Starting phenix.real_space_refine on Fri Jul 3 01:06:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7occ_12803/07_2026/7occ_12803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7occ_12803/07_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_12803/07_2026/7occ_12803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7occ_12803/07_2026/7occ_12803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7occ_12803/07_2026/7occ_12803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7occ_12803/07_2026/7occ_12803.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7occ_12803/07_2026/7occ_12803.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7occ_12803/07_2026/7occ_12803.cif" } 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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 2.69, per 1000 atoms: 0.24 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: 0.88 Conformation dependent library (CDL) restraints added in 410.5 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: 0.27 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: 1.51 Time building geometry restraints manager: 1.14 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 - 17.70: 5907 17.70 - 35.40: 479 35.40 - 53.10: 80 53.10 - 70.80: 10 70.80 - 88.50: 10 Dihedral angle restraints: 6486 sinusoidal: 2196 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 6483 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: 0.01 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: 2.980 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.080 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 13.593 88.496 3718 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/Z covalent geometry : bond 0.00992 / 0.39 (11448) covalent geometry : angle 0.76157 / 0.38 (15626) SS BOND : bond 0.00226 / 0.11 ( 4) SS BOND : angle 0.42673 / 0.26 ( 8) hydrogen bonds : bond 0.17749 / 11.85 ( 516) hydrogen bonds : angle 6.51865 / 4.65 ( 1518) link_BETA1-4 : bond 0.00801 / 0.53 ( 8) link_BETA1-4 : angle 2.41514 / 1.69 ( 24) link_NAG-ASN : bond 0.00865 / 0.59 ( 12) link_NAG-ASN : angle 2.15646 / 1.38 ( 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 : 0.271 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: 0.0933 time to fit residues: 22.6594 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 : 0.289 ------------------------------------------------------------------------------- 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... B 284 GLN D 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.169454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136312 restraints weight = 13741.396| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.75 r_work: 0.3111 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11472 Z= 0.135 Angle : 0.551 7.335 15694 Z= 0.285 Chirality : 0.045 0.293 1858 Planarity : 0.004 0.040 1994 Dihedral : 4.601 42.778 1588 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.96 % Allowed : 6.07 % Favored : 92.97 % 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: -0.00 (0.21), residues: 1468 helix: 1.48 (0.21), residues: 578 sheet: -0.70 (0.31), residues: 242 loop : -1.07 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 325 TYR 0.021 0.002 TYR B 367 PHE 0.012 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/Z covalent geometry : bond 0.00303 / 0.13 (11448) covalent geometry : angle 0.53964 / 0.28 (15626) SS BOND : bond 0.00974 / 0.50 ( 4) SS BOND : angle 0.54361 / 0.30 ( 8) hydrogen bonds : bond 0.04058 / 2.74 ( 516) hydrogen bonds : angle 4.64912 / 3.34 ( 1518) link_BETA1-4 : bond 0.00385 / 0.23 ( 8) link_BETA1-4 : angle 1.84892 / 1.24 ( 24) link_NAG-ASN : bond 0.00358 / 0.25 ( 12) link_NAG-ASN : angle 1.90233 / 1.16 ( 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 : 0.289 Fit side-chains REVERT: A 120 ASP cc_start: 0.6957 (t0) cc_final: 0.6757 (t70) REVERT: C 359 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7432 (mtt90) outliers start: 10 outliers final: 8 residues processed: 180 average time/residue: 0.0951 time to fit residues: 23.8853 Evaluate side-chains 161 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET 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: 0.7980 chunk 53 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 95 optimal weight: 0.0970 chunk 137 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.166911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135669 restraints weight = 13855.094| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.89 r_work: 0.3032 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 0.038 11472 Z= 0.141 Angle : 0.509 6.686 15694 Z= 0.262 Chirality : 0.043 0.277 1858 Planarity : 0.004 0.039 1994 Dihedral : 3.923 25.929 1582 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 0.45 (0.22), residues: 1468 helix: 1.89 (0.21), residues: 580 sheet: -0.21 (0.32), residues: 238 loop : -0.98 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 253 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 0.004 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (11448) covalent geometry : angle 0.50027 / 0.26 (15626) SS BOND : bond 0.00251 / 0.12 ( 4) SS BOND : angle 0.66183 / 0.43 ( 8) hydrogen bonds : bond 0.03546 / 2.42 ( 516) hydrogen bonds : angle 4.29445 / 3.09 ( 1518) link_BETA1-4 : bond 0.00645 / 0.36 ( 8) link_BETA1-4 : angle 1.43667 / 0.93 ( 24) link_NAG-ASN : bond 0.00360 / 0.25 ( 12) link_NAG-ASN : angle 1.64706 / 1.03 ( 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 171 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.303 Fit side-chains REVERT: A 52 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7879 (mtp) REVERT: A 55 ARG cc_start: 0.8444 (mmt180) cc_final: 0.8187 (mmt180) REVERT: A 151 ASN cc_start: 0.7561 (t0) cc_final: 0.7084 (t0) REVERT: C 52 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7932 (mtp) REVERT: C 151 ASN cc_start: 0.7592 (t0) cc_final: 0.7038 (t0) REVERT: C 352 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7093 (tm-30) REVERT: C 359 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7351 (mtt90) outliers start: 14 outliers final: 7 residues processed: 164 average time/residue: 0.0978 time to fit residues: 22.2730 Evaluate side-chains 156 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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: 0.0770 chunk 140 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3909 r_free = 0.3909 target = 0.167083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134866 restraints weight = 13925.711| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.97 r_work: 0.3022 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.003 0.028 11472 Z= 0.114 Angle : 0.471 5.830 15694 Z= 0.242 Chirality : 0.042 0.276 1858 Planarity : 0.003 0.039 1994 Dihedral : 3.745 23.725 1582 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.54 % Allowed : 10.21 % Favored : 88.25 % 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: 2.04 (0.21), residues: 584 sheet: -0.12 (0.31), residues: 248 loop : -0.87 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 325 TYR 0.020 0.002 TYR D 367 PHE 0.009 0.001 PHE B 56 TRP 0.023 0.001 TRP A 152 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (11448) covalent geometry : angle 0.46170 / 0.24 (15626) SS BOND : bond 0.00224 / 0.11 ( 4) SS BOND : angle 0.94167 / 0.57 ( 8) hydrogen bonds : bond 0.03072 / 2.10 ( 516) hydrogen bonds : angle 4.11717 / 2.95 ( 1518) link_BETA1-4 : bond 0.00267 / 0.18 ( 8) link_BETA1-4 : angle 1.48341 / 0.99 ( 24) link_NAG-ASN : bond 0.00291 / 0.20 ( 12) link_NAG-ASN : angle 1.54055 / 0.96 ( 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 177 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.371 Fit side-chains REVERT: A 52 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7877 (mtp) REVERT: A 55 ARG cc_start: 0.8418 (mmt180) cc_final: 0.8179 (mmt180) REVERT: A 151 ASN cc_start: 0.7569 (t0) cc_final: 0.7209 (t0) REVERT: C 151 ASN cc_start: 0.7603 (t0) cc_final: 0.7092 (t0) REVERT: C 359 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7410 (mtt90) outliers start: 16 outliers final: 6 residues processed: 169 average time/residue: 0.0966 time to fit residues: 22.7552 Evaluate side-chains 157 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET 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 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: 0.7980 chunk 72 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 141 optimal weight: 0.0060 chunk 86 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3910 r_free = 0.3910 target = 0.167048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135361 restraints weight = 13856.169| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.99 r_work: 0.3036 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11472 Z= 0.106 Angle : 0.466 7.652 15694 Z= 0.238 Chirality : 0.042 0.274 1858 Planarity : 0.003 0.038 1994 Dihedral : 3.605 21.988 1582 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.83 % Allowed : 11.08 % Favored : 87.09 % 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: 2.14 (0.21), residues: 586 sheet: -0.08 (0.31), residues: 250 loop : -0.85 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 359 TYR 0.019 0.001 TYR D 367 PHE 0.010 0.001 PHE A 328 TRP 0.018 0.001 TRP A 152 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11448) covalent geometry : angle 0.45807 / 0.24 (15626) SS BOND : bond 0.00187 / 0.09 ( 4) SS BOND : angle 0.73612 / 0.45 ( 8) hydrogen bonds : bond 0.02943 / 2.01 ( 516) hydrogen bonds : angle 4.00741 / 2.87 ( 1518) link_BETA1-4 : bond 0.00357 / 0.23 ( 8) link_BETA1-4 : angle 1.35053 / 0.90 ( 24) link_NAG-ASN : bond 0.00295 / 0.21 ( 12) link_NAG-ASN : angle 1.45246 / 0.92 ( 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 173 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.369 Fit side-chains REVERT: A 52 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7829 (mtp) REVERT: A 55 ARG cc_start: 0.8451 (mmt180) cc_final: 0.8243 (mmt180) REVERT: A 151 ASN cc_start: 0.7594 (t0) cc_final: 0.7118 (t0) REVERT: C 151 ASN cc_start: 0.7598 (t0) cc_final: 0.7266 (t0) REVERT: C 359 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7347 (mtt90) outliers start: 19 outliers final: 8 residues processed: 163 average time/residue: 0.0999 time to fit residues: 22.9768 Evaluate side-chains 156 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain B residue 92 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 1 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 19 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 134 optimal weight: 0.0000 overall best weight: 0.7966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN 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 = 0.3899 r_free = 0.3899 target = 0.166841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132338 restraints weight = 14001.549| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.34 r_work: 0.3034 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11472 Z= 0.122 Angle : 0.478 6.465 15694 Z= 0.246 Chirality : 0.042 0.285 1858 Planarity : 0.003 0.037 1994 Dihedral : 3.609 21.878 1582 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.93 % Allowed : 11.56 % 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: 0.78 (0.22), residues: 1468 helix: 2.15 (0.21), residues: 586 sheet: -0.05 (0.31), residues: 250 loop : -0.81 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.021 0.002 TYR D 367 PHE 0.009 0.001 PHE A 127 TRP 0.017 0.001 TRP C 152 HIS 0.003 0.001 HIS C 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (11448) covalent geometry : angle 0.47037 / 0.24 (15626) SS BOND : bond 0.00206 / 0.10 ( 4) SS BOND : angle 0.74111 / 0.46 ( 8) hydrogen bonds : bond 0.03013 / 2.05 ( 516) hydrogen bonds : angle 3.99211 / 2.86 ( 1518) link_BETA1-4 : bond 0.00346 / 0.23 ( 8) link_BETA1-4 : angle 1.39511 / 0.94 ( 24) link_NAG-ASN : bond 0.00358 / 0.25 ( 12) link_NAG-ASN : angle 1.48532 / 0.93 ( 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 174 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.423 Fit side-chains REVERT: A 52 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7759 (mtp) REVERT: A 55 ARG cc_start: 0.8498 (mmt180) cc_final: 0.8286 (mmt180) REVERT: A 151 ASN cc_start: 0.7676 (t0) cc_final: 0.7179 (t0) REVERT: A 185 ASP cc_start: 0.8408 (t0) cc_final: 0.8102 (t0) REVERT: C 151 ASN cc_start: 0.7642 (t0) cc_final: 0.7149 (t0) REVERT: C 359 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7355 (mtt90) outliers start: 20 outliers final: 11 residues processed: 165 average time/residue: 0.1099 time to fit residues: 24.7234 Evaluate side-chains 158 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET 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 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 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: 0.6980 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 112 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN 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 = 0.3902 r_free = 0.3902 target = 0.166848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135603 restraints weight = 14012.857| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.78 r_work: 0.3044 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2936 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= 0.146 Angle : 0.498 6.145 15694 Z= 0.257 Chirality : 0.043 0.284 1858 Planarity : 0.003 0.036 1994 Dihedral : 3.704 22.170 1582 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.83 % Allowed : 12.04 % Favored : 86.13 % 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: 2.11 (0.21), residues: 586 sheet: -0.06 (0.31), residues: 250 loop : -0.82 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.020 0.002 TYR D 367 PHE 0.010 0.001 PHE C 127 TRP 0.019 0.001 TRP A 152 HIS 0.003 0.001 HIS C 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11448) covalent geometry : angle 0.49063 / 0.26 (15626) SS BOND : bond 0.00230 / 0.11 ( 4) SS BOND : angle 0.85408 / 0.55 ( 8) hydrogen bonds : bond 0.03158 / 2.15 ( 516) hydrogen bonds : angle 4.01916 / 2.88 ( 1518) link_BETA1-4 : bond 0.00323 / 0.21 ( 8) link_BETA1-4 : angle 1.41069 / 0.96 ( 24) link_NAG-ASN : bond 0.00441 / 0.31 ( 12) link_NAG-ASN : angle 1.53536 / 0.96 ( 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 163 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.394 Fit side-chains REVERT: A 52 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7860 (mtp) REVERT: A 55 ARG cc_start: 0.8474 (mmt180) cc_final: 0.8246 (mmt180) REVERT: A 151 ASN cc_start: 0.7598 (t0) cc_final: 0.7164 (t0) REVERT: A 359 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7688 (mtt90) REVERT: B 27 MET cc_start: 0.7881 (mmt) cc_final: 0.7418 (mmt) REVERT: C 151 ASN cc_start: 0.7634 (t0) cc_final: 0.7185 (t0) REVERT: D 27 MET cc_start: 0.7931 (mmt) cc_final: 0.7454 (mmt) outliers start: 19 outliers final: 14 residues processed: 156 average time/residue: 0.0912 time to fit residues: 20.1262 Evaluate side-chains 154 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 140 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 9 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 56 optimal weight: 0.0050 chunk 102 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN 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 = 0.3918 r_free = 0.3918 target = 0.168409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137240 restraints weight = 14005.106| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.78 r_work: 0.3063 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11472 Z= 0.106 Angle : 0.479 9.169 15694 Z= 0.244 Chirality : 0.042 0.271 1858 Planarity : 0.003 0.034 1994 Dihedral : 3.598 21.312 1582 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.35 % Allowed : 12.33 % Favored : 86.32 % 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: 0.86 (0.22), residues: 1468 helix: 2.25 (0.21), residues: 586 sheet: -0.04 (0.31), residues: 250 loop : -0.79 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.018 0.001 TYR B 367 PHE 0.014 0.001 PHE C 328 TRP 0.017 0.001 TRP A 152 HIS 0.003 0.001 HIS C 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (11448) covalent geometry : angle 0.47154 / 0.24 (15626) SS BOND : bond 0.00201 / 0.10 ( 4) SS BOND : angle 0.67751 / 0.43 ( 8) hydrogen bonds : bond 0.02895 / 1.97 ( 516) hydrogen bonds : angle 3.94347 / 2.82 ( 1518) link_BETA1-4 : bond 0.00346 / 0.22 ( 8) link_BETA1-4 : angle 1.33138 / 0.89 ( 24) link_NAG-ASN : bond 0.00299 / 0.21 ( 12) link_NAG-ASN : angle 1.44006 / 0.90 ( 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 161 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.438 Fit side-chains REVERT: A 52 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7856 (mtp) REVERT: A 55 ARG cc_start: 0.8499 (mmt180) cc_final: 0.8274 (mmt180) REVERT: A 151 ASN cc_start: 0.7597 (t0) cc_final: 0.7186 (t0) REVERT: A 185 ASP cc_start: 0.8399 (t0) cc_final: 0.8075 (t0) REVERT: A 352 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7020 (tt0) REVERT: C 151 ASN cc_start: 0.7616 (t0) cc_final: 0.7180 (t0) REVERT: D 27 MET cc_start: 0.7860 (mmt) cc_final: 0.7426 (mmt) outliers start: 14 outliers final: 10 residues processed: 157 average time/residue: 0.1246 time to fit residues: 26.9886 Evaluate side-chains 153 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain B residue 28 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 24 optimal weight: 0.0570 chunk 123 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN 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 = 0.3917 r_free = 0.3917 target = 0.168194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134085 restraints weight = 13969.577| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.06 r_work: 0.3052 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3086 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= 0.113 Angle : 0.489 8.894 15694 Z= 0.249 Chirality : 0.042 0.278 1858 Planarity : 0.003 0.035 1994 Dihedral : 3.597 20.640 1582 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.35 % Allowed : 12.81 % Favored : 85.84 % 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: 0.87 (0.22), residues: 1468 helix: 2.25 (0.21), residues: 586 sheet: -0.03 (0.31), residues: 250 loop : -0.78 (0.24), 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 0.036 0.001 PHE B 23 TRP 0.017 0.001 TRP A 152 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (11448) covalent geometry : angle 0.48147 / 0.25 (15626) SS BOND : bond 0.00240 / 0.12 ( 4) SS BOND : angle 0.72078 / 0.43 ( 8) hydrogen bonds : bond 0.02920 / 1.99 ( 516) hydrogen bonds : angle 3.93138 / 2.81 ( 1518) link_BETA1-4 : bond 0.00349 / 0.23 ( 8) link_BETA1-4 : angle 1.32067 / 0.89 ( 24) link_NAG-ASN : bond 0.00334 / 0.23 ( 12) link_NAG-ASN : angle 1.46666 / 0.92 ( 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: 14 poor density : 151 time to evaluate : 0.382 Fit side-chains REVERT: A 52 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7834 (mtp) REVERT: A 55 ARG cc_start: 0.8497 (mmt180) cc_final: 0.8270 (mmt180) REVERT: A 151 ASN cc_start: 0.7675 (t0) cc_final: 0.7253 (t0) REVERT: A 185 ASP cc_start: 0.8395 (t0) cc_final: 0.8063 (t0) REVERT: C 151 ASN cc_start: 0.7661 (t0) cc_final: 0.7235 (t0) REVERT: C 339 GLU cc_start: 0.7315 (tp30) cc_final: 0.6652 (tm-30) outliers start: 14 outliers final: 9 residues processed: 161 average time/residue: 0.1129 time to fit residues: 25.8039 Evaluate side-chains 153 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 5 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 0.0870 chunk 14 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN 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 = 0.3920 r_free = 0.3920 target = 0.168504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.134704 restraints weight = 13976.375| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.07 r_work: 0.3074 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11472 Z= 0.108 Angle : 0.499 9.799 15694 Z= 0.253 Chirality : 0.042 0.276 1858 Planarity : 0.003 0.035 1994 Dihedral : 3.565 20.567 1582 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.16 % Allowed : 13.58 % Favored : 85.26 % 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: 0.90 (0.22), residues: 1468 helix: 2.28 (0.21), residues: 586 sheet: -0.02 (0.32), residues: 250 loop : -0.76 (0.24), 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 0.039 0.001 PHE D 23 TRP 0.016 0.001 TRP A 152 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (11448) covalent geometry : angle 0.49275 / 0.25 (15626) SS BOND : bond 0.00228 / 0.11 ( 4) SS BOND : angle 0.60698 / 0.37 ( 8) hydrogen bonds : bond 0.02878 / 1.97 ( 516) hydrogen bonds : angle 3.90993 / 2.79 ( 1518) link_BETA1-4 : bond 0.00355 / 0.23 ( 8) link_BETA1-4 : angle 1.28921 / 0.87 ( 24) link_NAG-ASN : bond 0.00294 / 0.20 ( 12) link_NAG-ASN : angle 1.42485 / 0.89 ( 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 162 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.372 Fit side-chains REVERT: A 55 ARG cc_start: 0.8408 (mmt180) cc_final: 0.8170 (mmt180) REVERT: A 151 ASN cc_start: 0.7637 (t0) cc_final: 0.7228 (t0) REVERT: A 185 ASP cc_start: 0.8395 (t0) cc_final: 0.8076 (t0) REVERT: A 339 GLU cc_start: 0.7217 (tp30) cc_final: 0.6636 (tm-30) REVERT: A 352 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6987 (tt0) REVERT: C 151 ASN cc_start: 0.7669 (t0) cc_final: 0.7252 (t0) REVERT: C 339 GLU cc_start: 0.7339 (tp30) cc_final: 0.6711 (tm-30) outliers start: 12 outliers final: 9 residues processed: 159 average time/residue: 0.1139 time to fit residues: 25.0414 Evaluate side-chains 151 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.0010 chunk 111 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN 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 = 0.3916 r_free = 0.3916 target = 0.168129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137628 restraints weight = 14060.889| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.93 r_work: 0.3054 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3232 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= 0.115 Angle : 0.499 9.467 15694 Z= 0.253 Chirality : 0.042 0.277 1858 Planarity : 0.003 0.034 1994 Dihedral : 3.568 20.424 1582 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.25 % Allowed : 13.68 % 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: 0.91 (0.22), residues: 1468 helix: 2.30 (0.21), residues: 584 sheet: -0.04 (0.32), residues: 250 loop : -0.75 (0.24), residues: 634 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 0.033 0.001 PHE D 23 TRP 0.016 0.001 TRP A 152 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11448) covalent geometry : angle 0.49273 / 0.25 (15626) SS BOND : bond 0.00221 / 0.11 ( 4) SS BOND : angle 0.58081 / 0.36 ( 8) hydrogen bonds : bond 0.02906 / 1.98 ( 516) hydrogen bonds : angle 3.89856 / 2.78 ( 1518) link_BETA1-4 : bond 0.00348 / 0.23 ( 8) link_BETA1-4 : angle 1.28728 / 0.87 ( 24) link_NAG-ASN : bond 0.00330 / 0.23 ( 12) link_NAG-ASN : angle 1.43857 / 0.90 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.55 seconds wall clock time: 37 minutes 42.45 seconds (2262.45 seconds total)