Starting phenix.real_space_refine on Sun May 18 20:36:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3v_22034/05_2025/6x3v_22034.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3v_22034/05_2025/6x3v_22034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x3v_22034/05_2025/6x3v_22034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3v_22034/05_2025/6x3v_22034.map" model { file = "/net/cci-nas-00/data/ceres_data/6x3v_22034/05_2025/6x3v_22034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3v_22034/05_2025/6x3v_22034.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11253 2.51 5 N 2833 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17426 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} 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: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'ABU': 1, 'NAG': 1, 'V8D': 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: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'ABU': 1, 'NAG': 1, 'V8D': 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 Time building chain proxies: 10.23, per 1000 atoms: 0.59 Number of scatterers: 17426 At special positions: 0 Unit cell: (135.779, 121.618, 129.948, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 3243 8.00 N 2833 7.00 C 11253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, 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 139 " - pdb=" SG CYS D 153 " 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 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 2.3 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 32 sheets defined 31.4% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.552A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 226 through 238 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.954A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 340 removed outlier: 3.969A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 23 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.654A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.526A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 243 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 275 removed outlier: 3.665A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 removed outlier: 3.597A pdb=" N TRP B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.938A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.609A pdb=" N ASN B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.549A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.763A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 248 through 270 Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 339 removed outlier: 3.549A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 11 through 24 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.589A pdb=" N SER D 92 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 243 removed outlier: 4.319A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.871A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 346 removed outlier: 4.151A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.803A pdb=" N LYS E 105 " --> pdb=" O MET E 102 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 106' Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.426A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 261 through 287 removed outlier: 3.701A pdb=" N ARG E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 324 removed outlier: 3.584A pdb=" N PHE E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 356 removed outlier: 3.843A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 87 through 91 removed outlier: 4.140A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.701A pdb=" N GLN K 65 " --> pdb=" O PRO K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.740A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 132 removed outlier: 6.922A pdb=" N ASP A 56 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL A 50 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR A 58 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.845A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 54 removed outlier: 4.649A pdb=" N THR B 61 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL B 53 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU B 59 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 86 removed outlier: 4.200A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL B 180 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 45 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.063A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.063A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR B 210 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE B 202 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 212 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER B 200 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR B 214 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL B 198 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS B 216 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN B 196 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS B 218 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.642A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.642A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.829A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.829A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL C 199 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR C 205 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS C 197 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG C 207 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR C 195 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER C 209 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 193 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER C 211 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR C 191 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS C 213 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 39 through 43 removed outlier: 6.062A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 removed outlier: 4.338A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 130 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 108 " --> pdb=" O THR D 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 86 removed outlier: 4.338A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 130 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 49 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.995A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.995A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 61 through 66 removed outlier: 3.705A pdb=" N SER E 61 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR E 73 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL E 65 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU E 71 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.595A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS E 184 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N MET E 57 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N SER E 186 " --> pdb=" O MET E 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.541A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.540A pdb=" N THR I 101 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR I 86 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.540A pdb=" N THR I 101 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR I 86 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN I 90 " --> pdb=" O THR I 96 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.161A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.161A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.541A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.422A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.596A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.707A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR K 94 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.707A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR K 94 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 814 hydrogen bonds defined for protein. 2325 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: 5.86 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2670 1.31 - 1.43: 5257 1.43 - 1.56: 9767 1.56 - 1.69: 1 1.69 - 1.82: 167 Bond restraints: 17862 Sorted by residual: bond pdb=" C13 V8D A 406 " pdb=" O02 V8D A 406 " ideal model delta sigma weight residual 1.209 1.398 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C13 V8D C 406 " pdb=" O02 V8D C 406 " ideal model delta sigma weight residual 1.209 1.397 -0.188 2.00e-02 2.50e+03 8.86e+01 bond pdb=" C13 V8D C 406 " pdb=" O01 V8D C 406 " ideal model delta sigma weight residual 1.325 1.180 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C13 V8D A 406 " pdb=" O01 V8D A 406 " ideal model delta sigma weight residual 1.325 1.182 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C08 V8D C 406 " pdb=" C13 V8D C 406 " ideal model delta sigma weight residual 1.459 1.530 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 17857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 23859 1.99 - 3.98: 347 3.98 - 5.98: 67 5.98 - 7.97: 12 7.97 - 9.96: 3 Bond angle restraints: 24288 Sorted by residual: angle pdb=" C08 V8D A 406 " pdb=" C13 V8D A 406 " pdb=" O01 V8D A 406 " ideal model delta sigma weight residual 110.46 120.42 -9.96 3.00e+00 1.11e-01 1.10e+01 angle pdb=" N GLY K 56 " pdb=" CA GLY K 56 " pdb=" C GLY K 56 " ideal model delta sigma weight residual 115.63 110.77 4.86 1.49e+00 4.50e-01 1.07e+01 angle pdb=" C08 V8D C 406 " pdb=" C13 V8D C 406 " pdb=" O01 V8D C 406 " ideal model delta sigma weight residual 110.46 120.24 -9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" N MET B 114 " pdb=" CA MET B 114 " pdb=" C MET B 114 " ideal model delta sigma weight residual 110.13 106.39 3.74 1.15e+00 7.56e-01 1.06e+01 angle pdb=" N ALA B 161 " pdb=" CA ALA B 161 " pdb=" CB ALA B 161 " ideal model delta sigma weight residual 114.17 110.83 3.34 1.14e+00 7.69e-01 8.56e+00 ... (remaining 24283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 10032 21.78 - 43.56: 681 43.56 - 65.34: 70 65.34 - 87.12: 32 87.12 - 108.90: 17 Dihedral angle restraints: 10832 sinusoidal: 4576 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -24.88 -61.12 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -31.80 -54.20 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" CA CYS A 150 " pdb=" C CYS A 150 " pdb=" N THR A 151 " pdb=" CA THR A 151 " ideal model delta harmonic sigma weight residual -180.00 -152.15 -27.85 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 10829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2372 0.060 - 0.121: 406 0.121 - 0.181: 24 0.181 - 0.241: 4 0.241 - 0.302: 3 Chirality restraints: 2809 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 111 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.98e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2806 not shown) Planarity restraints: 2995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 227 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C VAL D 227 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL D 227 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE D 228 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 227 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C VAL B 227 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL B 227 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE B 228 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 277 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO D 278 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 278 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 278 " -0.022 5.00e-02 4.00e+02 ... (remaining 2992 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 413 2.69 - 3.24: 16500 3.24 - 3.79: 26585 3.79 - 4.35: 36158 4.35 - 4.90: 61897 Nonbonded interactions: 141553 Sorted by model distance: nonbonded pdb=" OG1 THR B 99 " pdb=" OH TYR B 169 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR E 111 " pdb=" OH TYR E 181 " model vdw 2.144 3.040 nonbonded pdb=" NE2 HIS C 107 " pdb=" OG1 THR C 131 " model vdw 2.194 3.120 nonbonded pdb=" OG1 THR D 99 " pdb=" OH TYR D 169 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR L 63 " pdb=" OG1 THR L 74 " model vdw 2.213 3.040 ... (remaining 141548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } 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: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.040 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.100 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.189 17894 Z= 0.259 Angle : 0.662 9.958 24375 Z= 0.342 Chirality : 0.046 0.302 2809 Planarity : 0.004 0.040 2988 Dihedral : 15.050 108.897 6785 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.58 % Allowed : 10.67 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.16), residues: 2103 helix: 0.10 (0.19), residues: 564 sheet: -2.64 (0.17), residues: 675 loop : -2.46 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 67 HIS 0.004 0.001 HIS C 267 PHE 0.014 0.001 PHE D 226 TYR 0.016 0.002 TYR C 299 ARG 0.002 0.000 ARG B 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 7) link_NAG-ASN : angle 1.70203 ( 21) link_ALPHA1-6 : bond 0.00185 ( 2) link_ALPHA1-6 : angle 2.05863 ( 6) link_BETA1-4 : bond 0.00579 ( 9) link_BETA1-4 : angle 2.15780 ( 27) link_ALPHA1-2 : bond 0.00305 ( 3) link_ALPHA1-2 : angle 1.88416 ( 9) link_ALPHA1-3 : bond 0.00707 ( 2) link_ALPHA1-3 : angle 1.52452 ( 6) hydrogen bonds : bond 0.10740 ( 749) hydrogen bonds : angle 6.18481 ( 2325) SS BOND : bond 0.00128 ( 9) SS BOND : angle 1.90630 ( 18) covalent geometry : bond 0.00567 (17862) covalent geometry : angle 0.65273 (24288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 284 time to evaluate : 1.830 Fit side-chains REVERT: A 99 LEU cc_start: 0.9129 (tp) cc_final: 0.8923 (tp) REVERT: A 283 MET cc_start: 0.7392 (tpp) cc_final: 0.7122 (tpp) REVERT: A 304 TYR cc_start: 0.8540 (t80) cc_final: 0.8227 (t80) REVERT: B 308 ASN cc_start: 0.8642 (t0) cc_final: 0.8324 (t0) REVERT: C 321 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7856 (mtt180) REVERT: D 58 MET cc_start: 0.8000 (mtt) cc_final: 0.7710 (mtm) REVERT: D 323 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7660 (ttp80) REVERT: E 338 PHE cc_start: 0.7538 (t80) cc_final: 0.7291 (t80) REVERT: I 11 MET cc_start: 0.7911 (ppp) cc_final: 0.7696 (ppp) REVERT: L 106 LYS cc_start: 0.5232 (tptt) cc_final: 0.5031 (tptt) outliers start: 11 outliers final: 7 residues processed: 295 average time/residue: 0.3496 time to fit residues: 147.7847 Evaluate side-chains 249 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 242 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 90 GLN B 102 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN E 90 ASN E 324 GLN E 347 ASN K 5 GLN ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.097902 restraints weight = 21492.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099503 restraints weight = 18935.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100556 restraints weight = 14522.316| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17894 Z= 0.129 Angle : 0.548 7.588 24375 Z= 0.279 Chirality : 0.043 0.189 2809 Planarity : 0.004 0.041 2988 Dihedral : 8.875 74.516 2852 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.28 % Allowed : 13.49 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.18), residues: 2103 helix: 1.55 (0.21), residues: 563 sheet: -2.23 (0.18), residues: 690 loop : -1.81 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 67 HIS 0.004 0.001 HIS C 267 PHE 0.012 0.001 PHE B 146 TYR 0.027 0.001 TYR L 49 ARG 0.002 0.000 ARG D 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 7) link_NAG-ASN : angle 1.53071 ( 21) link_ALPHA1-6 : bond 0.00620 ( 2) link_ALPHA1-6 : angle 1.53510 ( 6) link_BETA1-4 : bond 0.00485 ( 9) link_BETA1-4 : angle 1.91183 ( 27) link_ALPHA1-2 : bond 0.00425 ( 3) link_ALPHA1-2 : angle 1.82094 ( 9) link_ALPHA1-3 : bond 0.01331 ( 2) link_ALPHA1-3 : angle 1.03848 ( 6) hydrogen bonds : bond 0.03649 ( 749) hydrogen bonds : angle 4.87555 ( 2325) SS BOND : bond 0.00174 ( 9) SS BOND : angle 1.61889 ( 18) covalent geometry : bond 0.00288 (17862) covalent geometry : angle 0.53999 (24288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 1.945 Fit side-chains REVERT: A 283 MET cc_start: 0.7405 (tpp) cc_final: 0.7183 (tpp) REVERT: A 304 TYR cc_start: 0.8621 (t80) cc_final: 0.8285 (t80) REVERT: B 308 ASN cc_start: 0.8533 (t0) cc_final: 0.8252 (t0) REVERT: C 265 ASN cc_start: 0.8572 (t0) cc_final: 0.8224 (t0) REVERT: C 321 ARG cc_start: 0.8292 (mtm180) cc_final: 0.7843 (mtt180) REVERT: D 323 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7608 (ttp80) REVERT: E 223 MET cc_start: 0.8046 (mmm) cc_final: 0.7394 (mmm) REVERT: E 338 PHE cc_start: 0.7220 (t80) cc_final: 0.6961 (t80) REVERT: I 20 THR cc_start: 0.8610 (t) cc_final: 0.8404 (m) REVERT: I 45 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8127 (mtpt) outliers start: 43 outliers final: 31 residues processed: 274 average time/residue: 0.3229 time to fit residues: 130.6480 Evaluate side-chains 261 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 96 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 170 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 275 ASN D 116 ASN L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.099335 restraints weight = 21438.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.101096 restraints weight = 15449.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.102430 restraints weight = 12557.062| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17894 Z= 0.111 Angle : 0.515 9.913 24375 Z= 0.260 Chirality : 0.042 0.183 2809 Planarity : 0.004 0.040 2988 Dihedral : 6.940 62.629 2851 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.76 % Allowed : 14.07 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.18), residues: 2103 helix: 2.18 (0.21), residues: 563 sheet: -1.82 (0.18), residues: 694 loop : -1.39 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 67 HIS 0.003 0.001 HIS C 267 PHE 0.010 0.001 PHE B 336 TYR 0.031 0.001 TYR L 49 ARG 0.004 0.000 ARG E 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 7) link_NAG-ASN : angle 1.35420 ( 21) link_ALPHA1-6 : bond 0.00484 ( 2) link_ALPHA1-6 : angle 1.57132 ( 6) link_BETA1-4 : bond 0.00487 ( 9) link_BETA1-4 : angle 1.79569 ( 27) link_ALPHA1-2 : bond 0.00387 ( 3) link_ALPHA1-2 : angle 1.56765 ( 9) link_ALPHA1-3 : bond 0.01271 ( 2) link_ALPHA1-3 : angle 1.02960 ( 6) hydrogen bonds : bond 0.03257 ( 749) hydrogen bonds : angle 4.47996 ( 2325) SS BOND : bond 0.00130 ( 9) SS BOND : angle 1.68333 ( 18) covalent geometry : bond 0.00246 (17862) covalent geometry : angle 0.50727 (24288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 2.032 Fit side-chains REVERT: A 9 MET cc_start: 0.8205 (tpp) cc_final: 0.7949 (tpp) REVERT: A 283 MET cc_start: 0.7344 (tpp) cc_final: 0.7133 (tpp) REVERT: A 304 TYR cc_start: 0.8611 (t80) cc_final: 0.8244 (t80) REVERT: B 308 ASN cc_start: 0.8499 (t0) cc_final: 0.7953 (t0) REVERT: C 164 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9225 (tt) REVERT: C 265 ASN cc_start: 0.8522 (t0) cc_final: 0.8234 (t0) REVERT: C 321 ARG cc_start: 0.8268 (mtm180) cc_final: 0.7752 (mtt180) REVERT: D 141 MET cc_start: 0.8291 (mtt) cc_final: 0.8042 (mtt) REVERT: D 213 MET cc_start: 0.8497 (mmm) cc_final: 0.7274 (mmm) REVERT: E 223 MET cc_start: 0.8072 (mmm) cc_final: 0.7389 (mmm) REVERT: E 338 PHE cc_start: 0.7176 (t80) cc_final: 0.6908 (t80) REVERT: I 45 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8046 (mtpt) REVERT: J 90 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8056 (t0) outliers start: 52 outliers final: 39 residues processed: 284 average time/residue: 0.3136 time to fit residues: 132.7252 Evaluate side-chains 276 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 103 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.123233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.095617 restraints weight = 21647.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.098463 restraints weight = 13270.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100219 restraints weight = 9795.715| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17894 Z= 0.155 Angle : 0.536 8.969 24375 Z= 0.270 Chirality : 0.043 0.199 2809 Planarity : 0.004 0.041 2988 Dihedral : 6.311 55.204 2850 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.45 % Allowed : 15.40 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 2103 helix: 2.33 (0.21), residues: 563 sheet: -1.64 (0.19), residues: 694 loop : -1.28 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 67 HIS 0.003 0.001 HIS C 267 PHE 0.012 0.001 PHE E 236 TYR 0.032 0.001 TYR L 49 ARG 0.004 0.000 ARG E 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 7) link_NAG-ASN : angle 1.64658 ( 21) link_ALPHA1-6 : bond 0.00296 ( 2) link_ALPHA1-6 : angle 1.76830 ( 6) link_BETA1-4 : bond 0.00485 ( 9) link_BETA1-4 : angle 1.72683 ( 27) link_ALPHA1-2 : bond 0.00421 ( 3) link_ALPHA1-2 : angle 1.66779 ( 9) link_ALPHA1-3 : bond 0.01230 ( 2) link_ALPHA1-3 : angle 0.99678 ( 6) hydrogen bonds : bond 0.03371 ( 749) hydrogen bonds : angle 4.40049 ( 2325) SS BOND : bond 0.00195 ( 9) SS BOND : angle 1.70204 ( 18) covalent geometry : bond 0.00365 (17862) covalent geometry : angle 0.52803 (24288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 252 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8281 (tpp) cc_final: 0.7933 (tpp) REVERT: A 283 MET cc_start: 0.7423 (tpp) cc_final: 0.7201 (tpp) REVERT: A 304 TYR cc_start: 0.8611 (t80) cc_final: 0.8206 (t80) REVERT: B 164 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7857 (ttp80) REVERT: B 308 ASN cc_start: 0.8515 (t0) cc_final: 0.7995 (t0) REVERT: C 164 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9238 (tt) REVERT: C 265 ASN cc_start: 0.8570 (t0) cc_final: 0.8313 (t0) REVERT: C 321 ARG cc_start: 0.8310 (mtm180) cc_final: 0.7807 (mtt180) REVERT: D 338 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6954 (mp) REVERT: E 223 MET cc_start: 0.8106 (mmm) cc_final: 0.7406 (mmm) REVERT: E 338 PHE cc_start: 0.7145 (t80) cc_final: 0.6876 (t80) REVERT: I 45 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8004 (mtpt) REVERT: K 5 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7529 (mm110) REVERT: K 91 THR cc_start: 0.8279 (p) cc_final: 0.7928 (t) outliers start: 65 outliers final: 49 residues processed: 294 average time/residue: 0.2997 time to fit residues: 131.4397 Evaluate side-chains 295 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 139 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 40 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 193 optimal weight: 0.0270 chunk 130 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.096784 restraints weight = 21791.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099674 restraints weight = 13278.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101493 restraints weight = 9746.000| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17894 Z= 0.120 Angle : 0.515 8.513 24375 Z= 0.258 Chirality : 0.042 0.181 2809 Planarity : 0.003 0.041 2988 Dihedral : 5.925 56.970 2850 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.40 % Allowed : 16.41 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.19), residues: 2103 helix: 2.48 (0.21), residues: 565 sheet: -1.49 (0.19), residues: 693 loop : -1.11 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 103 HIS 0.003 0.001 HIS D 216 PHE 0.018 0.001 PHE E 158 TYR 0.032 0.001 TYR L 49 ARG 0.004 0.000 ARG E 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 7) link_NAG-ASN : angle 1.80499 ( 21) link_ALPHA1-6 : bond 0.00324 ( 2) link_ALPHA1-6 : angle 1.69971 ( 6) link_BETA1-4 : bond 0.00490 ( 9) link_BETA1-4 : angle 1.55223 ( 27) link_ALPHA1-2 : bond 0.00376 ( 3) link_ALPHA1-2 : angle 1.58029 ( 9) link_ALPHA1-3 : bond 0.01232 ( 2) link_ALPHA1-3 : angle 1.00739 ( 6) hydrogen bonds : bond 0.03161 ( 749) hydrogen bonds : angle 4.27084 ( 2325) SS BOND : bond 0.00146 ( 9) SS BOND : angle 1.52864 ( 18) covalent geometry : bond 0.00276 (17862) covalent geometry : angle 0.50721 (24288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 249 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8299 (tpp) cc_final: 0.7981 (tpp) REVERT: B 308 ASN cc_start: 0.8416 (t0) cc_final: 0.7892 (t0) REVERT: C 164 ILE cc_start: 0.9462 (tt) cc_final: 0.9246 (tt) REVERT: C 265 ASN cc_start: 0.8477 (t0) cc_final: 0.8214 (t0) REVERT: C 321 ARG cc_start: 0.8253 (mtm180) cc_final: 0.7743 (mtt180) REVERT: D 58 MET cc_start: 0.8168 (mtt) cc_final: 0.7874 (mtp) REVERT: D 338 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6944 (mp) REVERT: E 223 MET cc_start: 0.8096 (mmm) cc_final: 0.7396 (mmm) REVERT: E 338 PHE cc_start: 0.7141 (t80) cc_final: 0.6883 (t80) REVERT: I 45 LYS cc_start: 0.8454 (mmmt) cc_final: 0.7949 (mtpt) REVERT: I 79 GLN cc_start: 0.8368 (mp10) cc_final: 0.8135 (mp10) REVERT: K 5 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7525 (mm110) outliers start: 64 outliers final: 51 residues processed: 288 average time/residue: 0.3110 time to fit residues: 134.3395 Evaluate side-chains 289 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 119 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 166 optimal weight: 0.0050 chunk 128 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 242 GLN B 308 ASN D 204 GLN L 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.097777 restraints weight = 21632.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100643 restraints weight = 13185.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102546 restraints weight = 9683.718| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17894 Z= 0.108 Angle : 0.502 7.965 24375 Z= 0.251 Chirality : 0.042 0.179 2809 Planarity : 0.003 0.040 2988 Dihedral : 5.661 59.443 2850 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.29 % Allowed : 17.53 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 2103 helix: 2.62 (0.21), residues: 565 sheet: -1.37 (0.19), residues: 697 loop : -0.98 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 103 HIS 0.003 0.000 HIS C 267 PHE 0.016 0.001 PHE E 158 TYR 0.033 0.001 TYR L 49 ARG 0.005 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 7) link_NAG-ASN : angle 1.44898 ( 21) link_ALPHA1-6 : bond 0.00298 ( 2) link_ALPHA1-6 : angle 1.70665 ( 6) link_BETA1-4 : bond 0.00464 ( 9) link_BETA1-4 : angle 1.47063 ( 27) link_ALPHA1-2 : bond 0.00365 ( 3) link_ALPHA1-2 : angle 1.54825 ( 9) link_ALPHA1-3 : bond 0.01381 ( 2) link_ALPHA1-3 : angle 1.07301 ( 6) hydrogen bonds : bond 0.03004 ( 749) hydrogen bonds : angle 4.15441 ( 2325) SS BOND : bond 0.00141 ( 9) SS BOND : angle 1.41831 ( 18) covalent geometry : bond 0.00243 (17862) covalent geometry : angle 0.49486 (24288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 250 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8261 (tpp) cc_final: 0.7953 (tpp) REVERT: A 132 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 294 MET cc_start: 0.7778 (mmm) cc_final: 0.7557 (mmm) REVERT: B 308 ASN cc_start: 0.8284 (t0) cc_final: 0.7856 (t0) REVERT: C 321 ARG cc_start: 0.8209 (mtm180) cc_final: 0.7679 (mtt180) REVERT: D 58 MET cc_start: 0.8163 (mtt) cc_final: 0.7951 (mtp) REVERT: D 213 MET cc_start: 0.8488 (mmm) cc_final: 0.7207 (mmm) REVERT: E 223 MET cc_start: 0.8098 (mmm) cc_final: 0.7367 (mmm) REVERT: E 338 PHE cc_start: 0.7100 (t80) cc_final: 0.6835 (t80) REVERT: I 45 LYS cc_start: 0.8394 (mmmt) cc_final: 0.7861 (mtpt) REVERT: I 79 GLN cc_start: 0.8404 (mp10) cc_final: 0.8159 (mp10) REVERT: K 5 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7560 (mm110) outliers start: 62 outliers final: 52 residues processed: 288 average time/residue: 0.3103 time to fit residues: 133.2011 Evaluate side-chains 293 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 18 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 169 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 242 GLN D 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.095373 restraints weight = 21882.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.098213 restraints weight = 13322.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100099 restraints weight = 9804.155| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17894 Z= 0.157 Angle : 0.542 7.735 24375 Z= 0.271 Chirality : 0.043 0.186 2809 Planarity : 0.004 0.039 2988 Dihedral : 5.635 55.865 2850 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.14 % Allowed : 17.37 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 2103 helix: 2.60 (0.21), residues: 565 sheet: -1.34 (0.19), residues: 678 loop : -0.95 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 103 HIS 0.003 0.001 HIS C 267 PHE 0.014 0.001 PHE E 158 TYR 0.034 0.001 TYR L 49 ARG 0.006 0.000 ARG B 164 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 7) link_NAG-ASN : angle 1.48891 ( 21) link_ALPHA1-6 : bond 0.00161 ( 2) link_ALPHA1-6 : angle 1.83862 ( 6) link_BETA1-4 : bond 0.00489 ( 9) link_BETA1-4 : angle 1.49990 ( 27) link_ALPHA1-2 : bond 0.00347 ( 3) link_ALPHA1-2 : angle 1.67500 ( 9) link_ALPHA1-3 : bond 0.01292 ( 2) link_ALPHA1-3 : angle 1.15682 ( 6) hydrogen bonds : bond 0.03281 ( 749) hydrogen bonds : angle 4.21914 ( 2325) SS BOND : bond 0.00139 ( 9) SS BOND : angle 1.59134 ( 18) covalent geometry : bond 0.00371 (17862) covalent geometry : angle 0.53512 (24288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 245 time to evaluate : 1.966 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8903 (tp) cc_final: 0.8644 (tp) REVERT: A 132 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 145 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8300 (mt) REVERT: A 294 MET cc_start: 0.7929 (mmm) cc_final: 0.7409 (mmp) REVERT: B 308 ASN cc_start: 0.8323 (t0) cc_final: 0.7927 (t0) REVERT: C 164 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9198 (tt) REVERT: C 265 ASN cc_start: 0.8572 (t0) cc_final: 0.8317 (t0) REVERT: C 321 ARG cc_start: 0.8242 (mtm180) cc_final: 0.7685 (mtt180) REVERT: E 45 ASP cc_start: 0.8428 (p0) cc_final: 0.8205 (p0) REVERT: E 223 MET cc_start: 0.8135 (mmm) cc_final: 0.7456 (mmm) REVERT: E 338 PHE cc_start: 0.7154 (t80) cc_final: 0.6900 (t80) REVERT: I 45 LYS cc_start: 0.8430 (mmmt) cc_final: 0.7920 (mtpt) REVERT: I 79 GLN cc_start: 0.8392 (mp10) cc_final: 0.8157 (mp10) REVERT: K 5 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7537 (mm110) outliers start: 78 outliers final: 62 residues processed: 294 average time/residue: 0.3023 time to fit residues: 134.3978 Evaluate side-chains 305 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.106312 restraints weight = 21101.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109409 restraints weight = 12462.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111403 restraints weight = 8978.874| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17894 Z= 0.113 Angle : 0.513 7.648 24375 Z= 0.256 Chirality : 0.042 0.178 2809 Planarity : 0.003 0.040 2988 Dihedral : 5.501 55.104 2850 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.51 % Allowed : 17.90 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 2103 helix: 2.71 (0.21), residues: 565 sheet: -1.26 (0.19), residues: 678 loop : -0.85 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 237 HIS 0.003 0.000 HIS C 267 PHE 0.014 0.001 PHE E 158 TYR 0.035 0.001 TYR L 49 ARG 0.004 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 7) link_NAG-ASN : angle 1.33953 ( 21) link_ALPHA1-6 : bond 0.00280 ( 2) link_ALPHA1-6 : angle 1.71990 ( 6) link_BETA1-4 : bond 0.00464 ( 9) link_BETA1-4 : angle 1.46169 ( 27) link_ALPHA1-2 : bond 0.00367 ( 3) link_ALPHA1-2 : angle 1.54136 ( 9) link_ALPHA1-3 : bond 0.01392 ( 2) link_ALPHA1-3 : angle 1.07722 ( 6) hydrogen bonds : bond 0.03037 ( 749) hydrogen bonds : angle 4.13287 ( 2325) SS BOND : bond 0.00146 ( 9) SS BOND : angle 1.41990 ( 18) covalent geometry : bond 0.00256 (17862) covalent geometry : angle 0.50659 (24288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 246 time to evaluate : 1.782 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 145 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8284 (mt) REVERT: A 294 MET cc_start: 0.7946 (mmm) cc_final: 0.7723 (mmm) REVERT: B 308 ASN cc_start: 0.8276 (t0) cc_final: 0.7901 (t0) REVERT: C 321 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7655 (mtt180) REVERT: E 223 MET cc_start: 0.8084 (mmm) cc_final: 0.7396 (mmm) REVERT: E 338 PHE cc_start: 0.7196 (t80) cc_final: 0.6925 (t80) REVERT: I 45 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7935 (mtpt) REVERT: I 79 GLN cc_start: 0.8481 (mp10) cc_final: 0.8254 (mp10) REVERT: K 5 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7557 (mm110) outliers start: 66 outliers final: 54 residues processed: 287 average time/residue: 0.2931 time to fit residues: 126.1501 Evaluate side-chains 298 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 21 optimal weight: 0.0000 chunk 43 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN L 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.098214 restraints weight = 21783.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101354 restraints weight = 12680.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.103397 restraints weight = 9064.411| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17894 Z= 0.112 Angle : 0.519 8.339 24375 Z= 0.257 Chirality : 0.042 0.180 2809 Planarity : 0.003 0.039 2988 Dihedral : 5.385 53.460 2850 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.40 % Allowed : 18.53 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 2103 helix: 2.74 (0.21), residues: 565 sheet: -1.18 (0.19), residues: 678 loop : -0.77 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 237 HIS 0.003 0.000 HIS C 267 PHE 0.014 0.001 PHE E 158 TYR 0.035 0.001 TYR L 49 ARG 0.007 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 7) link_NAG-ASN : angle 1.28857 ( 21) link_ALPHA1-6 : bond 0.00250 ( 2) link_ALPHA1-6 : angle 1.75053 ( 6) link_BETA1-4 : bond 0.00457 ( 9) link_BETA1-4 : angle 1.44895 ( 27) link_ALPHA1-2 : bond 0.00338 ( 3) link_ALPHA1-2 : angle 1.58140 ( 9) link_ALPHA1-3 : bond 0.01215 ( 2) link_ALPHA1-3 : angle 1.10032 ( 6) hydrogen bonds : bond 0.02992 ( 749) hydrogen bonds : angle 4.09196 ( 2325) SS BOND : bond 0.00309 ( 9) SS BOND : angle 1.35924 ( 18) covalent geometry : bond 0.00256 (17862) covalent geometry : angle 0.51280 (24288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 244 time to evaluate : 1.985 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8382 (p) REVERT: A 145 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 294 MET cc_start: 0.7985 (mmm) cc_final: 0.7740 (mmm) REVERT: B 164 ARG cc_start: 0.8106 (ttp-110) cc_final: 0.7857 (ttp80) REVERT: B 242 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7499 (mt0) REVERT: B 308 ASN cc_start: 0.8229 (t0) cc_final: 0.7880 (t0) REVERT: C 321 ARG cc_start: 0.8181 (mtm180) cc_final: 0.7635 (mtt180) REVERT: E 223 MET cc_start: 0.8091 (mmm) cc_final: 0.7391 (mmm) REVERT: E 338 PHE cc_start: 0.7187 (t80) cc_final: 0.6916 (t80) REVERT: I 45 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7911 (mtpt) REVERT: I 79 GLN cc_start: 0.8507 (mp10) cc_final: 0.8273 (mp10) REVERT: K 5 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7603 (mm110) outliers start: 64 outliers final: 56 residues processed: 283 average time/residue: 0.3117 time to fit residues: 131.2248 Evaluate side-chains 297 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 167 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 242 GLN D 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.097254 restraints weight = 21782.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100089 restraints weight = 13333.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.101963 restraints weight = 9774.627| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17894 Z= 0.129 Angle : 0.532 9.692 24375 Z= 0.263 Chirality : 0.043 0.184 2809 Planarity : 0.003 0.040 2988 Dihedral : 5.378 53.295 2850 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.51 % Allowed : 18.48 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 2103 helix: 2.69 (0.21), residues: 565 sheet: -1.15 (0.19), residues: 677 loop : -0.76 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 103 HIS 0.003 0.001 HIS C 267 PHE 0.024 0.001 PHE E 308 TYR 0.035 0.001 TYR L 49 ARG 0.007 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 7) link_NAG-ASN : angle 1.30444 ( 21) link_ALPHA1-6 : bond 0.00200 ( 2) link_ALPHA1-6 : angle 1.76867 ( 6) link_BETA1-4 : bond 0.00466 ( 9) link_BETA1-4 : angle 1.46163 ( 27) link_ALPHA1-2 : bond 0.00344 ( 3) link_ALPHA1-2 : angle 1.60876 ( 9) link_ALPHA1-3 : bond 0.01356 ( 2) link_ALPHA1-3 : angle 1.13352 ( 6) hydrogen bonds : bond 0.03039 ( 749) hydrogen bonds : angle 4.10647 ( 2325) SS BOND : bond 0.00136 ( 9) SS BOND : angle 1.45282 ( 18) covalent geometry : bond 0.00301 (17862) covalent geometry : angle 0.52616 (24288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 244 time to evaluate : 1.835 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8267 (mt) REVERT: A 294 MET cc_start: 0.7987 (mmm) cc_final: 0.7736 (mmm) REVERT: B 164 ARG cc_start: 0.8121 (ttp-110) cc_final: 0.7884 (ttp80) REVERT: B 308 ASN cc_start: 0.8258 (t0) cc_final: 0.7903 (t0) REVERT: C 321 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7635 (mtt180) REVERT: E 197 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7754 (ttp-110) REVERT: E 223 MET cc_start: 0.8136 (mmm) cc_final: 0.7436 (mmm) REVERT: E 338 PHE cc_start: 0.7185 (t80) cc_final: 0.6909 (t80) REVERT: I 45 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7916 (mtpt) REVERT: I 79 GLN cc_start: 0.8516 (mp10) cc_final: 0.8268 (mp10) REVERT: K 5 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7592 (mm110) outliers start: 66 outliers final: 61 residues processed: 286 average time/residue: 0.2983 time to fit residues: 128.5348 Evaluate side-chains 304 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 241 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.9009 > 50: distance: 61 - 66: 29.315 distance: 66 - 67: 26.212 distance: 67 - 68: 30.874 distance: 67 - 70: 37.935 distance: 68 - 69: 31.261 distance: 68 - 73: 14.585 distance: 70 - 71: 39.329 distance: 73 - 74: 8.045 distance: 74 - 75: 26.891 distance: 75 - 76: 29.483 distance: 75 - 77: 10.363 distance: 77 - 78: 28.453 distance: 78 - 79: 20.806 distance: 78 - 81: 27.468 distance: 79 - 80: 46.582 distance: 79 - 84: 7.006 distance: 81 - 82: 28.263 distance: 81 - 83: 35.865 distance: 84 - 85: 15.461 distance: 85 - 86: 40.846 distance: 86 - 87: 18.938 distance: 86 - 91: 24.657 distance: 88 - 90: 53.830 distance: 91 - 92: 15.814 distance: 92 - 93: 5.236 distance: 92 - 95: 30.607 distance: 93 - 94: 37.873 distance: 93 - 100: 4.440 distance: 95 - 96: 24.667 distance: 96 - 97: 16.684 distance: 97 - 98: 18.704 distance: 98 - 99: 5.856 distance: 100 - 101: 27.213 distance: 101 - 102: 9.341 distance: 101 - 104: 17.860 distance: 102 - 103: 23.362 distance: 102 - 108: 17.747 distance: 104 - 105: 28.560 distance: 104 - 106: 13.024 distance: 105 - 107: 6.798 distance: 108 - 109: 10.187 distance: 109 - 110: 39.075 distance: 109 - 112: 35.064 distance: 110 - 111: 11.782 distance: 110 - 117: 11.555 distance: 112 - 113: 6.002 distance: 113 - 114: 15.873 distance: 114 - 115: 25.989 distance: 114 - 116: 36.178 distance: 118 - 121: 8.845 distance: 121 - 122: 36.056 distance: 122 - 123: 24.302 distance: 122 - 124: 22.669 distance: 125 - 126: 26.829 distance: 125 - 131: 11.869 distance: 126 - 127: 17.061 distance: 126 - 129: 12.619 distance: 127 - 128: 20.319 distance: 127 - 132: 10.185 distance: 130 - 131: 41.380 distance: 132 - 133: 40.011 distance: 133 - 134: 10.121 distance: 133 - 136: 25.451 distance: 134 - 135: 11.540 distance: 134 - 141: 29.645 distance: 136 - 137: 25.638 distance: 138 - 139: 18.291