.67624 ( 8) hydrogen bonds : bond 0.03186 ( 516) hydrogen bonds : angle 4.01826 ( 1518) link_BETA1-4 : bond 0.00404 ( 8) link_BETA1-4 : angle 2.14212 ( 24) link_NAG-ASN : bond 0.00428 ( 12) link_NAG-ASN : angle 2.28355 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.24 seconds wall clock time: 39 minutes 43.41 seconds (2383.41 seconds total)