Starting phenix.real_space_refine on Tue Jul 29 11:22:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7occ_12803/07_2025/7occ_12803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7occ_12803/07_2025/7occ_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7occ_12803/07_2025/7occ_12803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7occ_12803/07_2025/7occ_12803.map" model { file = "/net/cci-nas-00/data/ceres_data/7occ_12803/07_2025/7occ_12803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7occ_12803/07_2025/7occ_12803.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 9, 'HIS:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 14} 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: {'GLN:plan1': 5, 'GLU:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 5, 'ARG:plan': 5} 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: {'GLN:plan1': 9, 'HIS:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 14} 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: {'GLN:plan1': 5, 'GLU:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 5, 'ARG:plan': 5} 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: 7.81, per 1000 atoms: 0.70 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: 3.17 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.32 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: 3.66 Time building geometry restraints manager: 3.72 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: 0.00 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.900 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (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 TRP 0.046 0.002 TRP C 152 HIS 0.008 0.002 HIS B 87 PHE 0.033 0.002 PHE A 82 TYR 0.029 0.002 TYR B 71 ARG 0.007 0.001 ARG D 14 Details of bonding type rmsd link_NAG-ASN : bond 0.00865 ( 12) link_NAG-ASN : angle 2.15646 ( 36) link_BETA1-4 : bond 0.00801 ( 8) link_BETA1-4 : angle 2.41514 ( 24) hydrogen bonds : bond 0.17749 ( 516) hydrogen bonds : angle 6.51865 ( 1518) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.42673 ( 8) covalent geometry : bond 0.00992 (11448) covalent geometry : angle 0.76157 (15626) *********************** 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 : 1.165 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: 0.2516 time to fit residues: 60.5094 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 : 1.163 ------------------------------------------------------------------------------- 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 123 optimal weight: 0.8980 chunk 110 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** C 209 HIS D 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.133109 restraints weight = 13589.126| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.14 r_work: 0.3099 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11472 Z= 0.139 Angle : 0.616 10.240 15694 Z= 0.300 Chirality : 0.046 0.189 1858 Planarity : 0.004 0.041 1994 Dihedral : 14.682 84.307 2004 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.96 % Allowed : 5.88 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1468 helix: 1.51 (0.21), residues: 576 sheet: -0.71 (0.31), residues: 242 loop : -1.05 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 152 HIS 0.007 0.001 HIS B 87 PHE 0.013 0.002 PHE B 50 TYR 0.023 0.002 TYR B 367 ARG 0.004 0.000 ARG D 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 12) link_NAG-ASN : angle 2.28347 ( 36) link_BETA1-4 : bond 0.00456 ( 8) link_BETA1-4 : angle 2.43275 ( 24) hydrogen bonds : bond 0.03827 ( 516) hydrogen bonds : angle 4.59068 ( 1518) SS BOND : bond 0.00379 ( 4) SS BOND : angle 0.75687 ( 8) covalent geometry : bond 0.00313 (11448) covalent geometry : angle 0.60020 (15626) *********************** 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 185 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 1.313 Fit side-chains REVERT: A 52 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7837 (mtp) REVERT: A 55 ARG cc_start: 0.8325 (mmt180) cc_final: 0.7781 (mmt180) REVERT: B 121 TYR cc_start: 0.8940 (t80) cc_final: 0.8668 (t80) REVERT: C 120 ASP cc_start: 0.7187 (t0) cc_final: 0.6984 (t70) REVERT: C 359 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7390 (mtt90) REVERT: D 121 TYR cc_start: 0.8870 (t80) cc_final: 0.8640 (t80) outliers start: 10 outliers final: 7 residues processed: 179 average time/residue: 0.2518 time to fit residues: 62.3513 Evaluate side-chains 162 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 18 GLN 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 18 GLN D 59 GLN D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.163257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130219 restraints weight = 13962.214| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.90 r_work: 0.2964 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11472 Z= 0.227 Angle : 0.655 10.974 15694 Z= 0.316 Chirality : 0.047 0.206 1858 Planarity : 0.004 0.043 1994 Dihedral : 10.772 76.060 1998 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.73 % Allowed : 9.34 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1468 helix: 1.57 (0.21), residues: 580 sheet: -0.30 (0.30), residues: 248 loop : -1.07 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 152 HIS 0.004 0.001 HIS C 121 PHE 0.016 0.002 PHE C 127 TYR 0.023 0.003 TYR B 71 ARG 0.005 0.000 ARG B 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 12) link_NAG-ASN : angle 2.71978 ( 36) link_BETA1-4 : bond 0.00288 ( 8) link_BETA1-4 : angle 2.37164 ( 24) hydrogen bonds : bond 0.04175 ( 516) hydrogen bonds : angle 4.47351 ( 1518) SS BOND : bond 0.00461 ( 4) SS BOND : angle 0.93655 ( 8) covalent geometry : bond 0.00545 (11448) covalent geometry : angle 0.63656 (15626) *********************** 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 180 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.202 Fit side-chains REVERT: A 151 ASN cc_start: 0.7729 (t0) cc_final: 0.7159 (t0) REVERT: A 359 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7311 (mtt90) REVERT: C 151 ASN cc_start: 0.7706 (t0) cc_final: 0.7138 (t0) REVERT: C 352 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7041 (tm-30) REVERT: C 359 ARG cc_start: 0.7614 (mtm110) cc_final: 0.7215 (mtt90) outliers start: 18 outliers final: 12 residues processed: 171 average time/residue: 0.2595 time to fit residues: 61.5022 Evaluate side-chains 163 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 125 ASP 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 326 VAL Chi-restraints excluded: chain D residue 106 GLN 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 3 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.162548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129205 restraints weight = 13743.743| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.88 r_work: 0.2970 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11472 Z= 0.210 Angle : 0.617 7.712 15694 Z= 0.302 Chirality : 0.045 0.186 1858 Planarity : 0.004 0.044 1994 Dihedral : 9.310 75.087 1998 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.31 % Allowed : 10.69 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1468 helix: 1.57 (0.21), residues: 582 sheet: -0.22 (0.30), residues: 256 loop : -1.06 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 152 HIS 0.005 0.001 HIS B 87 PHE 0.014 0.002 PHE C 127 TYR 0.018 0.002 TYR D 367 ARG 0.002 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00732 ( 12) link_NAG-ASN : angle 3.06008 ( 36) link_BETA1-4 : bond 0.00351 ( 8) link_BETA1-4 : angle 2.39300 ( 24) hydrogen bonds : bond 0.03770 ( 516) hydrogen bonds : angle 4.37978 ( 1518) SS BOND : bond 0.00327 ( 4) SS BOND : angle 0.95638 ( 8) covalent geometry : bond 0.00504 (11448) covalent geometry : angle 0.59331 (15626) *********************** 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 181 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.172 Fit side-chains REVERT: A 55 ARG cc_start: 0.8394 (mmt180) cc_final: 0.8132 (mmt180) REVERT: A 151 ASN cc_start: 0.7770 (t0) cc_final: 0.7229 (t0) REVERT: A 359 ARG cc_start: 0.7662 (mtm110) cc_final: 0.7296 (mtt90) REVERT: C 151 ASN cc_start: 0.7673 (t0) cc_final: 0.7135 (t0) REVERT: C 359 ARG cc_start: 0.7529 (mtm110) cc_final: 0.7236 (mtt90) outliers start: 24 outliers final: 17 residues processed: 173 average time/residue: 0.2533 time to fit residues: 60.9676 Evaluate side-chains 166 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 106 GLN 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 C residue 326 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 106 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.163298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129882 restraints weight = 13754.642| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.87 r_work: 0.2974 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2780 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= 0.171 Angle : 0.580 7.423 15694 Z= 0.284 Chirality : 0.043 0.178 1858 Planarity : 0.004 0.041 1994 Dihedral : 8.652 73.324 1998 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.31 % Allowed : 11.46 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1468 helix: 1.65 (0.21), residues: 582 sheet: -0.19 (0.30), residues: 260 loop : -1.05 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 152 HIS 0.004 0.001 HIS A 209 PHE 0.012 0.001 PHE A 127 TYR 0.017 0.002 TYR B 367 ARG 0.002 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 12) link_NAG-ASN : angle 2.81905 ( 36) link_BETA1-4 : bond 0.00345 ( 8) link_BETA1-4 : angle 2.33354 ( 24) hydrogen bonds : bond 0.03508 ( 516) hydrogen bonds : angle 4.30158 ( 1518) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.87896 ( 8) covalent geometry : bond 0.00408 (11448) covalent geometry : angle 0.55756 (15626) *********************** 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 179 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.233 Fit side-chains REVERT: A 55 ARG cc_start: 0.8379 (mmt180) cc_final: 0.8150 (mmt180) REVERT: A 151 ASN cc_start: 0.7721 (t0) cc_final: 0.7184 (t0) REVERT: A 277 ASP cc_start: 0.8591 (m-30) cc_final: 0.8360 (m-30) REVERT: C 151 ASN cc_start: 0.7692 (t0) cc_final: 0.7149 (t0) REVERT: C 359 ARG cc_start: 0.7637 (mtm110) cc_final: 0.7231 (mtt90) outliers start: 24 outliers final: 17 residues processed: 170 average time/residue: 0.2881 time to fit residues: 68.6606 Evaluate side-chains 165 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 326 VAL 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 325 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 22 optimal weight: 6.9990 chunk 102 optimal weight: 0.0970 chunk 139 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.165766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133604 restraints weight = 13815.012| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.91 r_work: 0.3009 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11472 Z= 0.121 Angle : 0.545 9.608 15694 Z= 0.264 Chirality : 0.042 0.164 1858 Planarity : 0.003 0.038 1994 Dihedral : 7.881 69.111 1998 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.02 % Allowed : 12.24 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1468 helix: 1.85 (0.21), residues: 584 sheet: -0.12 (0.30), residues: 260 loop : -0.97 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 152 HIS 0.003 0.001 HIS D 87 PHE 0.014 0.001 PHE C 286 TYR 0.018 0.001 TYR D 367 ARG 0.003 0.000 ARG B 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 12) link_NAG-ASN : angle 2.63286 ( 36) link_BETA1-4 : bond 0.00431 ( 8) link_BETA1-4 : angle 2.23865 ( 24) hydrogen bonds : bond 0.03130 ( 516) hydrogen bonds : angle 4.14919 ( 1518) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.71320 ( 8) covalent geometry : bond 0.00281 (11448) covalent geometry : angle 0.52409 (15626) *********************** 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 170 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.291 Fit side-chains REVERT: A 55 ARG cc_start: 0.8463 (mmt180) cc_final: 0.8262 (mmt180) REVERT: A 151 ASN cc_start: 0.7716 (t0) cc_final: 0.7225 (t0) REVERT: A 185 ASP cc_start: 0.8408 (t0) cc_final: 0.8107 (t0) REVERT: A 277 ASP cc_start: 0.8623 (m-30) cc_final: 0.8413 (m-30) REVERT: C 151 ASN cc_start: 0.7731 (t0) cc_final: 0.7236 (t0) outliers start: 21 outliers final: 16 residues processed: 162 average time/residue: 0.2637 time to fit residues: 59.2252 Evaluate side-chains 161 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 275 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 76 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 275 THR Chi-restraints excluded: chain D residue 325 ARG 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 56 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.165179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132750 restraints weight = 13882.271| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.92 r_work: 0.2999 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11472 Z= 0.133 Angle : 0.544 8.779 15694 Z= 0.265 Chirality : 0.042 0.162 1858 Planarity : 0.003 0.037 1994 Dihedral : 7.403 64.848 1998 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.99 % Allowed : 11.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1468 helix: 1.91 (0.21), residues: 584 sheet: -0.13 (0.32), residues: 250 loop : -0.91 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 152 HIS 0.003 0.001 HIS A 209 PHE 0.037 0.001 PHE D 23 TYR 0.019 0.001 TYR D 367 ARG 0.005 0.000 ARG A 359 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 12) link_NAG-ASN : angle 2.53721 ( 36) link_BETA1-4 : bond 0.00414 ( 8) link_BETA1-4 : angle 2.31145 ( 24) hydrogen bonds : bond 0.03195 ( 516) hydrogen bonds : angle 4.10225 ( 1518) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.80784 ( 8) covalent geometry : bond 0.00314 (11448) covalent geometry : angle 0.52350 (15626) *********************** 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 176 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.192 Fit side-chains REVERT: A 55 ARG cc_start: 0.8476 (mmt180) cc_final: 0.8276 (mmt180) REVERT: A 151 ASN cc_start: 0.7747 (t0) cc_final: 0.7262 (t0) REVERT: A 185 ASP cc_start: 0.8364 (t0) cc_final: 0.8072 (t0) REVERT: A 277 ASP cc_start: 0.8627 (m-30) cc_final: 0.8408 (m-30) REVERT: C 151 ASN cc_start: 0.7738 (t0) cc_final: 0.7238 (t0) outliers start: 31 outliers final: 20 residues processed: 164 average time/residue: 0.2545 time to fit residues: 57.8468 Evaluate side-chains 166 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ILE 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 275 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 79 ILE 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 275 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 77 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 0.0770 chunk 109 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.159369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112243 restraints weight = 13887.417| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.14 r_work: 0.2969 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.005 0.047 11472 Z= 0.198 Angle : 0.586 8.470 15694 Z= 0.289 Chirality : 0.044 0.165 1858 Planarity : 0.004 0.038 1994 Dihedral : 7.159 61.310 1998 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.41 % Allowed : 12.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1468 helix: 1.71 (0.21), residues: 584 sheet: -0.12 (0.32), residues: 250 loop : -0.98 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 152 HIS 0.004 0.001 HIS A 209 PHE 0.025 0.002 PHE D 23 TYR 0.018 0.002 TYR B 367 ARG 0.004 0.000 ARG D 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 12) link_NAG-ASN : angle 2.50383 ( 36) link_BETA1-4 : bond 0.00369 ( 8) link_BETA1-4 : angle 2.48020 ( 24) hydrogen bonds : bond 0.03589 ( 516) hydrogen bonds : angle 4.21534 ( 1518) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.85797 ( 8) covalent geometry : bond 0.00476 (11448) covalent geometry : angle 0.56611 (15626) *********************** 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 168 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.290 Fit side-chains REVERT: A 55 ARG cc_start: 0.8310 (mmt180) cc_final: 0.8096 (mmt180) REVERT: A 151 ASN cc_start: 0.7638 (t0) cc_final: 0.7187 (t0) REVERT: A 185 ASP cc_start: 0.8344 (t0) cc_final: 0.8039 (t0) REVERT: A 277 ASP cc_start: 0.8507 (m-30) cc_final: 0.8281 (m-30) REVERT: C 151 ASN cc_start: 0.7636 (t0) cc_final: 0.7172 (t0) REVERT: C 185 ASP cc_start: 0.8326 (t0) cc_final: 0.7990 (t0) outliers start: 25 outliers final: 23 residues processed: 161 average time/residue: 0.2628 time to fit residues: 58.6472 Evaluate side-chains 167 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 79 ILE 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 275 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 79 ILE 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 275 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 7 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 0.0370 chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 144 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 = 0.167627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136773 restraints weight = 13979.303| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.90 r_work: 0.3040 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11472 Z= 0.105 Angle : 0.526 8.750 15694 Z= 0.258 Chirality : 0.041 0.154 1858 Planarity : 0.003 0.037 1994 Dihedral : 6.586 56.732 1998 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.93 % Allowed : 13.10 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1468 helix: 2.02 (0.21), residues: 584 sheet: -0.05 (0.32), residues: 250 loop : -0.85 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 152 HIS 0.003 0.000 HIS B 87 PHE 0.024 0.001 PHE D 23 TYR 0.018 0.001 TYR D 367 ARG 0.003 0.000 ARG D 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 12) link_NAG-ASN : angle 2.37942 ( 36) link_BETA1-4 : bond 0.00448 ( 8) link_BETA1-4 : angle 2.24301 ( 24) hydrogen bonds : bond 0.03005 ( 516) hydrogen bonds : angle 4.04273 ( 1518) SS BOND : bond 0.00185 ( 4) SS BOND : angle 0.62737 ( 8) covalent geometry : bond 0.00242 (11448) covalent geometry : angle 0.50695 (15626) *********************** 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 171 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.165 Fit side-chains REVERT: A 151 ASN cc_start: 0.7758 (t0) cc_final: 0.7305 (t0) REVERT: A 185 ASP cc_start: 0.8420 (t0) cc_final: 0.8140 (t0) REVERT: A 277 ASP cc_start: 0.8672 (m-30) cc_final: 0.8451 (m-30) REVERT: A 352 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7046 (tt0) REVERT: B 229 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8664 (tt) REVERT: C 65 TYR cc_start: 0.7687 (m-80) cc_final: 0.7428 (m-80) REVERT: C 151 ASN cc_start: 0.7776 (t0) cc_final: 0.7326 (t0) REVERT: C 185 ASP cc_start: 0.8370 (t0) cc_final: 0.8085 (t0) REVERT: C 352 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7185 (tt0) REVERT: D 229 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8657 (tt) outliers start: 20 outliers final: 16 residues processed: 166 average time/residue: 0.2720 time to fit residues: 61.2912 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 : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ILE 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 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 79 ILE 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 275 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 111 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 18 optimal weight: 0.0030 chunk 83 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.161943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116051 restraints weight = 13791.492| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.22 r_work: 0.3028 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11472 Z= 0.120 Angle : 0.532 8.447 15694 Z= 0.261 Chirality : 0.042 0.176 1858 Planarity : 0.003 0.036 1994 Dihedral : 6.237 57.198 1998 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.31 % Allowed : 12.91 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1468 helix: 2.08 (0.21), residues: 584 sheet: 0.00 (0.32), residues: 250 loop : -0.78 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 152 HIS 0.003 0.001 HIS A 209 PHE 0.022 0.001 PHE D 23 TYR 0.019 0.001 TYR D 367 ARG 0.003 0.000 ARG D 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 12) link_NAG-ASN : angle 2.28590 ( 36) link_BETA1-4 : bond 0.00436 ( 8) link_BETA1-4 : angle 2.24686 ( 24) hydrogen bonds : bond 0.03062 ( 516) hydrogen bonds : angle 4.01433 ( 1518) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.67581 ( 8) covalent geometry : bond 0.00282 (11448) covalent geometry : angle 0.51392 (15626) ********************** 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: 24 poor density : 144 time to evaluate : 1.163 Fit side-chains REVERT: A 65 TYR cc_start: 0.7663 (m-80) cc_final: 0.7408 (m-80) REVERT: A 151 ASN cc_start: 0.7595 (t0) cc_final: 0.7175 (t0) REVERT: A 185 ASP cc_start: 0.8297 (t0) cc_final: 0.7998 (t0) REVERT: A 277 ASP cc_start: 0.8529 (m-30) cc_final: 0.8315 (m-30) REVERT: A 339 GLU cc_start: 0.7511 (tp30) cc_final: 0.6748 (tm-30) REVERT: A 352 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6899 (tt0) REVERT: B 229 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8671 (tt) REVERT: C 65 TYR cc_start: 0.7657 (m-80) cc_final: 0.7402 (m-80) REVERT: C 151 ASN cc_start: 0.7551 (t0) cc_final: 0.7136 (t0) REVERT: C 339 GLU cc_start: 0.7545 (tp30) cc_final: 0.6729 (tm-30) outliers start: 24 outliers final: 20 residues processed: 162 average time/residue: 0.2659 time to fit residues: 58.7594 Evaluate side-chains 163 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 79 ILE 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 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 79 ILE 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 275 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 139 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.160010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112970 restraints weight = 13705.001| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.21 r_work: 0.2996 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11472 Z= 0.168 Angle : 0.568 10.208 15694 Z= 0.280 Chirality : 0.043 0.183 1858 Planarity : 0.003 0.036 1994 Dihedral : 6.048 54.139 1998 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.02 % Allowed : 13.29 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1468 helix: 1.93 (0.21), residues: 584 sheet: -0.06 (0.32), residues: 250 loop : -0.85 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 152 HIS 0.004 0.001 HIS C 209 PHE 0.023 0.002 PHE D 23 TYR 0.019 0.002 TYR B 367 ARG 0.002 0.000 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 12) link_NAG-ASN : angle 2.30025 ( 36) link_BETA1-4 : bond 0.00389 ( 8) link_BETA1-4 : angle 2.27342 ( 24) hydrogen bonds : bond 0.03343 ( 516) hydrogen bonds : angle 4.08607 ( 1518) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.77390 ( 8) covalent geometry : bond 0.00404 (11448) covalent geometry : angle 0.55063 (15626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5248.84 seconds wall clock time: 92 minutes 55.54 seconds (5575.54 seconds total)