Starting phenix.real_space_refine on Fri Jul 3 13:56:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctp_45914/07_2026/9ctp_45914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctp_45914/07_2026/9ctp_45914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctp_45914/07_2026/9ctp_45914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctp_45914/07_2026/9ctp_45914.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctp_45914/07_2026/9ctp_45914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctp_45914/07_2026/9ctp_45914.cif" } resolution = 3.62 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= 0.003 sd= 0.028 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 8 5.49 5 S 79 5.16 5 C 9451 2.51 5 N 2342 2.21 5 O 2707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 14587 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2692 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 313} Chain breaks: 1 Chain: "B" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2720 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2711 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2625 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1734 Classifications: {'peptide': 209} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 199} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "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: "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: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'NAG': 1, 'PIO': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.06, per 1000 atoms: 0.21 Number of scatterers: 14587 At special positions: 0 Unit cell: (123.42, 114.07, 134.64, 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 79 16.00 P 8 15.00 O 2707 8.00 N 2342 7.00 C 9451 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=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 163 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " 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 Q 3 " - " MAN Q 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " NAG-ASN " NAG C 501 " - " ASN C 80 " " NAG D 503 " - " ASN D 135 " " NAG E 501 " - " ASN E 208 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN A 80 " " NAG H 1 " - " ASN C 149 " " NAG Q 1 " - " ASN B 111 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 618.6 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: 3324 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 24 sheets defined 30.2% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 removed outlier: 3.682A pdb=" N LEU A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 20 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.886A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.720A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 247 through 269 removed outlier: 4.123A pdb=" N LEU A 268 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 279 through 307 Processing helix chain 'A' and resid 462 through 486 removed outlier: 4.084A pdb=" N ILE A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) Proline residue: A 472 - end of helix Processing helix chain 'B' and resid 11 through 23 removed outlier: 4.379A pdb=" N PHE B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 19 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 removed outlier: 3.529A pdb=" N SER B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 230 through 243 removed outlier: 3.561A pdb=" N VAL B 238 " --> pdb=" O CYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 247 removed outlier: 3.560A pdb=" N LEU B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 244 through 247' Processing helix chain 'B' and resid 251 through 274 removed outlier: 3.724A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 310 removed outlier: 4.054A pdb=" N VAL B 292 " --> pdb=" O TRP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 415 removed outlier: 3.968A pdb=" N ILE B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Proline residue: B 401 - end of helix Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.593A pdb=" N VAL C 87 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 88 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 246 through 270 removed outlier: 3.742A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 308 Processing helix chain 'C' and resid 460 through 487 removed outlier: 4.139A pdb=" N ILE C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE C 471 " --> pdb=" O SER C 467 " (cutoff:3.500A) Proline residue: C 472 - end of helix Processing helix chain 'D' and resid 37 through 48 removed outlier: 3.516A pdb=" N LEU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 100 removed outlier: 3.527A pdb=" N LYS D 100 " --> pdb=" O GLU D 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 100' Processing helix chain 'D' and resid 111 through 115 removed outlier: 3.737A pdb=" N LEU D 114 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.732A pdb=" N ILE D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.543A pdb=" N CYS D 258 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL D 262 " --> pdb=" O CYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.982A pdb=" N PHE D 269 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 271 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 299 removed outlier: 3.633A pdb=" N ARG D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR D 286 " --> pdb=" O PHE D 282 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 334 removed outlier: 3.608A pdb=" N ALA D 324 " --> pdb=" O PHE D 320 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 325 " --> pdb=" O VAL D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 432 removed outlier: 3.571A pdb=" N SER D 431 " --> pdb=" O VAL D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 450 removed outlier: 3.656A pdb=" N VAL D 437 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU D 444 " --> pdb=" O ALA D 440 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR D 450 " --> pdb=" O TYR D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.523A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.371A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 67 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.131A pdb=" N ASP A 101 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA A 135 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 103 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 105 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 67 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.771A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.771A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.449A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 44 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 117 through 121 removed outlier: 7.449A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 44 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N VAL B 180 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 45 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.485A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.485A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.315A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 127 " --> pdb=" O MET C 115 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.967A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP C 56 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL C 50 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR C 58 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.886A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 205 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS C 197 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG C 207 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR C 195 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER C 209 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU C 193 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER C 211 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR C 191 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS C 213 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 71 through 78 removed outlier: 7.754A pdb=" N THR D 72 " --> pdb=" O PHE D 89 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N PHE D 89 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE D 74 " --> pdb=" O ASP D 87 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP D 87 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP D 94 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 110 removed outlier: 4.016A pdb=" N LEU D 143 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR D 150 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP D 94 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS D 95 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU D 64 " --> pdb=" O HIS D 95 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR D 63 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER D 194 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL D 65 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=AB6, first strand: chain 'D' and resid 124 through 125 removed outlier: 3.648A pdb=" N GLY D 232 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 219 " --> pdb=" O HIS D 242 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS D 244 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU D 217 " --> pdb=" O LYS D 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.645A pdb=" N ILE E 133 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS E 118 " --> pdb=" O ASP E 148 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU E 150 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N SER E 116 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.645A pdb=" N ILE E 133 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR E 58 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N THR E 51 " --> pdb=" O TYR E 181 " (cutoff:3.500A) removed outlier: 10.800A pdb=" N TRP E 183 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N ILE E 53 " --> pdb=" O TRP E 183 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N ARG E 185 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 10.846A pdb=" N THR E 55 " --> pdb=" O ARG E 185 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER E 187 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.805A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.690A pdb=" N GLU I 104 " --> pdb=" O MET I 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AC3, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AC4, first strand: chain 'I' and resid 45 through 48 removed outlier: 6.639A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.707A pdb=" N VAL J 18 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.672A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.43 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: 2445 1.32 - 1.45: 4199 1.45 - 1.57: 8151 1.57 - 1.70: 12 1.70 - 1.82: 138 Bond restraints: 14945 Sorted by residual: bond pdb=" N PRO B 278 " pdb=" CD PRO B 278 " ideal model delta sigma weight residual 1.473 1.555 -0.082 1.40e-02 5.10e+03 3.43e+01 bond pdb=" O4 PIO D 501 " pdb=" P4 PIO D 501 " ideal model delta sigma weight residual 1.710 1.626 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" O4 PIO B 601 " pdb=" P4 PIO B 601 " ideal model delta sigma weight residual 1.710 1.626 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O5 PIO B 601 " pdb=" P5 PIO B 601 " ideal model delta sigma weight residual 1.699 1.625 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O5 PIO D 501 " pdb=" P5 PIO D 501 " ideal model delta sigma weight residual 1.699 1.626 0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 14940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 19290 2.36 - 4.72: 893 4.72 - 7.08: 94 7.08 - 9.44: 24 9.44 - 11.80: 5 Bond angle restraints: 20306 Sorted by residual: angle pdb=" N ALA B 413 " pdb=" CA ALA B 413 " pdb=" C ALA B 413 " ideal model delta sigma weight residual 114.04 104.71 9.33 1.24e+00 6.50e-01 5.66e+01 angle pdb=" N ALA A 300 " pdb=" CA ALA A 300 " pdb=" C ALA A 300 " ideal model delta sigma weight residual 111.07 103.67 7.40 1.07e+00 8.73e-01 4.78e+01 angle pdb=" N ILE D 259 " pdb=" CA ILE D 259 " pdb=" C ILE D 259 " ideal model delta sigma weight residual 110.74 104.52 6.22 9.10e-01 1.21e+00 4.67e+01 angle pdb=" N ARG B 249 " pdb=" CA ARG B 249 " pdb=" C ARG B 249 " ideal model delta sigma weight residual 113.30 105.42 7.88 1.34e+00 5.57e-01 3.46e+01 angle pdb=" C SER D 268 " pdb=" CA SER D 268 " pdb=" CB SER D 268 " ideal model delta sigma weight residual 110.31 98.51 11.80 2.09e+00 2.29e-01 3.19e+01 ... (remaining 20301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 8799 34.62 - 69.23: 157 69.23 - 103.85: 31 103.85 - 138.47: 6 138.47 - 173.08: 2 Dihedral angle restraints: 8995 sinusoidal: 3830 harmonic: 5165 Sorted by residual: dihedral pdb=" CA MET D 136 " pdb=" C MET D 136 " pdb=" N THR D 137 " pdb=" CA THR D 137 " ideal model delta harmonic sigma weight residual -180.00 -45.09 -134.91 0 5.00e+00 4.00e-02 7.28e+02 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 -0.47 173.08 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 POV B 602 " pdb="C210 POV B 602 " pdb="C211 POV B 602 " pdb="C212 POV B 602 " ideal model delta sinusoidal sigma weight residual 112.25 -97.79 -149.96 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 2219 0.147 - 0.293: 112 0.293 - 0.440: 1 0.440 - 0.586: 2 0.586 - 0.733: 2 Chirality restraints: 2336 Sorted by residual: chirality pdb=" C1 MAN Q 4 " pdb=" O6 BMA Q 3 " pdb=" C2 MAN Q 4 " pdb=" O5 MAN Q 4 " both_signs ideal model delta sigma weight residual False 2.40 1.76 0.64 2.00e-02 2.50e+03 1.01e+03 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 -1.90 -0.50 2.00e-02 2.50e+03 6.23e+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 -2.22 -0.18 2.00e-02 2.50e+03 7.83e+01 ... (remaining 2333 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " 0.338 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG E 501 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " 0.125 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " 0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 2 " -0.330 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG Q 2 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG Q 2 " -0.115 2.00e-02 2.50e+03 pdb=" N2 NAG Q 2 " 0.512 2.00e-02 2.50e+03 pdb=" O7 NAG Q 2 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 503 " 0.248 2.00e-02 2.50e+03 2.08e-01 5.43e+02 pdb=" C7 NAG D 503 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG D 503 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG D 503 " -0.353 2.00e-02 2.50e+03 pdb=" O7 NAG D 503 " 0.002 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 78 2.50 - 3.10: 10037 3.10 - 3.70: 22005 3.70 - 4.30: 32697 4.30 - 4.90: 54265 Nonbonded interactions: 119082 Sorted by model distance: nonbonded pdb=" OD1 ASP C 95 " pdb=" OG1 THR D 138 " model vdw 1.904 3.040 nonbonded pdb=" OG1 THR D 187 " pdb=" O GLU D 233 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP E 56 " pdb=" O SER E 187 " model vdw 2.219 3.040 nonbonded pdb=" O ALA C 252 " pdb=" OG1 THR C 256 " model vdw 2.255 3.040 nonbonded pdb=" O VAL D 276 " pdb=" OG1 THR D 280 " model vdw 2.272 3.040 ... (remaining 119077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 7 through 307 or resid 461 through 487)) } ncs_group { reference = chain 'F' selection = chain 'H' } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.000 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.007 0.084 14967 Z= 0.454 Angle : 1.119 15.500 20365 Z= 0.688 Chirality : 0.071 0.733 2336 Planarity : 0.018 0.292 2479 Dihedral : 15.415 173.084 5650 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.21 % Allowed : 2.03 % Favored : 96.76 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.77 (0.18), residues: 1729 helix: -2.07 (0.20), residues: 443 sheet: -1.28 (0.22), residues: 521 loop : -1.95 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 18 TYR 0.034 0.002 TYR A 74 PHE 0.029 0.002 PHE D 269 TRP 0.019 0.002 TRP A 92 HIS 0.020 0.002 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.45 (14945) covalent geometry : angle 1.09678 / 0.68 (20306) SS BOND : bond 0.00146 / 0.08 ( 7) SS BOND : angle 0.58652 / 0.36 ( 14) hydrogen bonds : bond 0.21986 / 14.72 ( 586) hydrogen bonds : angle 9.27319 / 6.33 ( 1842) link_ALPHA1-6 : bond 0.01576 / 0.83 ( 1) link_ALPHA1-6 : angle 6.77531 / 3.79 ( 3) link_BETA1-4 : bond 0.00622 / 0.36 ( 7) link_BETA1-4 : angle 3.90745 / 2.49 ( 21) link_NAG-ASN : bond 0.01544 / 0.95 ( 7) link_NAG-ASN : angle 5.48903 / 3.64 ( 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 614 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 595 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8364 (mmt) cc_final: 0.8008 (mmt) REVERT: A 89 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7326 (t0) REVERT: A 100 ASN cc_start: 0.7842 (p0) cc_final: 0.7552 (p0) REVERT: A 232 ILE cc_start: 0.8966 (mt) cc_final: 0.8675 (pt) REVERT: A 294 MET cc_start: 0.8133 (mmm) cc_final: 0.7899 (tpt) REVERT: A 297 LEU cc_start: 0.9053 (mp) cc_final: 0.8745 (mp) REVERT: A 465 ARG cc_start: 0.7872 (tmt170) cc_final: 0.7552 (ptt90) REVERT: A 466 TRP cc_start: 0.7104 (m100) cc_final: 0.6880 (m100) REVERT: B 229 GLN cc_start: 0.8289 (tp40) cc_final: 0.7951 (tp40) REVERT: B 265 THR cc_start: 0.8661 (m) cc_final: 0.8441 (p) REVERT: B 268 THR cc_start: 0.9141 (t) cc_final: 0.8899 (p) REVERT: B 392 ILE cc_start: 0.8430 (mt) cc_final: 0.7748 (mt) REVERT: B 415 TYR cc_start: 0.8591 (m-80) cc_final: 0.7837 (m-80) REVERT: C 194 ILE cc_start: 0.9133 (mp) cc_final: 0.8931 (mt) REVERT: C 286 MET cc_start: 0.8681 (mtp) cc_final: 0.8466 (mtm) REVERT: D 70 TYR cc_start: 0.8514 (t80) cc_final: 0.8297 (t80) REVERT: D 116 SER cc_start: 0.8686 (m) cc_final: 0.8458 (p) REVERT: D 253 GLN cc_start: 0.8155 (mm110) cc_final: 0.7829 (mm-40) REVERT: D 328 PHE cc_start: 0.8980 (t80) cc_final: 0.8657 (t80) REVERT: E 66 ASN cc_start: 0.7751 (t0) cc_final: 0.7191 (t0) REVERT: E 210 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8498 (p) REVERT: J 39 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7847 (tp40) outliers start: 19 outliers final: 4 residues processed: 606 average time/residue: 0.1082 time to fit residues: 95.0131 Evaluate side-chains 337 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 331 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS A 303 ASN B 56 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097623 restraints weight = 30463.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100617 restraints weight = 14881.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.102500 restraints weight = 9419.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.103667 restraints weight = 7087.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.104352 restraints weight = 5967.455| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14967 Z= 0.227 Angle : 0.770 11.175 20365 Z= 0.390 Chirality : 0.049 0.277 2336 Planarity : 0.006 0.057 2479 Dihedral : 12.096 147.941 2375 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 3.81 % Allowed : 13.86 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.81 (0.19), residues: 1729 helix: -0.47 (0.23), residues: 448 sheet: -1.13 (0.21), residues: 531 loop : -1.58 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 228 TYR 0.025 0.002 TYR E 72 PHE 0.027 0.002 PHE C 293 TRP 0.028 0.002 TRP I 35 HIS 0.011 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (14945) covalent geometry : angle 0.75727 / 0.39 (20306) SS BOND : bond 0.00372 / 0.28 ( 7) SS BOND : angle 1.92453 / 1.26 ( 14) hydrogen bonds : bond 0.04896 / 3.25 ( 586) hydrogen bonds : angle 5.96205 / 4.10 ( 1842) link_ALPHA1-6 : bond 0.02508 / 1.32 ( 1) link_ALPHA1-6 : angle 2.71980 / 1.41 ( 3) link_BETA1-4 : bond 0.00452 / 0.28 ( 7) link_BETA1-4 : angle 2.84166 / 1.97 ( 21) link_NAG-ASN : bond 0.00670 / 0.38 ( 7) link_NAG-ASN : angle 2.90629 / 2.01 ( 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 405 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 345 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8582 (mmt) cc_final: 0.7204 (mtp) REVERT: A 100 ASN cc_start: 0.7926 (p0) cc_final: 0.7543 (p0) REVERT: A 153 GLU cc_start: 0.8341 (mp0) cc_final: 0.8002 (mp0) REVERT: A 155 GLU cc_start: 0.8123 (tt0) cc_final: 0.7691 (tt0) REVERT: A 223 LEU cc_start: 0.9095 (tt) cc_final: 0.8880 (tp) REVERT: A 232 ILE cc_start: 0.8871 (mt) cc_final: 0.8557 (pt) REVERT: A 294 MET cc_start: 0.8319 (mmm) cc_final: 0.8107 (tpt) REVERT: A 465 ARG cc_start: 0.8014 (tmt170) cc_final: 0.7534 (ptt90) REVERT: B 63 ASP cc_start: 0.8073 (t0) cc_final: 0.7782 (t0) REVERT: B 229 GLN cc_start: 0.8417 (tp40) cc_final: 0.7778 (tp40) REVERT: C 470 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7404 (t80) REVERT: D 83 GLU cc_start: 0.8416 (pt0) cc_final: 0.8209 (pt0) REVERT: D 96 ASP cc_start: 0.8177 (t0) cc_final: 0.7934 (t0) REVERT: D 116 SER cc_start: 0.8857 (m) cc_final: 0.8566 (p) REVERT: D 253 GLN cc_start: 0.8501 (mm110) cc_final: 0.8288 (mm110) REVERT: D 258 CYS cc_start: 0.8523 (t) cc_final: 0.7813 (t) REVERT: E 66 ASN cc_start: 0.8150 (t0) cc_final: 0.7705 (t0) REVERT: E 105 LYS cc_start: 0.9279 (mmmt) cc_final: 0.9036 (mmtp) REVERT: I 4 MET cc_start: 0.7873 (mmt) cc_final: 0.7662 (mmp) REVERT: J 39 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7925 (tp40) REVERT: J 41 PRO cc_start: 0.8926 (Cg_exo) cc_final: 0.8688 (Cg_endo) outliers start: 60 outliers final: 45 residues processed: 379 average time/residue: 0.0855 time to fit residues: 51.3519 Evaluate side-chains 354 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 312 TRP Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 64 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS B 56 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.125517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099173 restraints weight = 31041.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102196 restraints weight = 14858.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.104084 restraints weight = 9341.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105203 restraints weight = 7031.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105857 restraints weight = 5960.290| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14967 Z= 0.157 Angle : 0.667 10.137 20365 Z= 0.332 Chirality : 0.046 0.222 2336 Planarity : 0.004 0.045 2479 Dihedral : 10.483 148.876 2370 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 4.51 % Allowed : 14.69 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.36 (0.20), residues: 1729 helix: 0.16 (0.24), residues: 450 sheet: -1.02 (0.21), residues: 542 loop : -1.36 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 142 TYR 0.018 0.002 TYR E 72 PHE 0.027 0.002 PHE D 442 TRP 0.012 0.001 TRP E 82 HIS 0.013 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (14945) covalent geometry : angle 0.65531 / 0.33 (20306) SS BOND : bond 0.00316 / 0.25 ( 7) SS BOND : angle 1.66897 / 1.09 ( 14) hydrogen bonds : bond 0.04008 / 2.72 ( 586) hydrogen bonds : angle 5.25573 / 3.60 ( 1842) link_ALPHA1-6 : bond 0.02812 / 1.48 ( 1) link_ALPHA1-6 : angle 2.80739 / 1.45 ( 3) link_BETA1-4 : bond 0.00717 / 0.44 ( 7) link_BETA1-4 : angle 2.82628 / 1.94 ( 21) link_NAG-ASN : bond 0.00418 / 0.25 ( 7) link_NAG-ASN : angle 2.36892 / 1.63 ( 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 409 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 338 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8473 (mmt) cc_final: 0.7149 (mtp) REVERT: A 75 ASN cc_start: 0.8938 (p0) cc_final: 0.8614 (p0) REVERT: A 100 ASN cc_start: 0.7830 (p0) cc_final: 0.7504 (p0) REVERT: A 153 GLU cc_start: 0.8408 (mp0) cc_final: 0.7936 (mp0) REVERT: A 155 GLU cc_start: 0.8015 (tt0) cc_final: 0.7656 (tt0) REVERT: A 222 ILE cc_start: 0.8617 (tt) cc_final: 0.8367 (pt) REVERT: A 294 MET cc_start: 0.8235 (mmm) cc_final: 0.8006 (tpt) REVERT: A 465 ARG cc_start: 0.7878 (tmt170) cc_final: 0.7402 (ptt90) REVERT: B 63 ASP cc_start: 0.8061 (t0) cc_final: 0.7798 (t0) REVERT: B 229 GLN cc_start: 0.8558 (tp40) cc_final: 0.7868 (tp40) REVERT: B 241 SER cc_start: 0.8901 (t) cc_final: 0.8461 (p) REVERT: B 412 TRP cc_start: 0.9143 (m100) cc_final: 0.8840 (m100) REVERT: B 415 TYR cc_start: 0.8697 (m-80) cc_final: 0.8340 (m-80) REVERT: C 14 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7113 (tm-30) REVERT: C 224 GLN cc_start: 0.8641 (mt0) cc_final: 0.8285 (mt0) REVERT: C 274 LYS cc_start: 0.8380 (mmtp) cc_final: 0.8036 (mppt) REVERT: C 283 MET cc_start: 0.8867 (tpt) cc_final: 0.8478 (tpt) REVERT: D 116 SER cc_start: 0.8804 (m) cc_final: 0.8519 (p) REVERT: D 253 GLN cc_start: 0.8621 (mm110) cc_final: 0.8331 (tp40) REVERT: D 258 CYS cc_start: 0.8439 (t) cc_final: 0.8171 (t) REVERT: D 328 PHE cc_start: 0.8738 (t80) cc_final: 0.8358 (t80) REVERT: E 66 ASN cc_start: 0.8245 (t0) cc_final: 0.7734 (t0) REVERT: E 105 LYS cc_start: 0.9252 (mmmt) cc_final: 0.9012 (mmtp) REVERT: E 163 HIS cc_start: 0.6955 (m90) cc_final: 0.6753 (m90) REVERT: E 189 GLU cc_start: 0.7220 (tp30) cc_final: 0.6994 (tp30) REVERT: E 204 VAL cc_start: 0.8486 (t) cc_final: 0.8276 (m) REVERT: I 4 MET cc_start: 0.7910 (mmt) cc_final: 0.7630 (mmp) REVERT: J 39 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7897 (tp40) outliers start: 71 outliers final: 51 residues processed: 376 average time/residue: 0.0864 time to fit residues: 51.8634 Evaluate side-chains 356 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 305 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 312 TRP Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 134 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 109 optimal weight: 0.0670 overall best weight: 1.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS B 56 HIS B 242 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.124500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098853 restraints weight = 30625.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101816 restraints weight = 14475.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.103634 restraints weight = 9004.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104730 restraints weight = 6736.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.105375 restraints weight = 5688.376| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14967 Z= 0.137 Angle : 0.629 10.818 20365 Z= 0.310 Chirality : 0.045 0.248 2336 Planarity : 0.004 0.045 2479 Dihedral : 9.493 144.089 2368 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.39 % Allowed : 17.67 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.99 (0.20), residues: 1729 helix: 0.64 (0.24), residues: 450 sheet: -0.85 (0.22), residues: 542 loop : -1.21 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 228 TYR 0.019 0.001 TYR B 129 PHE 0.033 0.002 PHE C 475 TRP 0.010 0.001 TRP E 82 HIS 0.011 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (14945) covalent geometry : angle 0.61945 / 0.31 (20306) SS BOND : bond 0.00215 / 0.16 ( 7) SS BOND : angle 0.90738 / 0.58 ( 14) hydrogen bonds : bond 0.03531 / 2.39 ( 586) hydrogen bonds : angle 4.84308 / 3.33 ( 1842) link_ALPHA1-6 : bond 0.02503 / 1.32 ( 1) link_ALPHA1-6 : angle 2.78293 / 1.44 ( 3) link_BETA1-4 : bond 0.00548 / 0.34 ( 7) link_BETA1-4 : angle 2.67575 / 1.80 ( 21) link_NAG-ASN : bond 0.00365 / 0.21 ( 7) link_NAG-ASN : angle 1.97627 / 1.40 ( 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 415 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 346 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 55 MET cc_start: 0.8473 (mmt) cc_final: 0.7117 (mtp) REVERT: A 75 ASN cc_start: 0.8884 (p0) cc_final: 0.8521 (p0) REVERT: A 100 ASN cc_start: 0.7782 (p0) cc_final: 0.7469 (p0) REVERT: A 153 GLU cc_start: 0.8412 (mp0) cc_final: 0.7951 (mp0) REVERT: A 155 GLU cc_start: 0.7971 (tt0) cc_final: 0.7584 (tt0) REVERT: A 224 GLN cc_start: 0.7786 (mm110) cc_final: 0.7503 (mm110) REVERT: A 232 ILE cc_start: 0.8781 (tp) cc_final: 0.8510 (pt) REVERT: A 294 MET cc_start: 0.8394 (mmm) cc_final: 0.8008 (tpt) REVERT: A 465 ARG cc_start: 0.7809 (tmt170) cc_final: 0.7465 (ptt90) REVERT: A 466 TRP cc_start: 0.7363 (m100) cc_final: 0.7062 (t-100) REVERT: B 63 ASP cc_start: 0.8119 (t0) cc_final: 0.7819 (t0) REVERT: B 95 TRP cc_start: 0.8189 (t60) cc_final: 0.7913 (t60) REVERT: B 196 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8402 (mt0) REVERT: B 214 THR cc_start: 0.8818 (m) cc_final: 0.8420 (p) REVERT: B 229 GLN cc_start: 0.8730 (tp40) cc_final: 0.8033 (tp40) REVERT: B 241 SER cc_start: 0.8961 (t) cc_final: 0.8549 (p) REVERT: B 412 TRP cc_start: 0.9225 (m100) cc_final: 0.8498 (m100) REVERT: B 415 TYR cc_start: 0.8678 (m-80) cc_final: 0.8305 (m-80) REVERT: C 14 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7082 (tm-30) REVERT: C 224 GLN cc_start: 0.8733 (mt0) cc_final: 0.8149 (mm-40) REVERT: C 274 LYS cc_start: 0.8368 (mmtp) cc_final: 0.7927 (mppt) REVERT: C 297 LEU cc_start: 0.9269 (mm) cc_final: 0.8962 (mt) REVERT: D 116 SER cc_start: 0.8805 (m) cc_final: 0.8528 (p) REVERT: D 253 GLN cc_start: 0.8705 (mm110) cc_final: 0.8503 (mm-40) REVERT: D 258 CYS cc_start: 0.8554 (t) cc_final: 0.8328 (t) REVERT: D 328 PHE cc_start: 0.8766 (t80) cc_final: 0.8463 (t80) REVERT: E 66 ASN cc_start: 0.8306 (t0) cc_final: 0.8062 (t0) REVERT: E 75 ASP cc_start: 0.7977 (t0) cc_final: 0.7767 (t0) REVERT: E 105 LYS cc_start: 0.9255 (mmmt) cc_final: 0.9001 (mmtp) REVERT: E 160 MET cc_start: 0.6137 (mpp) cc_final: 0.4777 (ptt) REVERT: I 4 MET cc_start: 0.7958 (mmt) cc_final: 0.7670 (mmp) REVERT: I 38 GLN cc_start: 0.7840 (tp40) cc_final: 0.7552 (tp40) REVERT: I 90 GLN cc_start: 0.8767 (pp30) cc_final: 0.8504 (pp30) REVERT: J 39 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7842 (tp40) REVERT: J 59 LYS cc_start: 0.7132 (mtpt) cc_final: 0.6881 (mmtt) REVERT: J 78 THR cc_start: 0.7247 (m) cc_final: 0.6917 (p) outliers start: 69 outliers final: 54 residues processed: 377 average time/residue: 0.0866 time to fit residues: 51.3894 Evaluate side-chains 359 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 305 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 80 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 267 HIS B 56 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS C 479 ASN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.124172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.098343 restraints weight = 30347.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101289 restraints weight = 14513.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.103090 restraints weight = 9087.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104198 restraints weight = 6827.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104751 restraints weight = 5767.937| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14967 Z= 0.127 Angle : 0.619 9.429 20365 Z= 0.304 Chirality : 0.044 0.240 2336 Planarity : 0.004 0.047 2479 Dihedral : 9.234 159.073 2366 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.45 % Allowed : 18.56 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.80 (0.20), residues: 1729 helix: 0.90 (0.24), residues: 451 sheet: -0.76 (0.22), residues: 542 loop : -1.17 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 40 TYR 0.020 0.001 TYR B 129 PHE 0.033 0.002 PHE C 475 TRP 0.008 0.001 TRP C 67 HIS 0.011 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14945) covalent geometry : angle 0.60950 / 0.30 (20306) SS BOND : bond 0.00745 / 0.59 ( 7) SS BOND : angle 1.31373 / 0.84 ( 14) hydrogen bonds : bond 0.03399 / 2.30 ( 586) hydrogen bonds : angle 4.68023 / 3.21 ( 1842) link_ALPHA1-6 : bond 0.02523 / 1.33 ( 1) link_ALPHA1-6 : angle 2.87980 / 1.49 ( 3) link_BETA1-4 : bond 0.00558 / 0.35 ( 7) link_BETA1-4 : angle 2.52527 / 1.69 ( 21) link_NAG-ASN : bond 0.00315 / 0.19 ( 7) link_NAG-ASN : angle 1.79316 / 1.28 ( 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 391 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 321 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 55 MET cc_start: 0.8480 (mmt) cc_final: 0.7114 (mtp) REVERT: A 75 ASN cc_start: 0.8904 (p0) cc_final: 0.8540 (p0) REVERT: A 100 ASN cc_start: 0.7777 (p0) cc_final: 0.7375 (p0) REVERT: A 155 GLU cc_start: 0.7980 (tt0) cc_final: 0.7560 (tt0) REVERT: A 224 GLN cc_start: 0.7674 (mm110) cc_final: 0.7444 (mm110) REVERT: A 232 ILE cc_start: 0.8763 (tp) cc_final: 0.8431 (pt) REVERT: A 294 MET cc_start: 0.8236 (mmm) cc_final: 0.7979 (tpt) REVERT: A 304 TYR cc_start: 0.7794 (t80) cc_final: 0.7546 (t80) REVERT: A 465 ARG cc_start: 0.7767 (tmt170) cc_final: 0.7424 (ptt90) REVERT: A 466 TRP cc_start: 0.7445 (m100) cc_final: 0.7126 (t-100) REVERT: B 44 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8090 (p0) REVERT: B 95 TRP cc_start: 0.8164 (t60) cc_final: 0.7807 (t60) REVERT: B 196 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8428 (mt0) REVERT: B 214 THR cc_start: 0.8802 (m) cc_final: 0.8428 (p) REVERT: B 229 GLN cc_start: 0.8674 (tp40) cc_final: 0.8005 (tp40) REVERT: B 241 SER cc_start: 0.9060 (t) cc_final: 0.8621 (p) REVERT: B 310 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7893 (t80) REVERT: C 14 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7083 (tm-30) REVERT: C 155 GLU cc_start: 0.8151 (tt0) cc_final: 0.7755 (tt0) REVERT: C 218 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8357 (mp) REVERT: C 224 GLN cc_start: 0.8623 (mt0) cc_final: 0.8234 (mm-40) REVERT: C 274 LYS cc_start: 0.8383 (mmtp) cc_final: 0.8032 (mppt) REVERT: C 283 MET cc_start: 0.8914 (tpt) cc_final: 0.8669 (tpp) REVERT: C 297 LEU cc_start: 0.9240 (mm) cc_final: 0.8982 (mt) REVERT: D 82 MET cc_start: 0.8375 (mtp) cc_final: 0.8161 (mtm) REVERT: D 116 SER cc_start: 0.8813 (m) cc_final: 0.8532 (p) REVERT: D 203 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.9090 (t) REVERT: D 253 GLN cc_start: 0.8763 (mm110) cc_final: 0.8503 (mm-40) REVERT: D 328 PHE cc_start: 0.8794 (t80) cc_final: 0.8560 (t80) REVERT: E 56 ASP cc_start: 0.7468 (t0) cc_final: 0.6754 (m-30) REVERT: E 66 ASN cc_start: 0.8238 (t0) cc_final: 0.7886 (t0) REVERT: E 75 ASP cc_start: 0.7969 (t0) cc_final: 0.7714 (t0) REVERT: E 105 LYS cc_start: 0.9265 (mmmt) cc_final: 0.9004 (mmtp) REVERT: E 160 MET cc_start: 0.5979 (mpp) cc_final: 0.4672 (ptt) REVERT: I 4 MET cc_start: 0.7987 (mmt) cc_final: 0.7670 (mmp) REVERT: I 35 TRP cc_start: 0.8647 (m100) cc_final: 0.7829 (m-10) REVERT: I 49 TYR cc_start: 0.7943 (p90) cc_final: 0.7630 (p90) REVERT: I 90 GLN cc_start: 0.8771 (pp30) cc_final: 0.8486 (pp30) REVERT: J 39 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7823 (tp40) REVERT: J 59 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7169 (mmtt) REVERT: J 78 THR cc_start: 0.7334 (m) cc_final: 0.7046 (p) outliers start: 70 outliers final: 48 residues processed: 356 average time/residue: 0.0785 time to fit residues: 43.7436 Evaluate side-chains 355 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 301 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 63 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS B 56 HIS B 116 ASN B 216 HIS C 107 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.122050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.095313 restraints weight = 31267.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098196 restraints weight = 15165.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.099970 restraints weight = 9761.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.101079 restraints weight = 7522.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101715 restraints weight = 6435.967| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 14967 Z= 0.294 Angle : 0.761 11.789 20365 Z= 0.381 Chirality : 0.049 0.304 2336 Planarity : 0.005 0.051 2479 Dihedral : 9.832 167.236 2366 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.21 % Allowed : 19.26 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.99 (0.20), residues: 1729 helix: 0.78 (0.24), residues: 458 sheet: -0.96 (0.21), residues: 544 loop : -1.25 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 40 TYR 0.033 0.002 TYR C 205 PHE 0.033 0.003 PHE C 475 TRP 0.018 0.002 TRP J 103 HIS 0.008 0.002 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.29 (14945) covalent geometry : angle 0.75149 / 0.38 (20306) SS BOND : bond 0.00428 / 0.32 ( 7) SS BOND : angle 1.49379 / 1.01 ( 14) hydrogen bonds : bond 0.04106 / 2.79 ( 586) hydrogen bonds : angle 4.97519 / 3.41 ( 1842) link_ALPHA1-6 : bond 0.02168 / 1.14 ( 1) link_ALPHA1-6 : angle 2.93493 / 1.51 ( 3) link_BETA1-4 : bond 0.00460 / 0.28 ( 7) link_BETA1-4 : angle 2.69014 / 1.75 ( 21) link_NAG-ASN : bond 0.00659 / 0.34 ( 7) link_NAG-ASN : angle 2.36321 / 1.73 ( 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 391 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 309 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8442 (mmt) cc_final: 0.7129 (mtp) REVERT: A 75 ASN cc_start: 0.8925 (p0) cc_final: 0.8582 (p0) REVERT: A 155 GLU cc_start: 0.7982 (tt0) cc_final: 0.7658 (tt0) REVERT: A 224 GLN cc_start: 0.7824 (mm110) cc_final: 0.7544 (mm110) REVERT: A 232 ILE cc_start: 0.8808 (tp) cc_final: 0.8488 (pt) REVERT: A 465 ARG cc_start: 0.7782 (tmt170) cc_final: 0.7482 (ptt90) REVERT: A 466 TRP cc_start: 0.7435 (m100) cc_final: 0.7170 (t-100) REVERT: B 58 MET cc_start: 0.8623 (mtm) cc_final: 0.8353 (mtt) REVERT: B 196 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8377 (mt0) REVERT: B 214 THR cc_start: 0.8844 (m) cc_final: 0.8452 (p) REVERT: B 229 GLN cc_start: 0.8812 (tp40) cc_final: 0.7983 (tp40) REVERT: B 241 SER cc_start: 0.9201 (t) cc_final: 0.8728 (p) REVERT: C 14 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7027 (tm-30) REVERT: C 218 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8571 (mp) REVERT: C 224 GLN cc_start: 0.8748 (mt0) cc_final: 0.8428 (mm-40) REVERT: C 274 LYS cc_start: 0.8516 (mmtp) cc_final: 0.8256 (mppt) REVERT: C 283 MET cc_start: 0.8812 (tpt) cc_final: 0.8543 (tpp) REVERT: D 116 SER cc_start: 0.8739 (m) cc_final: 0.8490 (p) REVERT: D 237 MET cc_start: 0.8257 (mtt) cc_final: 0.7690 (mtt) REVERT: D 253 GLN cc_start: 0.8855 (mm110) cc_final: 0.8572 (tp40) REVERT: D 328 PHE cc_start: 0.9015 (t80) cc_final: 0.8789 (t80) REVERT: E 66 ASN cc_start: 0.8360 (t0) cc_final: 0.8123 (t0) REVERT: E 105 LYS cc_start: 0.9235 (mmmt) cc_final: 0.9034 (mmtp) REVERT: E 177 GLU cc_start: 0.8692 (tp30) cc_final: 0.8461 (tp30) REVERT: I 4 MET cc_start: 0.8181 (mmt) cc_final: 0.7769 (mmp) REVERT: I 32 TYR cc_start: 0.8729 (m-80) cc_final: 0.8450 (m-80) REVERT: J 39 GLN cc_start: 0.8321 (tp-100) cc_final: 0.7935 (tp40) REVERT: J 59 LYS cc_start: 0.7632 (mtpt) cc_final: 0.7134 (mmtt) outliers start: 82 outliers final: 66 residues processed: 355 average time/residue: 0.0790 time to fit residues: 44.8070 Evaluate side-chains 358 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 290 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 132 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS B 190 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.126539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.099988 restraints weight = 30470.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.102992 restraints weight = 14555.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.104860 restraints weight = 9242.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.105953 restraints weight = 7046.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106495 restraints weight = 6027.760| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14967 Z= 0.125 Angle : 0.662 13.804 20365 Z= 0.323 Chirality : 0.045 0.242 2336 Planarity : 0.004 0.048 2479 Dihedral : 9.288 163.886 2364 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.56 % Allowed : 21.17 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.72 (0.20), residues: 1729 helix: 1.05 (0.24), residues: 450 sheet: -0.73 (0.22), residues: 536 loop : -1.15 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 61 TYR 0.027 0.001 TYR E 72 PHE 0.026 0.002 PHE D 442 TRP 0.016 0.001 TRP J 36 HIS 0.007 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (14945) covalent geometry : angle 0.65565 / 0.32 (20306) SS BOND : bond 0.00236 / 0.19 ( 7) SS BOND : angle 0.64447 / 0.42 ( 14) hydrogen bonds : bond 0.03493 / 2.39 ( 586) hydrogen bonds : angle 4.67443 / 3.22 ( 1842) link_ALPHA1-6 : bond 0.02682 / 1.41 ( 1) link_ALPHA1-6 : angle 2.69459 / 1.41 ( 3) link_BETA1-4 : bond 0.00570 / 0.33 ( 7) link_BETA1-4 : angle 2.35733 / 1.56 ( 21) link_NAG-ASN : bond 0.00361 / 0.21 ( 7) link_NAG-ASN : angle 1.75658 / 1.26 ( 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 381 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 325 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8430 (mmt) cc_final: 0.7147 (mtp) REVERT: A 75 ASN cc_start: 0.8841 (p0) cc_final: 0.8481 (p0) REVERT: A 155 GLU cc_start: 0.7859 (tt0) cc_final: 0.7463 (tt0) REVERT: A 224 GLN cc_start: 0.7759 (mm110) cc_final: 0.7497 (mm110) REVERT: A 232 ILE cc_start: 0.8752 (tp) cc_final: 0.8449 (pt) REVERT: A 465 ARG cc_start: 0.7813 (tmt170) cc_final: 0.7477 (ptt90) REVERT: A 466 TRP cc_start: 0.7411 (m100) cc_final: 0.7116 (t-100) REVERT: B 15 PHE cc_start: 0.7611 (m-10) cc_final: 0.7330 (m-80) REVERT: B 58 MET cc_start: 0.8607 (mtm) cc_final: 0.8353 (mtt) REVERT: B 214 THR cc_start: 0.8824 (m) cc_final: 0.8507 (p) REVERT: B 229 GLN cc_start: 0.8745 (tp40) cc_final: 0.8084 (tp40) REVERT: B 241 SER cc_start: 0.9130 (t) cc_final: 0.8691 (p) REVERT: C 14 GLU cc_start: 0.7643 (tm-30) cc_final: 0.6939 (tm-30) REVERT: C 155 GLU cc_start: 0.8196 (tt0) cc_final: 0.7956 (tt0) REVERT: C 218 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8542 (mp) REVERT: C 227 MET cc_start: 0.7372 (tmm) cc_final: 0.6979 (tmm) REVERT: C 274 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8098 (mppt) REVERT: C 289 PHE cc_start: 0.8966 (t80) cc_final: 0.8592 (t80) REVERT: D 116 SER cc_start: 0.8715 (m) cc_final: 0.8464 (p) REVERT: D 237 MET cc_start: 0.7621 (mtt) cc_final: 0.7098 (mtt) REVERT: D 253 GLN cc_start: 0.8765 (mm110) cc_final: 0.8522 (tp40) REVERT: D 325 LEU cc_start: 0.9387 (mm) cc_final: 0.9157 (mp) REVERT: E 75 ASP cc_start: 0.8201 (t0) cc_final: 0.7955 (t0) REVERT: E 105 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8942 (mmtp) REVERT: E 177 GLU cc_start: 0.8581 (tp30) cc_final: 0.8325 (tp30) REVERT: I 4 MET cc_start: 0.8124 (mmt) cc_final: 0.7785 (mmp) REVERT: I 90 GLN cc_start: 0.8919 (pp30) cc_final: 0.8476 (pp30) REVERT: J 39 GLN cc_start: 0.8266 (tp-100) cc_final: 0.7846 (tp40) REVERT: J 59 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7327 (mmtt) outliers start: 56 outliers final: 45 residues processed: 350 average time/residue: 0.0899 time to fit residues: 48.7436 Evaluate side-chains 351 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 304 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 75 PHE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 130 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.125391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.099005 restraints weight = 31127.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101802 restraints weight = 15372.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103532 restraints weight = 9976.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104502 restraints weight = 7726.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105115 restraints weight = 6708.278| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14967 Z= 0.198 Angle : 0.681 13.102 20365 Z= 0.340 Chirality : 0.047 0.248 2336 Planarity : 0.004 0.057 2479 Dihedral : 9.287 167.389 2364 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 4.13 % Allowed : 21.68 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.73 (0.20), residues: 1729 helix: 1.13 (0.24), residues: 451 sheet: -0.70 (0.22), residues: 525 loop : -1.26 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 228 TYR 0.024 0.002 TYR E 72 PHE 0.022 0.002 PHE D 442 TRP 0.024 0.001 TRP B 95 HIS 0.006 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (14945) covalent geometry : angle 0.67329 / 0.34 (20306) SS BOND : bond 0.00207 / 0.15 ( 7) SS BOND : angle 0.86516 / 0.57 ( 14) hydrogen bonds : bond 0.03625 / 2.45 ( 586) hydrogen bonds : angle 4.72020 / 3.24 ( 1842) link_ALPHA1-6 : bond 0.02355 / 1.24 ( 1) link_ALPHA1-6 : angle 2.89248 / 1.51 ( 3) link_BETA1-4 : bond 0.00474 / 0.29 ( 7) link_BETA1-4 : angle 2.49192 / 1.64 ( 21) link_NAG-ASN : bond 0.00529 / 0.28 ( 7) link_NAG-ASN : angle 1.95376 / 1.43 ( 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 376 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 311 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8459 (mmt) cc_final: 0.7189 (mtp) REVERT: A 75 ASN cc_start: 0.8893 (p0) cc_final: 0.8530 (p0) REVERT: A 155 GLU cc_start: 0.7943 (tt0) cc_final: 0.7584 (tt0) REVERT: A 201 SER cc_start: 0.8415 (m) cc_final: 0.8165 (t) REVERT: A 224 GLN cc_start: 0.7740 (mm110) cc_final: 0.7437 (mm110) REVERT: A 232 ILE cc_start: 0.8800 (tp) cc_final: 0.8486 (pt) REVERT: A 465 ARG cc_start: 0.7805 (tmt170) cc_final: 0.7509 (ptt90) REVERT: A 466 TRP cc_start: 0.7402 (m100) cc_final: 0.7126 (t-100) REVERT: B 58 MET cc_start: 0.8636 (mtm) cc_final: 0.8389 (mtt) REVERT: B 214 THR cc_start: 0.8802 (m) cc_final: 0.8510 (p) REVERT: B 229 GLN cc_start: 0.8757 (tp40) cc_final: 0.7953 (tp40) REVERT: B 241 SER cc_start: 0.9171 (t) cc_final: 0.8717 (p) REVERT: C 14 GLU cc_start: 0.7607 (tm-30) cc_final: 0.6927 (tm-30) REVERT: C 155 GLU cc_start: 0.8234 (tt0) cc_final: 0.7995 (tt0) REVERT: C 218 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8549 (mp) REVERT: C 274 LYS cc_start: 0.8437 (mmtp) cc_final: 0.8156 (mppt) REVERT: C 289 PHE cc_start: 0.9008 (t80) cc_final: 0.8666 (t80) REVERT: C 294 MET cc_start: 0.8782 (mmt) cc_final: 0.8537 (mmp) REVERT: D 64 GLU cc_start: 0.7668 (pm20) cc_final: 0.7452 (pm20) REVERT: D 116 SER cc_start: 0.8750 (m) cc_final: 0.8484 (p) REVERT: D 237 MET cc_start: 0.7853 (mtt) cc_final: 0.7384 (mtt) REVERT: D 253 GLN cc_start: 0.8875 (mm110) cc_final: 0.8614 (tp40) REVERT: D 325 LEU cc_start: 0.9362 (mm) cc_final: 0.9128 (mp) REVERT: E 75 ASP cc_start: 0.8310 (t0) cc_final: 0.8030 (t0) REVERT: E 177 GLU cc_start: 0.8650 (tp30) cc_final: 0.8420 (tp30) REVERT: I 4 MET cc_start: 0.8209 (mmt) cc_final: 0.7840 (mmp) REVERT: I 90 GLN cc_start: 0.9007 (pp30) cc_final: 0.8579 (pp30) REVERT: J 39 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7825 (tp40) REVERT: J 59 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7276 (mmtt) outliers start: 65 outliers final: 55 residues processed: 345 average time/residue: 0.0866 time to fit residues: 46.9338 Evaluate side-chains 355 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 298 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 127 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 149 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.128311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.102220 restraints weight = 30942.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105093 restraints weight = 15039.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106862 restraints weight = 9638.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107922 restraints weight = 7406.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108353 restraints weight = 6361.922| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14967 Z= 0.124 Angle : 0.663 12.725 20365 Z= 0.323 Chirality : 0.046 0.296 2336 Planarity : 0.004 0.055 2479 Dihedral : 8.954 161.794 2364 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 3.62 % Allowed : 22.25 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % 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: 1.16 (0.24), residues: 450 sheet: -0.67 (0.22), residues: 532 loop : -1.17 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 228 TYR 0.025 0.001 TYR E 72 PHE 0.024 0.001 PHE D 442 TRP 0.021 0.001 TRP C 237 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (14945) covalent geometry : angle 0.65679 / 0.32 (20306) SS BOND : bond 0.00204 / 0.16 ( 7) SS BOND : angle 0.60301 / 0.41 ( 14) hydrogen bonds : bond 0.03373 / 2.26 ( 586) hydrogen bonds : angle 4.58596 / 3.16 ( 1842) link_ALPHA1-6 : bond 0.02497 / 1.31 ( 1) link_ALPHA1-6 : angle 2.58482 / 1.35 ( 3) link_BETA1-4 : bond 0.00566 / 0.34 ( 7) link_BETA1-4 : angle 2.32814 / 1.54 ( 21) link_NAG-ASN : bond 0.00401 / 0.22 ( 7) link_NAG-ASN : angle 1.68281 / 1.20 ( 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 376 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 319 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8504 (mmt) cc_final: 0.7306 (mtp) REVERT: A 75 ASN cc_start: 0.8829 (p0) cc_final: 0.8447 (p0) REVERT: A 155 GLU cc_start: 0.7936 (tt0) cc_final: 0.7539 (tt0) REVERT: A 201 SER cc_start: 0.8381 (m) cc_final: 0.8155 (t) REVERT: A 224 GLN cc_start: 0.7667 (mm110) cc_final: 0.7359 (mm110) REVERT: A 232 ILE cc_start: 0.8750 (tp) cc_final: 0.8449 (pt) REVERT: A 465 ARG cc_start: 0.7851 (tmt170) cc_final: 0.7504 (ptt90) REVERT: A 466 TRP cc_start: 0.7426 (m100) cc_final: 0.7116 (t-100) REVERT: B 15 PHE cc_start: 0.7643 (m-10) cc_final: 0.7364 (m-80) REVERT: B 58 MET cc_start: 0.8624 (mtm) cc_final: 0.8410 (mtt) REVERT: B 214 THR cc_start: 0.8857 (m) cc_final: 0.8619 (p) REVERT: B 229 GLN cc_start: 0.8736 (tp40) cc_final: 0.8017 (tp40) REVERT: B 241 SER cc_start: 0.9114 (t) cc_final: 0.8684 (p) REVERT: C 9 MET cc_start: 0.7923 (tpp) cc_final: 0.7685 (mmt) REVERT: C 14 GLU cc_start: 0.7651 (tm-30) cc_final: 0.6994 (tm-30) REVERT: C 274 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8163 (mppt) REVERT: C 289 PHE cc_start: 0.8889 (t80) cc_final: 0.8448 (t80) REVERT: D 116 SER cc_start: 0.8747 (m) cc_final: 0.8489 (p) REVERT: D 253 GLN cc_start: 0.8762 (mm110) cc_final: 0.8481 (tp40) REVERT: D 260 MET cc_start: 0.8674 (mmt) cc_final: 0.8290 (mmt) REVERT: D 269 PHE cc_start: 0.7575 (m-10) cc_final: 0.7293 (m-10) REVERT: D 327 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8174 (tt0) REVERT: E 56 ASP cc_start: 0.7303 (t0) cc_final: 0.6647 (m-30) REVERT: E 75 ASP cc_start: 0.8235 (t0) cc_final: 0.7953 (t0) REVERT: E 177 GLU cc_start: 0.8579 (tp30) cc_final: 0.8355 (tp30) REVERT: I 4 MET cc_start: 0.8213 (mmt) cc_final: 0.7931 (mmp) REVERT: I 49 TYR cc_start: 0.8027 (p90) cc_final: 0.7636 (p90) REVERT: I 90 GLN cc_start: 0.8918 (pp30) cc_final: 0.8489 (pp30) REVERT: J 39 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7706 (tp40) REVERT: J 59 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7358 (mmtt) outliers start: 57 outliers final: 52 residues processed: 348 average time/residue: 0.0840 time to fit residues: 45.6877 Evaluate side-chains 357 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 304 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 75 PHE Chi-restraints excluded: chain J residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 75 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 22 optimal weight: 0.0570 chunk 102 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 overall best weight: 1.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.125600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.098991 restraints weight = 30839.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.101958 restraints weight = 14857.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103808 restraints weight = 9450.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.104893 restraints weight = 7212.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105502 restraints weight = 6181.484| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14967 Z= 0.154 Angle : 0.689 15.434 20365 Z= 0.336 Chirality : 0.046 0.216 2336 Planarity : 0.004 0.057 2479 Dihedral : 8.877 157.429 2364 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.84 % Rotamer: Outliers : 3.50 % Allowed : 22.44 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % 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: -0.69 (0.20), residues: 1729 helix: 1.14 (0.24), residues: 451 sheet: -0.65 (0.22), residues: 529 loop : -1.24 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 228 TYR 0.024 0.002 TYR B 129 PHE 0.022 0.002 PHE D 442 TRP 0.051 0.001 TRP C 237 HIS 0.006 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (14945) covalent geometry : angle 0.68203 / 0.33 (20306) SS BOND : bond 0.00195 / 0.15 ( 7) SS BOND : angle 0.76345 / 0.51 ( 14) hydrogen bonds : bond 0.03477 / 2.32 ( 586) hydrogen bonds : angle 4.56357 / 3.13 ( 1842) link_ALPHA1-6 : bond 0.02435 / 1.28 ( 1) link_ALPHA1-6 : angle 2.73409 / 1.43 ( 3) link_BETA1-4 : bond 0.00509 / 0.30 ( 7) link_BETA1-4 : angle 2.36579 / 1.56 ( 21) link_NAG-ASN : bond 0.00442 / 0.24 ( 7) link_NAG-ASN : angle 1.74535 / 1.27 ( 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 368 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 313 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8476 (mmt) cc_final: 0.7200 (mtp) REVERT: A 75 ASN cc_start: 0.8821 (p0) cc_final: 0.8418 (p0) REVERT: A 155 GLU cc_start: 0.7884 (tt0) cc_final: 0.7502 (tt0) REVERT: A 224 GLN cc_start: 0.7573 (mm110) cc_final: 0.7269 (mm110) REVERT: A 232 ILE cc_start: 0.8782 (tp) cc_final: 0.8474 (pt) REVERT: A 465 ARG cc_start: 0.7781 (tmt170) cc_final: 0.7483 (ptt90) REVERT: A 466 TRP cc_start: 0.7419 (m100) cc_final: 0.7110 (t-100) REVERT: B 58 MET cc_start: 0.8626 (mtm) cc_final: 0.8407 (mtt) REVERT: B 214 THR cc_start: 0.8872 (m) cc_final: 0.8620 (p) REVERT: B 229 GLN cc_start: 0.8769 (tp40) cc_final: 0.7994 (tp40) REVERT: B 241 SER cc_start: 0.9114 (t) cc_final: 0.8660 (p) REVERT: C 9 MET cc_start: 0.7920 (tpp) cc_final: 0.7710 (mmt) REVERT: C 14 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6977 (tm-30) REVERT: C 182 GLU cc_start: 0.7044 (mp0) cc_final: 0.6737 (mp0) REVERT: C 274 LYS cc_start: 0.8417 (mmtp) cc_final: 0.8170 (mppt) REVERT: C 286 MET cc_start: 0.8961 (mtt) cc_final: 0.8686 (mtt) REVERT: C 289 PHE cc_start: 0.8969 (t80) cc_final: 0.8618 (t80) REVERT: D 116 SER cc_start: 0.8783 (m) cc_final: 0.8527 (p) REVERT: D 237 MET cc_start: 0.7587 (mtt) cc_final: 0.6991 (mtt) REVERT: D 253 GLN cc_start: 0.8820 (mm110) cc_final: 0.8529 (tp40) REVERT: E 56 ASP cc_start: 0.7380 (t0) cc_final: 0.6675 (m-30) REVERT: E 75 ASP cc_start: 0.8292 (t0) cc_final: 0.7996 (t0) REVERT: E 177 GLU cc_start: 0.8601 (tp30) cc_final: 0.8370 (tp30) REVERT: I 4 MET cc_start: 0.8247 (mmt) cc_final: 0.7977 (mmp) REVERT: I 37 GLN cc_start: 0.7169 (tm130) cc_final: 0.6961 (tm-30) REVERT: I 49 TYR cc_start: 0.8026 (p90) cc_final: 0.7656 (p90) REVERT: I 90 GLN cc_start: 0.8965 (pp30) cc_final: 0.8535 (pp30) REVERT: J 39 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7661 (tp40) REVERT: J 59 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7336 (mmtt) outliers start: 55 outliers final: 51 residues processed: 340 average time/residue: 0.0870 time to fit residues: 46.0951 Evaluate side-chains 360 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 155 optimal weight: 0.5980 chunk 167 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS B 88 ASN C 64 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.127852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.101461 restraints weight = 30561.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104465 restraints weight = 14631.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.106318 restraints weight = 9294.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107394 restraints weight = 7093.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107954 restraints weight = 6091.324| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14967 Z= 0.120 Angle : 0.670 13.569 20365 Z= 0.326 Chirality : 0.045 0.213 2336 Planarity : 0.004 0.059 2479 Dihedral : 8.618 150.343 2364 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 3.56 % Allowed : 22.70 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.24 % 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: -0.60 (0.20), residues: 1729 helix: 1.15 (0.25), residues: 452 sheet: -0.58 (0.22), residues: 524 loop : -1.16 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 228 TYR 0.024 0.001 TYR E 72 PHE 0.014 0.001 PHE B 157 TRP 0.049 0.001 TRP C 237 HIS 0.006 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14945) covalent geometry : angle 0.66435 / 0.32 (20306) SS BOND : bond 0.00227 / 0.18 ( 7) SS BOND : angle 0.58764 / 0.41 ( 14) hydrogen bonds : bond 0.03396 / 2.28 ( 586) hydrogen bonds : angle 4.51782 / 3.11 ( 1842) link_ALPHA1-6 : bond 0.02450 / 1.29 ( 1) link_ALPHA1-6 : angle 2.47102 / 1.29 ( 3) link_BETA1-4 : bond 0.00574 / 0.34 ( 7) link_BETA1-4 : angle 2.25792 / 1.48 ( 21) link_NAG-ASN : bond 0.00339 / 0.19 ( 7) link_NAG-ASN : angle 1.57892 / 1.13 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.09 seconds wall clock time: 38 minutes 16.93 seconds (2296.93 seconds total)