Starting phenix.real_space_refine on Fri Jul 3 13:56:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctv_45920/07_2026/9ctv_45920.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctv_45920/07_2026/9ctv_45920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctv_45920/07_2026/9ctv_45920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctv_45920/07_2026/9ctv_45920.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctv_45920/07_2026/9ctv_45920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctv_45920/07_2026/9ctv_45920.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 82 5.16 5 C 9411 2.51 5 N 2341 2.21 5 O 2726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14567 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2701 Classifications: {'peptide': 329} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "B" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2693 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain breaks: 1 Chain: "C" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1714 Classifications: {'peptide': 207} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 197} Chain: "D" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2673 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Chain: "E" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2678 Classifications: {'peptide': 332} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" 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: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'PIO': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" 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: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.21 Number of scatterers: 14567 At special positions: 0 Unit cell: (121.55, 115.94, 133.705, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 7 15.00 O 2726 8.00 N 2341 7.00 C 9411 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 ALPHA1-6 " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG C 501 " - " ASN C 208 " " NAG F 1 " - " ASN A 80 " " NAG G 1 " - " ASN A 149 " " NAG H 1 " - " ASN D 149 " " NAG I 1 " - " ASN D 80 " " NAG J 1 " - " ASN E 110 " " NAG M 1 " - " ASN B 111 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 618.1 milliseconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 23 sheets defined 29.0% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.760A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 removed outlier: 4.021A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 268 removed outlier: 3.769A pdb=" N MET A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 307 removed outlier: 3.505A pdb=" N TYR A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 486 Proline residue: A 472 - end of helix removed outlier: 3.824A pdb=" N PHE A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.508A pdb=" N ILE B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 4.504A pdb=" N ASP B 145 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 146 " --> pdb=" O LEU B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.894A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.549A pdb=" N LEU B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 273 removed outlier: 3.554A pdb=" N PHE B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 310 removed outlier: 3.604A pdb=" N PHE B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 416 removed outlier: 4.403A pdb=" N ILE B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Proline residue: B 401 - end of helix removed outlier: 3.511A pdb=" N TRP B 412 " --> pdb=" O ASN B 408 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.718A pdb=" N MET C 102 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 20 Processing helix chain 'D' and resid 139 through 143 removed outlier: 4.258A pdb=" N ARG D 142 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 225 through 237 Processing helix chain 'D' and resid 238 through 242 removed outlier: 3.551A pdb=" N ILE D 242 " --> pdb=" O SER D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 271 removed outlier: 3.506A pdb=" N LEU D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 266 " --> pdb=" O THR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 306 removed outlier: 4.084A pdb=" N PHE D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 445 removed outlier: 3.530A pdb=" N SER D 428 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET D 430 " --> pdb=" O LYS D 426 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) Proline residue: D 433 - end of helix removed outlier: 3.678A pdb=" N LEU D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 87 through 93 removed outlier: 4.286A pdb=" N SER E 91 " --> pdb=" O ASN E 87 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 145 removed outlier: 4.038A pdb=" N ASP E 144 " --> pdb=" O HIS E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 176 Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 229 through 242 removed outlier: 3.554A pdb=" N THR E 236 " --> pdb=" O PRO E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 246 removed outlier: 3.563A pdb=" N LEU E 246 " --> pdb=" O SER E 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 243 through 246' Processing helix chain 'E' and resid 250 through 273 removed outlier: 3.504A pdb=" N THR E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 262 " --> pdb=" O GLY E 258 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 309 removed outlier: 3.764A pdb=" N ALA E 299 " --> pdb=" O PHE E 295 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 412 removed outlier: 4.151A pdb=" N ILE E 395 " --> pdb=" O ARG E 391 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE E 397 " --> pdb=" O SER E 393 " (cutoff:3.500A) Proline residue: E 398 - end of helix removed outlier: 3.588A pdb=" N ALA E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.822A pdb=" N TRP A 67 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 removed outlier: 3.822A pdb=" N TRP A 67 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 62 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE A 44 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLN A 64 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE A 42 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.646A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 86 removed outlier: 4.246A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 130 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP B 70 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.518A pdb=" N TRP B 70 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.133A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.133A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 98 removed outlier: 3.691A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU C 71 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 58 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.949A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA C 121 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ARG C 144 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU C 71 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 58 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N GLU C 189 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N MET C 57 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.337A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.337A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 218 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 81 through 83 removed outlier: 3.534A pdb=" N LEU D 83 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE D 105 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 81 through 83 removed outlier: 3.534A pdb=" N LEU D 83 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP D 67 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS D 68 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP D 37 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR D 167 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.982A pdb=" N ASP D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 48 through 53 removed outlier: 3.588A pdb=" N SER E 48 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR E 60 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL E 52 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU E 58 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR E 38 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE E 169 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL E 40 " --> pdb=" O ILE E 169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 107 through 108 removed outlier: 8.829A pdb=" N GLN E 179 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE E 44 " --> pdb=" O GLN E 179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 83 through 85 removed outlier: 4.049A pdb=" N LEU E 118 " --> pdb=" O LEU E 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.304A pdb=" N SER E 158 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR E 210 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY E 207 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY E 194 " --> pdb=" O HIS E 217 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS E 219 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU E 192 " --> pdb=" O LYS E 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.606A pdb=" N THR K 71 " --> pdb=" O TYR K 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.896A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR K 115 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS K 59 " --> pdb=" O ARG K 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.507A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.009A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.729A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1887 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: 3.08 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2419 1.32 - 1.45: 4215 1.45 - 1.57: 8137 1.57 - 1.69: 10 1.69 - 1.81: 144 Bond restraints: 14925 Sorted by residual: bond pdb=" C GLY A 219 " pdb=" O GLY A 219 " ideal model delta sigma weight residual 1.234 1.293 -0.059 1.21e-02 6.83e+03 2.40e+01 bond pdb=" C HIS D 267 " pdb=" O HIS D 267 " ideal model delta sigma weight residual 1.237 1.292 -0.055 1.16e-02 7.43e+03 2.28e+01 bond pdb=" C PHE D 432 " pdb=" N PRO D 433 " ideal model delta sigma weight residual 1.335 1.391 -0.057 1.28e-02 6.10e+03 1.96e+01 bond pdb=" C SER D 265 " pdb=" O SER D 265 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.15e-02 7.56e+03 1.88e+01 bond pdb=" O4 PIO B 601 " pdb=" P4 PIO B 601 " ideal model delta sigma weight residual 1.710 1.625 0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 14920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 19506 2.20 - 4.40: 678 4.40 - 6.60: 77 6.60 - 8.81: 15 8.81 - 11.01: 3 Bond angle restraints: 20279 Sorted by residual: angle pdb=" O PHE D 166 " pdb=" C PHE D 166 " pdb=" N TYR D 167 " ideal model delta sigma weight residual 123.27 114.65 8.62 1.13e+00 7.83e-01 5.82e+01 angle pdb=" CA PHE D 166 " pdb=" C PHE D 166 " pdb=" N TYR D 167 " ideal model delta sigma weight residual 116.25 124.46 -8.21 1.23e+00 6.61e-01 4.45e+01 angle pdb=" C TYR A 220 " pdb=" N PHE A 221 " pdb=" CA PHE A 221 " ideal model delta sigma weight residual 120.44 112.87 7.57 1.30e+00 5.92e-01 3.39e+01 angle pdb=" C PHE D 166 " pdb=" N TYR D 167 " pdb=" CA TYR D 167 " ideal model delta sigma weight residual 121.85 131.62 -9.77 1.77e+00 3.19e-01 3.05e+01 angle pdb=" N HIS D 267 " pdb=" CA HIS D 267 " pdb=" C HIS D 267 " ideal model delta sigma weight residual 111.14 105.32 5.82 1.08e+00 8.57e-01 2.90e+01 ... (remaining 20274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 8800 34.36 - 68.72: 148 68.72 - 103.08: 40 103.08 - 137.44: 25 137.44 - 171.80: 1 Dihedral angle restraints: 9014 sinusoidal: 3853 harmonic: 5161 Sorted by residual: dihedral pdb=" C3 POV B 602 " pdb=" C31 POV B 602 " pdb=" O31 POV B 602 " pdb=" C32 POV B 602 " ideal model delta sinusoidal sigma weight residual 172.61 0.81 171.80 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA LEU B 133 " pdb=" C LEU B 133 " pdb=" N THR B 134 " pdb=" CA THR B 134 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CD ARG E 220 " pdb=" NE ARG E 220 " pdb=" CZ ARG E 220 " pdb=" NH1 ARG E 220 " ideal model delta sinusoidal sigma weight residual 0.00 36.02 -36.02 1 1.00e+01 1.00e-02 1.84e+01 ... (remaining 9011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 2216 0.129 - 0.257: 111 0.257 - 0.386: 6 0.386 - 0.515: 0 0.515 - 0.643: 1 Chirality restraints: 2334 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.61e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.61e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.74e+01 ... (remaining 2331 not shown) Planarity restraints: 2487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.294 2.00e-02 2.50e+03 2.55e-01 8.14e+02 pdb=" C7 NAG H 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.145 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.456 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.232 2.00e-02 2.50e+03 1.96e-01 4.81e+02 pdb=" C7 NAG J 2 " -0.054 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.334 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.187 2.00e-02 2.50e+03 1.57e-01 3.07e+02 pdb=" C7 NAG G 2 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.135 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.258 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.012 2.00e-02 2.50e+03 ... (remaining 2484 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3911 2.80 - 3.33: 12289 3.33 - 3.85: 24510 3.85 - 4.38: 28283 4.38 - 4.90: 48562 Nonbonded interactions: 117555 Sorted by model distance: nonbonded pdb=" O LEU E 413 " pdb=" C ASN E 414 " model vdw 2.278 3.270 nonbonded pdb=" OD2 ASP D 24 " pdb=" OG1 THR E 15 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR A 74 " pdb=" O LEU A 118 " model vdw 2.320 3.040 nonbonded pdb=" O PHE E 257 " pdb=" OG1 THR E 261 " model vdw 2.329 3.040 nonbonded pdb=" OD1 ASP D 139 " pdb=" CG ARG D 141 " model vdw 2.343 3.440 ... (remaining 117550 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' and (resid 8 through 10 or resid 12 through 36 or resid 38 through 40 \ or resid 42 through 43 or resid 45 through 65 or resid 67 or resid 69 through 7 \ 4 or resid 77 through 168 or resid 170 or resid 174 through 178 or resid 180 thr \ ough 192 or resid 196 through 198 or resid 200 or resid 202 through 203 or resid \ 205 through 212 or resid 214 through 229 or resid 231 through 264 or resid 266 \ through 282 or resid 284 through 293 or resid 295 through 300 or resid 302 throu \ gh 306 or resid 461 or resid 463 through 464 or resid 466 through 468 or resid 4 \ 70 through 472 or resid 475 through 476 or resid 478 through 479 or resid 481 th \ rough 487)) selection = (chain 'D' and (resid 8 through 10 or resid 12 through 36 or resid 38 through 40 \ or resid 42 through 43 or resid 45 through 65 or resid 67 or resid 69 through 7 \ 4 or resid 77 through 168 or resid 170 or resid 174 through 178 or resid 180 thr \ ough 192 or resid 196 through 198 or resid 200 or resid 202 through 203 or resid \ 205 through 212 or resid 214 through 229 or resid 231 through 264 or resid 266 \ through 282 or resid 284 through 293 or resid 295 through 300 or resid 302 throu \ gh 422 or resid 424 through 425 or resid 427 through 429 or resid 431 through 43 \ 3 or resid 436 through 437 or resid 439 through 440 or resid 442 through 448)) } ncs_group { reference = (chain 'B' and (resid 11 or resid 13 or resid 15 through 35 or resid 39 through \ 41 or resid 43 or resid 45 or resid 47 through 55 or resid 57 through 68 or resi \ d 70 through 81 or resid 84 through 121 or resid 124 through 135 or resid 137 th \ rough 151 or resid 153 through 163 or resid 166 through 167 or resid 169 or resi \ d 171 through 172 or resid 178 through 179 or resid 181 through 182 or resid 184 \ through 196 or resid 205 through 210 or resid 212 through 214 or resid 216 thro \ ugh 310 or resid 387 through 394 or resid 396 through 398 or resid 400 through 4 \ 01 or resid 403 through 405 or resid 407 through 601)) selection = (chain 'E' and (resid 10 or resid 12 or resid 14 through 34 or resid 38 through \ 40 or resid 42 or resid 44 or resid 46 through 54 or resid 56 through 67 or resi \ d 69 through 80 or resid 83 through 120 or resid 123 through 134 or resid 136 th \ rough 150 or resid 152 through 162 or resid 165 through 166 or resid 168 or resi \ d 170 through 171 or resid 177 through 178 or resid 180 through 181 or resid 183 \ through 195 or resid 204 through 209 or resid 211 through 213 or resid 215 thro \ ugh 391 or resid 393 through 395 or resid 397 through 398 or resid 400 through 4 \ 02 or resid 404 through 501)) } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'M' } 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.960 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.006 0.085 14950 Z= 0.392 Angle : 0.918 11.008 20347 Z= 0.551 Chirality : 0.062 0.643 2334 Planarity : 0.015 0.281 2480 Dihedral : 16.699 171.803 5675 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.57 % Allowed : 1.59 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.18), residues: 1729 helix: -3.11 (0.15), residues: 448 sheet: -1.47 (0.22), residues: 536 loop : -1.62 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 114 TYR 0.023 0.002 TYR A 220 PHE 0.035 0.001 PHE A 221 TRP 0.020 0.001 TRP K 36 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.39 (14925) covalent geometry : angle 0.90437 / 0.55 (20279) SS BOND : bond 0.00336 / 0.17 ( 7) SS BOND : angle 0.97966 / 0.59 ( 14) hydrogen bonds : bond 0.27611 / 17.88 ( 590) hydrogen bonds : angle 9.53921 / 6.69 ( 1887) link_ALPHA1-6 : bond 0.00917 / 0.48 ( 1) link_ALPHA1-6 : angle 3.99207 / 2.59 ( 3) link_BETA1-4 : bond 0.00614 / 0.38 ( 10) link_BETA1-4 : angle 2.72973 / 2.20 ( 30) link_NAG-ASN : bond 0.01506 / 0.71 ( 7) link_NAG-ASN : angle 3.51968 / 2.28 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 520 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.8508 (tt0) cc_final: 0.7851 (tt0) REVERT: A 197 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7924 (mppt) REVERT: A 269 ARG cc_start: 0.7413 (mtp-110) cc_final: 0.7048 (mtp-110) REVERT: B 24 ASP cc_start: 0.8139 (t0) cc_final: 0.7866 (p0) REVERT: B 123 GLU cc_start: 0.8262 (pt0) cc_final: 0.7829 (pp20) REVERT: B 234 CYS cc_start: 0.8895 (m) cc_final: 0.8012 (m) REVERT: B 282 TYR cc_start: 0.8281 (p90) cc_final: 0.7962 (p90) REVERT: B 286 MET cc_start: 0.8626 (ttp) cc_final: 0.8278 (tmm) REVERT: B 288 TRP cc_start: 0.8593 (m100) cc_final: 0.7980 (m-10) REVERT: B 290 ILE cc_start: 0.8685 (mt) cc_final: 0.8407 (mt) REVERT: C 56 ASP cc_start: 0.7950 (t0) cc_final: 0.7729 (t0) REVERT: C 70 MET cc_start: 0.8168 (mmt) cc_final: 0.7610 (mtm) REVERT: C 188 VAL cc_start: 0.8478 (t) cc_final: 0.8252 (p) REVERT: C 201 PHE cc_start: 0.8536 (m-80) cc_final: 0.8319 (m-80) REVERT: C 203 PHE cc_start: 0.6802 (t80) cc_final: 0.6452 (t80) REVERT: C 204 VAL cc_start: 0.8995 (t) cc_final: 0.8761 (t) REVERT: C 226 TYR cc_start: 0.7947 (m-80) cc_final: 0.7118 (m-80) REVERT: C 228 ASP cc_start: 0.6659 (m-30) cc_final: 0.6367 (t0) REVERT: D 140 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6763 (pt) REVERT: D 147 GLU cc_start: 0.8262 (tt0) cc_final: 0.7951 (tt0) REVERT: D 157 TYR cc_start: 0.8722 (t80) cc_final: 0.8020 (t80) REVERT: D 162 ASP cc_start: 0.8565 (m-30) cc_final: 0.7780 (t0) REVERT: D 240 PHE cc_start: 0.7631 (m-80) cc_final: 0.7430 (m-10) REVERT: D 286 MET cc_start: 0.7026 (mmt) cc_final: 0.6629 (mtt) REVERT: D 291 PHE cc_start: 0.8443 (m-10) cc_final: 0.8120 (m-10) REVERT: D 293 PHE cc_start: 0.8048 (t80) cc_final: 0.7459 (t80) REVERT: D 306 PHE cc_start: 0.6810 (t80) cc_final: 0.6347 (t80) REVERT: D 425 ASP cc_start: 0.7360 (t0) cc_final: 0.7061 (t0) REVERT: E 146 PRO cc_start: 0.8389 (Cg_endo) cc_final: 0.8003 (Cg_exo) REVERT: E 159 TYR cc_start: 0.9198 (t80) cc_final: 0.8917 (t80) REVERT: E 228 GLN cc_start: 0.8321 (tt0) cc_final: 0.7964 (mt0) REVERT: E 241 GLN cc_start: 0.8021 (mt0) cc_final: 0.7634 (tt0) REVERT: K 5 GLN cc_start: 0.8470 (mm110) cc_final: 0.8089 (mm-40) REVERT: K 38 LYS cc_start: 0.8368 (tptm) cc_final: 0.8021 (tptm) REVERT: L 19 VAL cc_start: 0.8732 (p) cc_final: 0.8441 (p) REVERT: L 38 GLN cc_start: 0.7332 (tp-100) cc_final: 0.6756 (tt0) outliers start: 9 outliers final: 0 residues processed: 526 average time/residue: 0.1107 time to fit residues: 84.6882 Evaluate side-chains 345 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 217 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 116 ASN B 151 HIS D 119 HIS D 169 ASN E 115 ASN E 141 HIS K 6 GLN L 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105912 restraints weight = 23781.924| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.93 r_work: 0.3266 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14950 Z= 0.256 Angle : 0.725 10.428 20347 Z= 0.370 Chirality : 0.047 0.259 2334 Planarity : 0.005 0.054 2480 Dihedral : 12.732 173.015 2385 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.37 % Allowed : 12.52 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.19), residues: 1729 helix: -0.53 (0.22), residues: 449 sheet: -1.46 (0.21), residues: 542 loop : -1.20 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 141 TYR 0.025 0.002 TYR E 293 PHE 0.028 0.002 PHE E 244 TRP 0.032 0.002 TRP K 36 HIS 0.005 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.26 (14925) covalent geometry : angle 0.71416 / 0.37 (20279) SS BOND : bond 0.00512 / 0.27 ( 7) SS BOND : angle 2.31029 / 1.35 ( 14) hydrogen bonds : bond 0.05198 / 3.38 ( 590) hydrogen bonds : angle 5.78315 / 4.02 ( 1887) link_ALPHA1-6 : bond 0.01638 / 0.86 ( 1) link_ALPHA1-6 : angle 3.66988 / 2.97 ( 3) link_BETA1-4 : bond 0.00832 / 0.50 ( 10) link_BETA1-4 : angle 2.19400 / 1.56 ( 30) link_NAG-ASN : bond 0.00487 / 0.25 ( 7) link_NAG-ASN : angle 2.18704 / 1.51 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 351 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8709 (ptm) REVERT: A 153 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8565 (mm-30) REVERT: A 155 GLU cc_start: 0.8442 (tt0) cc_final: 0.8230 (tt0) REVERT: A 197 LYS cc_start: 0.8325 (mtmt) cc_final: 0.8033 (mppt) REVERT: A 237 TRP cc_start: 0.8159 (m-10) cc_final: 0.7926 (m-10) REVERT: A 244 TYR cc_start: 0.7176 (p90) cc_final: 0.6732 (p90) REVERT: B 24 ASP cc_start: 0.8331 (t0) cc_final: 0.7729 (p0) REVERT: B 144 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 196 GLN cc_start: 0.8611 (pm20) cc_final: 0.8192 (pm20) REVERT: B 234 CYS cc_start: 0.8861 (m) cc_final: 0.8246 (m) REVERT: B 250 GLU cc_start: 0.7978 (mp0) cc_final: 0.7019 (tt0) REVERT: B 282 TYR cc_start: 0.8208 (p90) cc_final: 0.7896 (p90) REVERT: C 70 MET cc_start: 0.8134 (mmt) cc_final: 0.7622 (mmt) REVERT: C 102 MET cc_start: 0.8473 (tpp) cc_final: 0.8207 (tpp) REVERT: C 201 PHE cc_start: 0.8455 (m-80) cc_final: 0.8198 (m-80) REVERT: C 226 TYR cc_start: 0.7771 (m-80) cc_final: 0.7079 (m-80) REVERT: D 147 GLU cc_start: 0.8450 (tt0) cc_final: 0.7793 (tt0) REVERT: D 157 TYR cc_start: 0.8692 (t80) cc_final: 0.8140 (t80) REVERT: D 162 ASP cc_start: 0.8832 (m-30) cc_final: 0.8019 (t0) REVERT: D 181 ILE cc_start: 0.8069 (mt) cc_final: 0.7620 (mt) REVERT: D 207 ARG cc_start: 0.8262 (ttm170) cc_final: 0.7646 (ttm110) REVERT: D 286 MET cc_start: 0.6939 (mmt) cc_final: 0.6527 (mtt) REVERT: D 425 ASP cc_start: 0.7510 (t0) cc_final: 0.7185 (t0) REVERT: E 111 MET cc_start: 0.7882 (ttm) cc_final: 0.7594 (ttt) REVERT: E 146 PRO cc_start: 0.8345 (Cg_endo) cc_final: 0.7963 (Cg_exo) REVERT: E 159 TYR cc_start: 0.9184 (t80) cc_final: 0.8920 (t80) REVERT: E 309 PHE cc_start: 0.5463 (m-80) cc_final: 0.5244 (m-80) REVERT: K 5 GLN cc_start: 0.8526 (mm110) cc_final: 0.8188 (mm-40) REVERT: L 8 PRO cc_start: 0.7650 (Cg_endo) cc_final: 0.7211 (Cg_exo) REVERT: L 94 TYR cc_start: 0.8922 (m-80) cc_final: 0.8604 (m-80) outliers start: 53 outliers final: 31 residues processed: 376 average time/residue: 0.1051 time to fit residues: 59.7904 Evaluate side-chains 346 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 314 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 HIS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 107 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 143 optimal weight: 0.0670 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.144842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105673 restraints weight = 24239.365| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.35 r_work: 0.3244 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14950 Z= 0.176 Angle : 0.621 12.630 20347 Z= 0.313 Chirality : 0.044 0.218 2334 Planarity : 0.004 0.052 2480 Dihedral : 9.899 178.584 2385 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.07 % Allowed : 14.49 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.19), residues: 1729 helix: 0.29 (0.23), residues: 464 sheet: -1.31 (0.21), residues: 536 loop : -1.15 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 142 TYR 0.025 0.002 TYR B 225 PHE 0.021 0.002 PHE E 244 TRP 0.022 0.001 TRP C 183 HIS 0.031 0.002 HIS E 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (14925) covalent geometry : angle 0.61243 / 0.31 (20279) SS BOND : bond 0.00511 / 0.27 ( 7) SS BOND : angle 1.33097 / 0.78 ( 14) hydrogen bonds : bond 0.04090 / 2.68 ( 590) hydrogen bonds : angle 5.22702 / 3.62 ( 1887) link_ALPHA1-6 : bond 0.01737 / 0.91 ( 1) link_ALPHA1-6 : angle 3.10327 / 2.31 ( 3) link_BETA1-4 : bond 0.00526 / 0.31 ( 10) link_BETA1-4 : angle 2.10026 / 1.45 ( 30) link_NAG-ASN : bond 0.00265 / 0.14 ( 7) link_NAG-ASN : angle 1.68611 / 1.16 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 324 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8661 (ptm) REVERT: A 153 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8614 (mm-30) REVERT: A 197 LYS cc_start: 0.8328 (mtmt) cc_final: 0.8021 (mppt) REVERT: A 230 ILE cc_start: 0.8786 (pt) cc_final: 0.8258 (mt) REVERT: A 282 ASP cc_start: 0.8711 (m-30) cc_final: 0.8450 (m-30) REVERT: B 24 ASP cc_start: 0.8330 (t0) cc_final: 0.7685 (p0) REVERT: B 144 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7243 (tm-30) REVERT: B 196 GLN cc_start: 0.8701 (pm20) cc_final: 0.8285 (pm20) REVERT: B 234 CYS cc_start: 0.8858 (m) cc_final: 0.8149 (m) REVERT: B 250 GLU cc_start: 0.7945 (mp0) cc_final: 0.6849 (tt0) REVERT: B 282 TYR cc_start: 0.8113 (p90) cc_final: 0.7673 (p90) REVERT: B 288 TRP cc_start: 0.8585 (m100) cc_final: 0.7741 (m-10) REVERT: C 70 MET cc_start: 0.8113 (mmt) cc_final: 0.7637 (mtm) REVERT: C 201 PHE cc_start: 0.8459 (m-80) cc_final: 0.8121 (m-80) REVERT: C 203 PHE cc_start: 0.6710 (t80) cc_final: 0.6332 (t80) REVERT: C 226 TYR cc_start: 0.7748 (m-80) cc_final: 0.7115 (m-80) REVERT: D 157 TYR cc_start: 0.8598 (t80) cc_final: 0.8135 (t80) REVERT: D 162 ASP cc_start: 0.8821 (m-30) cc_final: 0.8029 (t0) REVERT: D 215 LYS cc_start: 0.8253 (tptp) cc_final: 0.7859 (tmtt) REVERT: D 286 MET cc_start: 0.6866 (mmt) cc_final: 0.6429 (mtt) REVERT: D 425 ASP cc_start: 0.7546 (t0) cc_final: 0.7266 (t0) REVERT: E 412 TYR cc_start: 0.6263 (m-80) cc_final: 0.5876 (t80) REVERT: K 5 GLN cc_start: 0.8543 (mm110) cc_final: 0.8199 (mm-40) REVERT: K 46 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7987 (pm20) REVERT: K 98 ARG cc_start: 0.8597 (ptm-80) cc_final: 0.8270 (ptt90) REVERT: L 11 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7807 (ppp) REVERT: L 34 SER cc_start: 0.9232 (m) cc_final: 0.9015 (p) REVERT: L 79 GLN cc_start: 0.8303 (mm110) cc_final: 0.7976 (mp10) outliers start: 64 outliers final: 46 residues processed: 359 average time/residue: 0.1019 time to fit residues: 55.7417 Evaluate side-chains 350 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 302 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 56 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.144954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107878 restraints weight = 23497.999| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.76 r_work: 0.3251 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14950 Z= 0.173 Angle : 0.601 12.496 20347 Z= 0.301 Chirality : 0.044 0.190 2334 Planarity : 0.004 0.062 2480 Dihedral : 8.874 174.738 2385 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.90 % Allowed : 14.62 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.20), residues: 1729 helix: 0.73 (0.24), residues: 455 sheet: -1.26 (0.20), residues: 542 loop : -0.90 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 207 TYR 0.018 0.001 TYR D 284 PHE 0.035 0.002 PHE A 475 TRP 0.016 0.001 TRP A 466 HIS 0.008 0.001 HIS E 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (14925) covalent geometry : angle 0.59367 / 0.30 (20279) SS BOND : bond 0.00143 / 0.07 ( 7) SS BOND : angle 1.22345 / 0.72 ( 14) hydrogen bonds : bond 0.03563 / 2.34 ( 590) hydrogen bonds : angle 4.95076 / 3.41 ( 1887) link_ALPHA1-6 : bond 0.01739 / 0.92 ( 1) link_ALPHA1-6 : angle 2.95936 / 2.08 ( 3) link_BETA1-4 : bond 0.00570 / 0.34 ( 10) link_BETA1-4 : angle 1.81061 / 1.25 ( 30) link_NAG-ASN : bond 0.00608 / 0.31 ( 7) link_NAG-ASN : angle 1.61151 / 1.11 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 317 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8631 (ptm) REVERT: A 153 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8573 (mm-30) REVERT: A 197 LYS cc_start: 0.8278 (mtmt) cc_final: 0.8010 (mppt) REVERT: A 230 ILE cc_start: 0.8770 (pt) cc_final: 0.8227 (mt) REVERT: A 282 ASP cc_start: 0.8703 (m-30) cc_final: 0.8234 (m-30) REVERT: B 17 ARG cc_start: 0.8589 (mtt90) cc_final: 0.8305 (mtt-85) REVERT: B 24 ASP cc_start: 0.8352 (t0) cc_final: 0.7716 (p0) REVERT: B 141 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7782 (mtt) REVERT: B 144 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7214 (tm-30) REVERT: B 196 GLN cc_start: 0.8759 (pm20) cc_final: 0.8362 (pm20) REVERT: B 213 MET cc_start: 0.8339 (mmm) cc_final: 0.7125 (mtp) REVERT: B 234 CYS cc_start: 0.8845 (m) cc_final: 0.8179 (m) REVERT: B 250 GLU cc_start: 0.8060 (mp0) cc_final: 0.6853 (tt0) REVERT: C 70 MET cc_start: 0.7987 (mmt) cc_final: 0.7592 (mtm) REVERT: C 201 PHE cc_start: 0.8418 (m-80) cc_final: 0.8033 (m-80) REVERT: C 203 PHE cc_start: 0.6729 (t80) cc_final: 0.6332 (t80) REVERT: D 147 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8436 (mm-30) REVERT: D 153 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8260 (mm-30) REVERT: D 157 TYR cc_start: 0.8650 (t80) cc_final: 0.8202 (t80) REVERT: D 162 ASP cc_start: 0.8761 (m-30) cc_final: 0.8022 (t0) REVERT: D 215 LYS cc_start: 0.8089 (tptp) cc_final: 0.7855 (tmtt) REVERT: D 286 MET cc_start: 0.6913 (mmt) cc_final: 0.6345 (mtt) REVERT: D 425 ASP cc_start: 0.7679 (t0) cc_final: 0.7357 (t0) REVERT: E 111 MET cc_start: 0.7816 (ttm) cc_final: 0.7573 (ttt) REVERT: E 412 TYR cc_start: 0.6487 (m-80) cc_final: 0.5947 (t80) REVERT: K 5 GLN cc_start: 0.8569 (mm110) cc_final: 0.8251 (mm-40) REVERT: K 43 GLN cc_start: 0.8609 (mt0) cc_final: 0.8160 (mm-40) REVERT: K 46 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7945 (pm20) REVERT: K 98 ARG cc_start: 0.8575 (ptm-80) cc_final: 0.8127 (ptt90) REVERT: L 11 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7844 (ppp) REVERT: L 34 SER cc_start: 0.9213 (m) cc_final: 0.8985 (p) REVERT: L 90 GLN cc_start: 0.9058 (pp30) cc_final: 0.8767 (pp30) outliers start: 77 outliers final: 51 residues processed: 359 average time/residue: 0.1049 time to fit residues: 56.9051 Evaluate side-chains 357 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 303 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 161 optimal weight: 0.2980 chunk 62 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109551 restraints weight = 23551.902| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.63 r_work: 0.3307 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14950 Z= 0.121 Angle : 0.566 12.243 20347 Z= 0.281 Chirality : 0.042 0.177 2334 Planarity : 0.004 0.055 2480 Dihedral : 8.533 162.498 2385 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.75 % Allowed : 17.16 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.20), residues: 1729 helix: 1.13 (0.25), residues: 454 sheet: -1.07 (0.21), residues: 540 loop : -0.78 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 61 TYR 0.022 0.001 TYR C 226 PHE 0.019 0.001 PHE E 244 TRP 0.019 0.001 TRP A 237 HIS 0.005 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14925) covalent geometry : angle 0.56044 / 0.28 (20279) SS BOND : bond 0.00222 / 0.11 ( 7) SS BOND : angle 0.85938 / 0.51 ( 14) hydrogen bonds : bond 0.03169 / 2.08 ( 590) hydrogen bonds : angle 4.70272 / 3.24 ( 1887) link_ALPHA1-6 : bond 0.01661 / 0.87 ( 1) link_ALPHA1-6 : angle 2.63662 / 1.88 ( 3) link_BETA1-4 : bond 0.00574 / 0.34 ( 10) link_BETA1-4 : angle 1.54051 / 1.06 ( 30) link_NAG-ASN : bond 0.00610 / 0.31 ( 7) link_NAG-ASN : angle 1.40350 / 0.96 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8351 (ttmm) REVERT: A 61 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8580 (ptm) REVERT: A 230 ILE cc_start: 0.8754 (pt) cc_final: 0.8205 (mt) REVERT: A 282 ASP cc_start: 0.8550 (m-30) cc_final: 0.8283 (t0) REVERT: B 17 ARG cc_start: 0.8511 (mtt90) cc_final: 0.8274 (mtt-85) REVERT: B 24 ASP cc_start: 0.8186 (t0) cc_final: 0.7731 (p0) REVERT: B 141 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7609 (mtt) REVERT: B 144 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8163 (tp30) REVERT: B 196 GLN cc_start: 0.8688 (pm20) cc_final: 0.8355 (pm20) REVERT: B 228 ILE cc_start: 0.8586 (pt) cc_final: 0.8375 (pt) REVERT: B 234 CYS cc_start: 0.8848 (m) cc_final: 0.8205 (m) REVERT: B 250 GLU cc_start: 0.8025 (mp0) cc_final: 0.6679 (tt0) REVERT: C 70 MET cc_start: 0.8022 (mmt) cc_final: 0.7668 (mtm) REVERT: C 201 PHE cc_start: 0.8380 (m-80) cc_final: 0.8132 (m-80) REVERT: C 203 PHE cc_start: 0.6649 (t80) cc_final: 0.6396 (t80) REVERT: C 226 TYR cc_start: 0.7431 (m-10) cc_final: 0.6946 (m-80) REVERT: D 153 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8232 (mt-10) REVERT: D 162 ASP cc_start: 0.8549 (m-30) cc_final: 0.7964 (t0) REVERT: D 215 LYS cc_start: 0.8090 (tptp) cc_final: 0.7839 (tmtt) REVERT: D 286 MET cc_start: 0.7179 (mmt) cc_final: 0.6572 (mtt) REVERT: D 425 ASP cc_start: 0.7718 (t0) cc_final: 0.7416 (t0) REVERT: E 146 PRO cc_start: 0.8442 (Cg_endo) cc_final: 0.8089 (Cg_exo) REVERT: E 228 GLN cc_start: 0.8376 (tt0) cc_final: 0.7793 (mt0) REVERT: E 245 TRP cc_start: 0.6512 (m-10) cc_final: 0.6310 (m-10) REVERT: E 412 TYR cc_start: 0.6538 (m-80) cc_final: 0.6233 (t80) REVERT: K 5 GLN cc_start: 0.8486 (mm110) cc_final: 0.8220 (mm-40) REVERT: K 38 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7726 (mmmm) REVERT: K 43 GLN cc_start: 0.8622 (mt0) cc_final: 0.8308 (mt0) outliers start: 59 outliers final: 45 residues processed: 359 average time/residue: 0.1100 time to fit residues: 58.6346 Evaluate side-chains 356 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 308 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain K residue 38 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.145694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109508 restraints weight = 23415.696| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.61 r_work: 0.3289 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14950 Z= 0.130 Angle : 0.571 11.051 20347 Z= 0.283 Chirality : 0.042 0.177 2334 Planarity : 0.004 0.054 2480 Dihedral : 8.334 154.892 2385 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.75 % Allowed : 17.93 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1729 helix: 1.27 (0.25), residues: 449 sheet: -1.00 (0.21), residues: 537 loop : -0.72 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.019 0.001 TYR D 284 PHE 0.016 0.001 PHE E 244 TRP 0.021 0.001 TRP A 237 HIS 0.003 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (14925) covalent geometry : angle 0.56575 / 0.28 (20279) SS BOND : bond 0.00487 / 0.26 ( 7) SS BOND : angle 0.83618 / 0.50 ( 14) hydrogen bonds : bond 0.03067 / 2.02 ( 590) hydrogen bonds : angle 4.62264 / 3.18 ( 1887) link_ALPHA1-6 : bond 0.01657 / 0.87 ( 1) link_ALPHA1-6 : angle 2.67539 / 1.94 ( 3) link_BETA1-4 : bond 0.00544 / 0.32 ( 10) link_BETA1-4 : angle 1.48672 / 1.04 ( 30) link_NAG-ASN : bond 0.00426 / 0.22 ( 7) link_NAG-ASN : angle 1.41151 / 0.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 323 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8574 (ptm) REVERT: A 230 ILE cc_start: 0.8770 (pt) cc_final: 0.8206 (mt) REVERT: A 267 HIS cc_start: 0.7245 (OUTLIER) cc_final: 0.6708 (m-70) REVERT: A 282 ASP cc_start: 0.8576 (m-30) cc_final: 0.8002 (m-30) REVERT: B 17 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8255 (mtt-85) REVERT: B 24 ASP cc_start: 0.8186 (t0) cc_final: 0.7703 (p0) REVERT: B 141 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7604 (mtt) REVERT: B 144 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8159 (tp30) REVERT: B 196 GLN cc_start: 0.8670 (pm20) cc_final: 0.8370 (pm20) REVERT: B 228 ILE cc_start: 0.8565 (pt) cc_final: 0.8356 (pt) REVERT: B 234 CYS cc_start: 0.8825 (m) cc_final: 0.8167 (m) REVERT: B 250 GLU cc_start: 0.8068 (mp0) cc_final: 0.6651 (tt0) REVERT: C 70 MET cc_start: 0.8019 (mmt) cc_final: 0.7669 (mtm) REVERT: C 201 PHE cc_start: 0.8414 (m-80) cc_final: 0.8212 (m-80) REVERT: C 203 PHE cc_start: 0.6659 (t80) cc_final: 0.6411 (t80) REVERT: C 226 TYR cc_start: 0.7505 (m-10) cc_final: 0.6940 (m-80) REVERT: D 55 MET cc_start: 0.8012 (mmm) cc_final: 0.7755 (mmm) REVERT: D 153 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8275 (mm-30) REVERT: D 157 TYR cc_start: 0.8486 (t80) cc_final: 0.8079 (t80) REVERT: D 162 ASP cc_start: 0.8532 (m-30) cc_final: 0.7962 (t0) REVERT: D 215 LYS cc_start: 0.8120 (tptp) cc_final: 0.7509 (tmtt) REVERT: D 286 MET cc_start: 0.7299 (mmt) cc_final: 0.6645 (mtt) REVERT: D 298 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7137 (tm-30) REVERT: D 425 ASP cc_start: 0.7695 (t0) cc_final: 0.7213 (t0) REVERT: E 228 GLN cc_start: 0.8397 (tt0) cc_final: 0.7871 (mt0) REVERT: E 241 GLN cc_start: 0.7894 (tt0) cc_final: 0.7675 (tp40) REVERT: E 245 TRP cc_start: 0.6545 (m-10) cc_final: 0.6277 (m-10) REVERT: E 412 TYR cc_start: 0.6770 (m-80) cc_final: 0.6372 (t80) REVERT: K 5 GLN cc_start: 0.8482 (mm110) cc_final: 0.8241 (mm-40) REVERT: K 38 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7805 (mmmm) REVERT: K 43 GLN cc_start: 0.8540 (mt0) cc_final: 0.8280 (mm110) REVERT: K 98 ARG cc_start: 0.8674 (ptm160) cc_final: 0.8317 (ptt90) REVERT: L 24 LYS cc_start: 0.8339 (tttm) cc_final: 0.7912 (mtmt) outliers start: 59 outliers final: 46 residues processed: 354 average time/residue: 0.1061 time to fit residues: 56.0735 Evaluate side-chains 356 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 306 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain K residue 38 LYS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 116 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.143614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.107727 restraints weight = 23537.573| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.54 r_work: 0.3272 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14950 Z= 0.180 Angle : 0.606 10.687 20347 Z= 0.302 Chirality : 0.043 0.172 2334 Planarity : 0.004 0.072 2480 Dihedral : 8.417 150.715 2385 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.39 % Allowed : 17.48 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1729 helix: 1.35 (0.25), residues: 447 sheet: -1.07 (0.21), residues: 544 loop : -0.71 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 61 TYR 0.019 0.002 TYR E 293 PHE 0.015 0.002 PHE A 240 TRP 0.022 0.001 TRP A 237 HIS 0.012 0.001 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (14925) covalent geometry : angle 0.60011 / 0.30 (20279) SS BOND : bond 0.00375 / 0.20 ( 7) SS BOND : angle 1.02569 / 0.61 ( 14) hydrogen bonds : bond 0.03235 / 2.13 ( 590) hydrogen bonds : angle 4.70795 / 3.24 ( 1887) link_ALPHA1-6 : bond 0.01710 / 0.90 ( 1) link_ALPHA1-6 : angle 3.00582 / 2.24 ( 3) link_BETA1-4 : bond 0.00600 / 0.37 ( 10) link_BETA1-4 : angle 1.55427 / 1.12 ( 30) link_NAG-ASN : bond 0.00305 / 0.16 ( 7) link_NAG-ASN : angle 1.52085 / 1.07 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 311 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8702 (ptm) REVERT: A 230 ILE cc_start: 0.8784 (pt) cc_final: 0.8179 (mt) REVERT: A 267 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.6726 (m-70) REVERT: A 282 ASP cc_start: 0.8755 (m-30) cc_final: 0.8282 (m-30) REVERT: B 17 ARG cc_start: 0.8643 (mtt90) cc_final: 0.8411 (mtt-85) REVERT: B 24 ASP cc_start: 0.8338 (t0) cc_final: 0.7752 (p0) REVERT: B 141 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7668 (mtt) REVERT: B 144 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8335 (tp30) REVERT: B 234 CYS cc_start: 0.8950 (m) cc_final: 0.8345 (m) REVERT: B 250 GLU cc_start: 0.8240 (mp0) cc_final: 0.6783 (tt0) REVERT: C 70 MET cc_start: 0.8173 (mmt) cc_final: 0.7673 (mtm) REVERT: C 201 PHE cc_start: 0.8610 (m-80) cc_final: 0.8274 (m-80) REVERT: C 203 PHE cc_start: 0.6871 (t80) cc_final: 0.6573 (t80) REVERT: C 226 TYR cc_start: 0.7715 (m-10) cc_final: 0.7066 (m-80) REVERT: D 157 TYR cc_start: 0.8660 (t80) cc_final: 0.8277 (t80) REVERT: D 162 ASP cc_start: 0.8741 (m-30) cc_final: 0.8078 (t0) REVERT: D 207 ARG cc_start: 0.8473 (ttm170) cc_final: 0.8240 (ttm-80) REVERT: D 215 LYS cc_start: 0.8151 (tptp) cc_final: 0.7834 (tmtt) REVERT: D 286 MET cc_start: 0.7410 (mmt) cc_final: 0.6732 (mtt) REVERT: D 298 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7344 (tm-30) REVERT: D 425 ASP cc_start: 0.7653 (t0) cc_final: 0.7311 (t0) REVERT: E 228 GLN cc_start: 0.8394 (tt0) cc_final: 0.7868 (mt0) REVERT: E 234 ILE cc_start: 0.7400 (tt) cc_final: 0.6979 (mt) REVERT: E 241 GLN cc_start: 0.7895 (tt0) cc_final: 0.7659 (tp40) REVERT: E 412 TYR cc_start: 0.6860 (m-80) cc_final: 0.6304 (t80) REVERT: K 5 GLN cc_start: 0.8595 (mm110) cc_final: 0.8333 (mm-40) REVERT: K 43 GLN cc_start: 0.8549 (mt0) cc_final: 0.8237 (mm110) REVERT: K 72 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7920 (p) REVERT: K 80 TYR cc_start: 0.7504 (m-80) cc_final: 0.7258 (m-10) REVERT: L 24 LYS cc_start: 0.8483 (tttm) cc_final: 0.7953 (mtmt) REVERT: L 38 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7145 (tt0) outliers start: 69 outliers final: 60 residues processed: 346 average time/residue: 0.0968 time to fit residues: 50.6173 Evaluate side-chains 367 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 302 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 31 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102987 restraints weight = 23695.388| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.64 r_work: 0.3209 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 14950 Z= 0.308 Angle : 0.706 11.096 20347 Z= 0.354 Chirality : 0.047 0.173 2334 Planarity : 0.005 0.064 2480 Dihedral : 8.998 158.330 2385 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.77 % Allowed : 17.99 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.20), residues: 1729 helix: 1.02 (0.24), residues: 453 sheet: -1.28 (0.21), residues: 533 loop : -0.88 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 207 TYR 0.023 0.002 TYR E 293 PHE 0.019 0.002 PHE A 105 TRP 0.024 0.002 TRP D 237 HIS 0.008 0.002 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.31 (14925) covalent geometry : angle 0.69885 / 0.35 (20279) SS BOND : bond 0.00346 / 0.18 ( 7) SS BOND : angle 1.42015 / 0.85 ( 14) hydrogen bonds : bond 0.03717 / 2.45 ( 590) hydrogen bonds : angle 5.01439 / 3.45 ( 1887) link_ALPHA1-6 : bond 0.02080 / 1.09 ( 1) link_ALPHA1-6 : angle 3.55501 / 2.69 ( 3) link_BETA1-4 : bond 0.00693 / 0.43 ( 10) link_BETA1-4 : angle 1.79649 / 1.34 ( 30) link_NAG-ASN : bond 0.00449 / 0.24 ( 7) link_NAG-ASN : angle 1.77316 / 1.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 305 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8657 (tptt) REVERT: A 61 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8770 (ptm) REVERT: A 230 ILE cc_start: 0.8813 (pt) cc_final: 0.8286 (mt) REVERT: B 17 ARG cc_start: 0.8710 (mtt90) cc_final: 0.8441 (mtt-85) REVERT: B 141 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7699 (mtt) REVERT: B 144 GLU cc_start: 0.8622 (tm-30) cc_final: 0.7525 (tm-30) REVERT: B 234 CYS cc_start: 0.8990 (m) cc_final: 0.8367 (m) REVERT: C 70 MET cc_start: 0.8205 (mmt) cc_final: 0.7769 (mmt) REVERT: C 201 PHE cc_start: 0.8689 (m-80) cc_final: 0.8357 (m-80) REVERT: C 203 PHE cc_start: 0.7084 (t80) cc_final: 0.6735 (t80) REVERT: C 226 TYR cc_start: 0.7843 (m-10) cc_final: 0.7198 (m-80) REVERT: D 20 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8783 (mm) REVERT: D 157 TYR cc_start: 0.8745 (t80) cc_final: 0.8383 (t80) REVERT: D 162 ASP cc_start: 0.8782 (m-30) cc_final: 0.8128 (t0) REVERT: D 215 LYS cc_start: 0.8184 (tptp) cc_final: 0.7849 (tmtt) REVERT: D 286 MET cc_start: 0.7554 (mmt) cc_final: 0.6865 (mtt) REVERT: D 298 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7093 (tm-30) REVERT: D 425 ASP cc_start: 0.7658 (t0) cc_final: 0.7196 (t0) REVERT: E 111 MET cc_start: 0.7477 (ttm) cc_final: 0.7276 (ttm) REVERT: E 228 GLN cc_start: 0.8398 (tt0) cc_final: 0.7811 (mt0) REVERT: E 234 ILE cc_start: 0.7513 (tt) cc_final: 0.7132 (mt) REVERT: E 241 GLN cc_start: 0.7978 (tt0) cc_final: 0.7754 (tp40) REVERT: E 412 TYR cc_start: 0.6894 (m-80) cc_final: 0.6198 (t80) REVERT: K 5 GLN cc_start: 0.8578 (mm110) cc_final: 0.8329 (mm-40) REVERT: K 43 GLN cc_start: 0.8593 (mt0) cc_final: 0.8291 (mm110) REVERT: K 72 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7998 (p) REVERT: K 105 MET cc_start: 0.8539 (mtm) cc_final: 0.8265 (mtt) REVERT: L 24 LYS cc_start: 0.8559 (tttm) cc_final: 0.8093 (mtmt) REVERT: L 38 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: L 41 GLU cc_start: 0.8792 (tp30) cc_final: 0.8579 (tm-30) REVERT: L 60 ASP cc_start: 0.8329 (p0) cc_final: 0.8117 (p0) outliers start: 75 outliers final: 57 residues processed: 347 average time/residue: 0.1012 time to fit residues: 52.7355 Evaluate side-chains 361 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 299 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.143678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107781 restraints weight = 23557.305| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.54 r_work: 0.3272 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14950 Z= 0.131 Angle : 0.611 10.473 20347 Z= 0.302 Chirality : 0.043 0.190 2334 Planarity : 0.004 0.066 2480 Dihedral : 8.608 149.983 2385 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.43 % Allowed : 20.41 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1729 helix: 1.25 (0.25), residues: 454 sheet: -1.12 (0.21), residues: 539 loop : -0.73 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 468 TYR 0.027 0.001 TYR E 293 PHE 0.020 0.001 PHE B 304 TRP 0.027 0.001 TRP A 237 HIS 0.009 0.001 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14925) covalent geometry : angle 0.60616 / 0.30 (20279) SS BOND : bond 0.00065 / 0.03 ( 7) SS BOND : angle 0.83861 / 0.50 ( 14) hydrogen bonds : bond 0.03152 / 2.08 ( 590) hydrogen bonds : angle 4.73085 / 3.26 ( 1887) link_ALPHA1-6 : bond 0.01874 / 0.99 ( 1) link_ALPHA1-6 : angle 2.73631 / 1.97 ( 3) link_BETA1-4 : bond 0.00558 / 0.34 ( 10) link_BETA1-4 : angle 1.48713 / 1.05 ( 30) link_NAG-ASN : bond 0.00313 / 0.16 ( 7) link_NAG-ASN : angle 1.49090 / 1.02 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8690 (ptm) REVERT: A 230 ILE cc_start: 0.8770 (pt) cc_final: 0.8249 (mt) REVERT: A 267 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6795 (m-70) REVERT: A 269 ARG cc_start: 0.8432 (mtp-110) cc_final: 0.8209 (ttm-80) REVERT: A 468 ARG cc_start: 0.7322 (ttp-170) cc_final: 0.7000 (ttp-170) REVERT: B 17 ARG cc_start: 0.8628 (mtt90) cc_final: 0.8379 (mtt-85) REVERT: B 141 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7597 (mtt) REVERT: B 144 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8276 (tp30) REVERT: B 234 CYS cc_start: 0.8943 (m) cc_final: 0.8358 (m) REVERT: C 70 MET cc_start: 0.8288 (mmt) cc_final: 0.7812 (mmt) REVERT: C 201 PHE cc_start: 0.8614 (m-80) cc_final: 0.8308 (m-80) REVERT: C 203 PHE cc_start: 0.6997 (t80) cc_final: 0.6685 (t80) REVERT: C 226 TYR cc_start: 0.7700 (m-10) cc_final: 0.7035 (m-80) REVERT: D 162 ASP cc_start: 0.8741 (m-30) cc_final: 0.8082 (t0) REVERT: D 207 ARG cc_start: 0.8450 (ttm170) cc_final: 0.8096 (ttm-80) REVERT: D 215 LYS cc_start: 0.8124 (tptp) cc_final: 0.7712 (tmtt) REVERT: D 286 MET cc_start: 0.7492 (mmt) cc_final: 0.6860 (mtt) REVERT: E 228 GLN cc_start: 0.8337 (tt0) cc_final: 0.7787 (mt0) REVERT: E 412 TYR cc_start: 0.6854 (m-80) cc_final: 0.6179 (t80) REVERT: K 5 GLN cc_start: 0.8535 (mm110) cc_final: 0.8289 (mm-40) REVERT: K 43 GLN cc_start: 0.8622 (mt0) cc_final: 0.8310 (mm110) REVERT: L 4 MET cc_start: 0.8555 (mmm) cc_final: 0.8254 (mmm) REVERT: L 24 LYS cc_start: 0.8512 (tttm) cc_final: 0.7954 (mtmt) REVERT: L 38 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7391 (tt0) outliers start: 54 outliers final: 46 residues processed: 334 average time/residue: 0.0978 time to fit residues: 49.3469 Evaluate side-chains 340 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 79 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 130 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 0.0010 chunk 167 optimal weight: 10.0000 chunk 19 optimal weight: 0.0070 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.145672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109616 restraints weight = 23489.296| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.61 r_work: 0.3299 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14950 Z= 0.114 Angle : 0.594 10.305 20347 Z= 0.291 Chirality : 0.042 0.179 2334 Planarity : 0.004 0.058 2480 Dihedral : 8.161 138.638 2385 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.31 % Allowed : 20.60 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1729 helix: 1.45 (0.25), residues: 450 sheet: -0.99 (0.21), residues: 529 loop : -0.64 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.031 0.001 TYR L 49 PHE 0.027 0.001 PHE E 309 TRP 0.029 0.001 TRP A 237 HIS 0.006 0.001 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (14925) covalent geometry : angle 0.58953 / 0.29 (20279) SS BOND : bond 0.00051 / 0.03 ( 7) SS BOND : angle 0.75573 / 0.46 ( 14) hydrogen bonds : bond 0.02879 / 1.90 ( 590) hydrogen bonds : angle 4.54363 / 3.13 ( 1887) link_ALPHA1-6 : bond 0.01720 / 0.91 ( 1) link_ALPHA1-6 : angle 2.62626 / 1.94 ( 3) link_BETA1-4 : bond 0.00553 / 0.32 ( 10) link_BETA1-4 : angle 1.41035 / 0.98 ( 30) link_NAG-ASN : bond 0.00288 / 0.15 ( 7) link_NAG-ASN : angle 1.29661 / 0.88 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8708 (ptm) REVERT: A 230 ILE cc_start: 0.8748 (pt) cc_final: 0.8210 (mt) REVERT: A 267 HIS cc_start: 0.7136 (OUTLIER) cc_final: 0.6525 (m-70) REVERT: A 269 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.8120 (ttm-80) REVERT: A 282 ASP cc_start: 0.8683 (m-30) cc_final: 0.8202 (t0) REVERT: B 90 MET cc_start: 0.8755 (tpt) cc_final: 0.8425 (tpt) REVERT: B 141 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7618 (mtt) REVERT: B 144 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8325 (tp30) REVERT: B 234 CYS cc_start: 0.8883 (m) cc_final: 0.8308 (m) REVERT: C 65 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8840 (m) REVERT: C 66 ASN cc_start: 0.8380 (t0) cc_final: 0.8128 (t0) REVERT: C 70 MET cc_start: 0.8327 (mmt) cc_final: 0.7742 (mmt) REVERT: C 201 PHE cc_start: 0.8567 (m-80) cc_final: 0.8260 (m-80) REVERT: C 203 PHE cc_start: 0.7014 (t80) cc_final: 0.6735 (t80) REVERT: D 61 MET cc_start: 0.8856 (ptt) cc_final: 0.8606 (ptt) REVERT: D 155 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: D 162 ASP cc_start: 0.8732 (m-30) cc_final: 0.7994 (t0) REVERT: D 215 LYS cc_start: 0.8118 (tptp) cc_final: 0.7640 (tmtt) REVERT: D 285 LEU cc_start: 0.8796 (mt) cc_final: 0.8499 (mp) REVERT: D 286 MET cc_start: 0.7572 (mmt) cc_final: 0.6915 (mtt) REVERT: E 228 GLN cc_start: 0.8258 (tt0) cc_final: 0.7704 (mt0) REVERT: E 234 ILE cc_start: 0.7254 (tt) cc_final: 0.6919 (mt) REVERT: E 412 TYR cc_start: 0.6840 (m-80) cc_final: 0.6217 (t80) REVERT: K 5 GLN cc_start: 0.8539 (mm110) cc_final: 0.8282 (mm-40) REVERT: K 43 GLN cc_start: 0.8592 (mt0) cc_final: 0.8252 (mm110) REVERT: K 80 TYR cc_start: 0.7943 (m-10) cc_final: 0.7325 (m-10) REVERT: L 4 MET cc_start: 0.8449 (mmm) cc_final: 0.8071 (mmm) REVERT: L 24 LYS cc_start: 0.8459 (tttm) cc_final: 0.7884 (mtmt) REVERT: L 38 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7279 (tt0) outliers start: 52 outliers final: 39 residues processed: 330 average time/residue: 0.1022 time to fit residues: 51.1334 Evaluate side-chains 327 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 282 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 8 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.1980 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104246 restraints weight = 23665.521| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.70 r_work: 0.3227 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14950 Z= 0.244 Angle : 0.675 10.938 20347 Z= 0.334 Chirality : 0.045 0.174 2334 Planarity : 0.004 0.059 2480 Dihedral : 8.574 143.702 2385 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.31 % Allowed : 20.66 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1729 helix: 1.25 (0.25), residues: 448 sheet: -1.12 (0.21), residues: 532 loop : -0.70 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 61 TYR 0.036 0.002 TYR L 49 PHE 0.016 0.002 PHE B 407 TRP 0.034 0.002 TRP A 237 HIS 0.006 0.001 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 (14925) covalent geometry : angle 0.66902 / 0.33 (20279) SS BOND : bond 0.00235 / 0.11 ( 7) SS BOND : angle 1.28374 / 0.77 ( 14) hydrogen bonds : bond 0.03405 / 2.24 ( 590) hydrogen bonds : angle 4.81463 / 3.32 ( 1887) link_ALPHA1-6 : bond 0.01968 / 1.04 ( 1) link_ALPHA1-6 : angle 3.26021 / 2.51 ( 3) link_BETA1-4 : bond 0.00642 / 0.39 ( 10) link_BETA1-4 : angle 1.62624 / 1.19 ( 30) link_NAG-ASN : bond 0.00361 / 0.19 ( 7) link_NAG-ASN : angle 1.62906 / 1.15 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3421.17 seconds wall clock time: 59 minutes 40.73 seconds (3580.73 seconds total)