Starting phenix.real_space_refine on Sun Dec 29 20:08:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7occ_12803/12_2024/7occ_12803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7occ_12803/12_2024/7occ_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_12803/12_2024/7occ_12803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7occ_12803/12_2024/7occ_12803.map" model { file = "/net/cci-nas-00/data/ceres_data/7occ_12803/12_2024/7occ_12803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7occ_12803/12_2024/7occ_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.62, per 1000 atoms: 0.68 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: 3.25 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: 1.38 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: 3.86 Time building geometry restraints manager: 3.60 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.870 Find NCS groups from input model: 0.450 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- 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 11448 Z= 0.644 Angle : 0.762 30.364 15626 Z= 0.381 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 *********************** 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 : 1.289 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: 0.2641 time to fit residues: 63.2265 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 : 1.210 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 11448 Z= 0.204 Angle : 0.600 10.240 15626 Z= 0.297 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 *********************** 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 : 1.152 Fit side-chains REVERT: A 52 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7080 (mtp) REVERT: A 55 ARG cc_start: 0.8017 (mmt180) cc_final: 0.7543 (mmt180) REVERT: A 120 ASP cc_start: 0.6553 (t0) cc_final: 0.6327 (t70) REVERT: B 121 TYR cc_start: 0.8630 (t80) cc_final: 0.8325 (t80) REVERT: C 120 ASP cc_start: 0.6848 (t0) cc_final: 0.6592 (t70) REVERT: D 121 TYR cc_start: 0.8567 (t80) cc_final: 0.8319 (t80) outliers start: 10 outliers final: 7 residues processed: 179 average time/residue: 0.2675 time to fit residues: 66.3059 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 : 1.330 ------------------------------------------------------------------------------- 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 73 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11448 Z= 0.226 Angle : 0.575 10.660 15626 Z= 0.278 Chirality : 0.044 0.193 1858 Planarity : 0.004 0.039 1994 Dihedral : 10.213 73.013 1998 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.54 % Allowed : 9.15 % Favored : 89.31 % 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: 0.50 (0.22), residues: 1468 helix: 1.91 (0.21), residues: 580 sheet: -0.13 (0.30), residues: 246 loop : -0.96 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 152 HIS 0.005 0.001 HIS B 87 PHE 0.012 0.001 PHE A 127 TYR 0.021 0.002 TYR D 367 ARG 0.004 0.001 ARG A 253 *********************** 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 177 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 1.328 Fit side-chains REVERT: A 52 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7049 (mtp) REVERT: A 55 ARG cc_start: 0.8074 (mmt180) cc_final: 0.7867 (mmt180) REVERT: C 352 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6829 (tm-30) REVERT: D 121 TYR cc_start: 0.8786 (t80) cc_final: 0.8509 (t80) outliers start: 16 outliers final: 7 residues processed: 169 average time/residue: 0.2664 time to fit residues: 62.5514 Evaluate side-chains 158 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain 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 131 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11448 Z= 0.203 Angle : 0.526 7.363 15626 Z= 0.260 Chirality : 0.042 0.177 1858 Planarity : 0.003 0.038 1994 Dihedral : 8.710 70.935 1998 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.73 % Allowed : 10.89 % Favored : 87.38 % 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: 0.59 (0.22), residues: 1468 helix: 1.98 (0.21), residues: 584 sheet: -0.14 (0.31), residues: 246 loop : -0.89 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 152 HIS 0.003 0.001 HIS B 87 PHE 0.010 0.001 PHE A 127 TYR 0.018 0.002 TYR D 367 ARG 0.004 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 1.241 Fit side-chains REVERT: A 55 ARG cc_start: 0.8056 (mmt180) cc_final: 0.7847 (mmt180) outliers start: 18 outliers final: 7 residues processed: 168 average time/residue: 0.2588 time to fit residues: 61.1138 Evaluate side-chains 154 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 chunk 120 optimal weight: 0.7980 chunk 97 optimal weight: 0.0060 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11448 Z= 0.156 Angle : 0.503 7.828 15626 Z= 0.247 Chirality : 0.041 0.171 1858 Planarity : 0.003 0.038 1994 Dihedral : 7.746 66.638 1998 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.54 % Allowed : 11.66 % Favored : 86.80 % 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: 0.75 (0.22), residues: 1468 helix: 2.15 (0.21), residues: 586 sheet: -0.08 (0.31), residues: 250 loop : -0.85 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 152 HIS 0.003 0.001 HIS D 87 PHE 0.009 0.001 PHE D 56 TYR 0.019 0.001 TYR D 367 ARG 0.002 0.000 ARG D 172 *********************** 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 171 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.334 Fit side-chains REVERT: A 185 ASP cc_start: 0.7743 (t0) cc_final: 0.7420 (t0) outliers start: 16 outliers final: 9 residues processed: 167 average time/residue: 0.2849 time to fit residues: 65.4446 Evaluate side-chains 155 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 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 47 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11448 Z= 0.294 Angle : 0.558 7.348 15626 Z= 0.279 Chirality : 0.043 0.178 1858 Planarity : 0.004 0.037 1994 Dihedral : 7.399 63.048 1998 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.31 % Allowed : 11.27 % Favored : 86.42 % 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: 0.57 (0.22), residues: 1468 helix: 1.91 (0.21), residues: 586 sheet: -0.11 (0.31), residues: 248 loop : -0.88 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 152 HIS 0.003 0.001 HIS C 209 PHE 0.013 0.002 PHE C 127 TYR 0.020 0.002 TYR D 367 ARG 0.003 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.349 Fit side-chains REVERT: A 185 ASP cc_start: 0.7726 (t0) cc_final: 0.7428 (t0) REVERT: C 282 MET cc_start: 0.8478 (mtm) cc_final: 0.8096 (mtm) outliers start: 24 outliers final: 17 residues processed: 162 average time/residue: 0.2837 time to fit residues: 63.2363 Evaluate side-chains 161 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 8 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 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 88 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11448 Z= 0.172 Angle : 0.514 7.245 15626 Z= 0.256 Chirality : 0.041 0.154 1858 Planarity : 0.003 0.036 1994 Dihedral : 6.890 60.954 1998 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.45 % Allowed : 12.14 % Favored : 86.42 % 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: 0.73 (0.22), residues: 1468 helix: 2.09 (0.21), residues: 586 sheet: -0.08 (0.31), residues: 248 loop : -0.81 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 152 HIS 0.003 0.001 HIS D 87 PHE 0.008 0.001 PHE D 70 TYR 0.018 0.001 TYR D 367 ARG 0.002 0.000 ARG D 291 *********************** 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 168 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.210 Fit side-chains REVERT: A 185 ASP cc_start: 0.7700 (t0) cc_final: 0.7416 (t0) REVERT: B 27 MET cc_start: 0.7177 (mmt) cc_final: 0.6742 (mmt) REVERT: C 282 MET cc_start: 0.8510 (mtm) cc_final: 0.8162 (mtm) REVERT: D 27 MET cc_start: 0.7272 (mmt) cc_final: 0.6807 (mmt) outliers start: 15 outliers final: 11 residues processed: 163 average time/residue: 0.2811 time to fit residues: 62.7242 Evaluate side-chains 156 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 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 87 optimal weight: 1.9990 chunk 56 optimal weight: 0.0030 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11448 Z= 0.191 Angle : 0.515 7.193 15626 Z= 0.257 Chirality : 0.041 0.148 1858 Planarity : 0.003 0.035 1994 Dihedral : 6.394 58.464 1998 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.83 % Allowed : 11.85 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.22), residues: 1468 helix: 2.16 (0.21), residues: 586 sheet: -0.09 (0.32), residues: 250 loop : -0.80 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 152 HIS 0.002 0.001 HIS A 209 PHE 0.015 0.001 PHE C 328 TYR 0.020 0.001 TYR D 367 ARG 0.003 0.000 ARG D 291 *********************** 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 166 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.198 Fit side-chains REVERT: A 185 ASP cc_start: 0.7687 (t0) cc_final: 0.7406 (t0) REVERT: C 282 MET cc_start: 0.8489 (mtm) cc_final: 0.8215 (mtm) outliers start: 19 outliers final: 15 residues processed: 158 average time/residue: 0.2651 time to fit residues: 57.8330 Evaluate side-chains 161 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 28 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 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 0.1980 chunk 40 optimal weight: 0.0070 chunk 118 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11448 Z= 0.152 Angle : 0.499 7.133 15626 Z= 0.250 Chirality : 0.041 0.160 1858 Planarity : 0.003 0.035 1994 Dihedral : 6.049 58.784 1998 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.54 % Allowed : 12.52 % Favored : 85.93 % 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: 0.89 (0.22), residues: 1468 helix: 2.26 (0.21), residues: 586 sheet: -0.06 (0.32), residues: 250 loop : -0.75 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 152 HIS 0.002 0.000 HIS D 87 PHE 0.037 0.001 PHE D 23 TYR 0.019 0.001 TYR D 367 ARG 0.002 0.000 ARG D 172 *********************** 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: 16 poor density : 155 time to evaluate : 1.257 Fit side-chains REVERT: A 185 ASP cc_start: 0.7684 (t0) cc_final: 0.7456 (t0) REVERT: A 352 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6609 (tt0) REVERT: B 229 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8580 (tt) REVERT: C 282 MET cc_start: 0.8486 (mtm) cc_final: 0.8217 (mtm) REVERT: C 339 GLU cc_start: 0.6560 (tp30) cc_final: 0.6318 (tm-30) outliers start: 16 outliers final: 11 residues processed: 168 average time/residue: 0.2824 time to fit residues: 66.2271 Evaluate side-chains 159 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 71 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11448 Z= 0.190 Angle : 0.514 7.034 15626 Z= 0.259 Chirality : 0.041 0.166 1858 Planarity : 0.003 0.035 1994 Dihedral : 5.743 55.158 1998 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.45 % Allowed : 12.91 % Favored : 85.65 % 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: 0.89 (0.22), residues: 1468 helix: 2.24 (0.21), residues: 586 sheet: -0.03 (0.32), residues: 248 loop : -0.72 (0.25), residues: 634 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 0.031 0.001 PHE D 23 TYR 0.020 0.001 TYR D 367 ARG 0.002 0.000 ARG D 172 ********************** 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 169 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.311 Fit side-chains REVERT: A 185 ASP cc_start: 0.7716 (t0) cc_final: 0.7454 (t0) REVERT: C 282 MET cc_start: 0.8496 (mtm) cc_final: 0.8233 (mtm) REVERT: C 339 GLU cc_start: 0.6593 (tp30) cc_final: 0.6310 (tm-30) outliers start: 15 outliers final: 11 residues processed: 166 average time/residue: 0.2758 time to fit residues: 63.1217 Evaluate side-chains 160 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 271 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134356 restraints weight = 13929.498| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.96 r_work: 0.3073 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11448 Z= 0.175 Angle : 0.514 9.662 15626 Z= 0.258 Chirality : 0.041 0.152 1858 Planarity : 0.003 0.035 1994 Dihedral : 5.522 53.999 1998 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.54 % Allowed : 13.29 % Favored : 85.16 % 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: 0.92 (0.22), residues: 1468 helix: 2.29 (0.21), residues: 584 sheet: -0.04 (0.32), residues: 250 loop : -0.72 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 152 HIS 0.003 0.001 HIS D 87 PHE 0.029 0.001 PHE D 23 TYR 0.020 0.001 TYR D 367 ARG 0.002 0.000 ARG D 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.90 seconds wall clock time: 42 minutes 25.98 seconds (2545.98 seconds total)