Starting phenix.real_space_refine on Thu Mar 5 00:03:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3v_22034/03_2026/6x3v_22034.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3v_22034/03_2026/6x3v_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_22034/03_2026/6x3v_22034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3v_22034/03_2026/6x3v_22034.map" model { file = "/net/cci-nas-00/data/ceres_data/6x3v_22034/03_2026/6x3v_22034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3v_22034/03_2026/6x3v_22034.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.93, per 1000 atoms: 0.23 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: 1.68 Conformation dependent library (CDL) restraints added in 782.0 milliseconds 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: 0.51 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: 3.16 Time building geometry restraints manager: 2.18 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.700 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- 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 : 7.44 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (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 ARG 0.002 0.000 ARG B 255 TYR 0.016 0.002 TYR C 299 PHE 0.014 0.001 PHE D 226 TRP 0.009 0.001 TRP A 67 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00567 (17862) covalent geometry : angle 0.65273 (24288) SS BOND : bond 0.00128 ( 9) SS BOND : angle 1.90630 ( 18) hydrogen bonds : bond 0.10740 ( 749) hydrogen bonds : angle 6.18481 ( 2325) 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) 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_NAG-ASN : bond 0.00275 ( 7) link_NAG-ASN : angle 1.70203 ( 21) *********************** 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 : 0.442 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: 0.8325 (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: 0.7716 (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: 0.1572 time to fit residues: 66.0465 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 : 0.624 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.096512 restraints weight = 21664.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098032 restraints weight = 19261.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.099187 restraints weight = 14512.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099620 restraints weight = 12149.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.099749 restraints weight = 11325.601| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17894 Z= 0.157 Angle : 0.561 7.693 24375 Z= 0.286 Chirality : 0.044 0.187 2809 Planarity : 0.004 0.041 2988 Dihedral : 8.818 73.650 2852 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.28 % Allowed : 13.97 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.18), residues: 2103 helix: 1.49 (0.21), residues: 563 sheet: -2.26 (0.18), residues: 690 loop : -1.85 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 50 TYR 0.028 0.001 TYR L 49 PHE 0.013 0.001 PHE B 146 TRP 0.010 0.001 TRP C 67 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00363 (17862) covalent geometry : angle 0.55266 (24288) SS BOND : bond 0.00208 ( 9) SS BOND : angle 1.69763 ( 18) hydrogen bonds : bond 0.03799 ( 749) hydrogen bonds : angle 4.90276 ( 2325) link_ALPHA1-2 : bond 0.00426 ( 3) link_ALPHA1-2 : angle 1.88568 ( 9) link_ALPHA1-3 : bond 0.01319 ( 2) link_ALPHA1-3 : angle 0.97737 ( 6) link_ALPHA1-6 : bond 0.00523 ( 2) link_ALPHA1-6 : angle 1.67171 ( 6) link_BETA1-4 : bond 0.00457 ( 9) link_BETA1-4 : angle 1.93039 ( 27) link_NAG-ASN : bond 0.00223 ( 7) link_NAG-ASN : angle 1.47708 ( 21) *********************** 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 290 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.640 Fit side-chains REVERT: A 304 TYR cc_start: 0.8620 (t80) cc_final: 0.8274 (t80) REVERT: B 308 ASN cc_start: 0.8568 (t0) cc_final: 0.7990 (t0) REVERT: C 265 ASN cc_start: 0.8600 (t0) cc_final: 0.8215 (t0) REVERT: C 321 ARG cc_start: 0.8354 (mtm180) cc_final: 0.7909 (mtt180) REVERT: D 323 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7585 (ttp80) REVERT: E 223 MET cc_start: 0.8070 (mmm) cc_final: 0.7412 (mmm) REVERT: E 327 ARG cc_start: 0.6608 (mtp180) cc_final: 0.6375 (mtp85) REVERT: E 338 PHE cc_start: 0.7241 (t80) cc_final: 0.6988 (t80) REVERT: I 45 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8120 (mtpt) outliers start: 43 outliers final: 31 residues processed: 276 average time/residue: 0.1423 time to fit residues: 58.1080 Evaluate side-chains 262 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 275 ASN 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 77 ILE 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 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 5 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 179 optimal weight: 0.0040 chunk 187 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN B 275 ASN C 267 HIS D 116 ASN L 79 GLN ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.122126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.096875 restraints weight = 21838.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098757 restraints weight = 15744.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.100036 restraints weight = 12726.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100940 restraints weight = 11018.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.101417 restraints weight = 10084.937| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17894 Z= 0.150 Angle : 0.545 10.132 24375 Z= 0.276 Chirality : 0.044 0.183 2809 Planarity : 0.004 0.040 2988 Dihedral : 7.284 64.042 2850 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.29 % Allowed : 14.71 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.18), residues: 2103 helix: 2.00 (0.21), residues: 563 sheet: -1.90 (0.18), residues: 681 loop : -1.54 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 164 TYR 0.031 0.001 TYR L 49 PHE 0.012 0.001 PHE B 146 TRP 0.009 0.001 TRP C 67 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00351 (17862) covalent geometry : angle 0.53636 (24288) SS BOND : bond 0.00309 ( 9) SS BOND : angle 1.94546 ( 18) hydrogen bonds : bond 0.03558 ( 749) hydrogen bonds : angle 4.62104 ( 2325) link_ALPHA1-2 : bond 0.00381 ( 3) link_ALPHA1-2 : angle 1.66526 ( 9) link_ALPHA1-3 : bond 0.01309 ( 2) link_ALPHA1-3 : angle 0.98942 ( 6) link_ALPHA1-6 : bond 0.00384 ( 2) link_ALPHA1-6 : angle 1.65703 ( 6) link_BETA1-4 : bond 0.00469 ( 9) link_BETA1-4 : angle 1.83426 ( 27) link_NAG-ASN : bond 0.00189 ( 7) link_NAG-ASN : angle 1.39980 ( 21) *********************** 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: 62 poor density : 242 time to evaluate : 0.589 Fit side-chains REVERT: A 9 MET cc_start: 0.8210 (tpp) cc_final: 0.7872 (tpp) REVERT: A 304 TYR cc_start: 0.8612 (t80) cc_final: 0.8243 (t80) REVERT: B 308 ASN cc_start: 0.8554 (t0) cc_final: 0.7997 (t0) REVERT: C 59 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8688 (pt) REVERT: C 164 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9248 (tt) REVERT: C 265 ASN cc_start: 0.8610 (t0) cc_final: 0.8295 (t0) REVERT: C 321 ARG cc_start: 0.8322 (mtm180) cc_final: 0.7854 (mtt180) REVERT: D 338 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6994 (mp) REVERT: E 150 GLU cc_start: 0.8185 (tt0) cc_final: 0.7976 (tt0) REVERT: E 197 ARG cc_start: 0.8552 (ttp-110) cc_final: 0.8350 (ttp-110) REVERT: E 223 MET cc_start: 0.8092 (mmm) cc_final: 0.7422 (mmm) REVERT: E 311 LEU cc_start: 0.8655 (tp) cc_final: 0.8452 (tp) REVERT: E 327 ARG cc_start: 0.6633 (mtp180) cc_final: 0.6389 (mtp85) REVERT: E 338 PHE cc_start: 0.7195 (t80) cc_final: 0.6941 (t80) REVERT: I 45 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8048 (mtpt) REVERT: K 5 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7582 (mm110) outliers start: 62 outliers final: 45 residues processed: 282 average time/residue: 0.1331 time to fit residues: 56.0888 Evaluate side-chains 282 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 222 ILE 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 275 ASN Chi-restraints excluded: chain B residue 286 MET 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 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 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 253 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 291 SER 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 56 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 89 optimal weight: 0.0270 chunk 162 optimal weight: 30.0000 chunk 191 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 142 HIS B 242 GLN L 79 GLN ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.091912 restraints weight = 22097.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.094743 restraints weight = 13510.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.096559 restraints weight = 9953.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097697 restraints weight = 8220.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.098442 restraints weight = 7270.123| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17894 Z= 0.253 Angle : 0.615 9.451 24375 Z= 0.312 Chirality : 0.046 0.201 2809 Planarity : 0.004 0.041 2988 Dihedral : 6.760 55.004 2850 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.98 % Allowed : 16.46 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.18), residues: 2103 helix: 2.02 (0.21), residues: 563 sheet: -1.84 (0.19), residues: 681 loop : -1.47 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 221 TYR 0.033 0.002 TYR L 49 PHE 0.015 0.002 PHE B 146 TRP 0.008 0.001 TRP C 67 HIS 0.004 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00603 (17862) covalent geometry : angle 0.60682 (24288) SS BOND : bond 0.00293 ( 9) SS BOND : angle 2.20466 ( 18) hydrogen bonds : bond 0.03981 ( 749) hydrogen bonds : angle 4.65279 ( 2325) link_ALPHA1-2 : bond 0.00420 ( 3) link_ALPHA1-2 : angle 1.88285 ( 9) link_ALPHA1-3 : bond 0.01355 ( 2) link_ALPHA1-3 : angle 1.08011 ( 6) link_ALPHA1-6 : bond 0.00078 ( 2) link_ALPHA1-6 : angle 2.03750 ( 6) link_BETA1-4 : bond 0.00466 ( 9) link_BETA1-4 : angle 1.78283 ( 27) link_NAG-ASN : bond 0.00161 ( 7) link_NAG-ASN : angle 1.52500 ( 21) *********************** 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 333 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 258 time to evaluate : 0.588 Fit side-chains REVERT: A 99 LEU cc_start: 0.9053 (tp) cc_final: 0.8796 (tp) REVERT: A 304 TYR cc_start: 0.8636 (t80) cc_final: 0.8246 (t80) REVERT: B 308 ASN cc_start: 0.8611 (t0) cc_final: 0.8091 (t0) REVERT: C 265 ASN cc_start: 0.8623 (t0) cc_final: 0.8207 (t0) REVERT: C 321 ARG cc_start: 0.8371 (mtm180) cc_final: 0.7915 (mtt180) REVERT: D 338 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7012 (mp) REVERT: E 197 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.8283 (ttp-110) REVERT: E 223 MET cc_start: 0.8214 (mmm) cc_final: 0.7567 (mmm) REVERT: E 338 PHE cc_start: 0.7172 (t80) cc_final: 0.6872 (t80) REVERT: K 5 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7527 (mm110) outliers start: 75 outliers final: 62 residues processed: 308 average time/residue: 0.1321 time to fit residues: 60.8627 Evaluate side-chains 312 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 248 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 ILE 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 118 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 131 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 232 LEU 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 77 ILE Chi-restraints excluded: chain C residue 109 VAL 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 294 MET Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 57 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 233 MET 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 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 352 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 23 optimal weight: 0.2980 chunk 202 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 B 275 ASN L 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.094714 restraints weight = 21810.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.097857 restraints weight = 12718.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099878 restraints weight = 9107.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101162 restraints weight = 7378.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101996 restraints weight = 6463.110| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17894 Z= 0.148 Angle : 0.547 8.951 24375 Z= 0.274 Chirality : 0.043 0.209 2809 Planarity : 0.004 0.040 2988 Dihedral : 6.229 56.588 2850 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.98 % Allowed : 17.74 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.19), residues: 2103 helix: 2.32 (0.21), residues: 563 sheet: -1.67 (0.19), residues: 691 loop : -1.26 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.032 0.001 TYR L 49 PHE 0.018 0.001 PHE E 158 TRP 0.008 0.001 TRP K 103 HIS 0.002 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00345 (17862) covalent geometry : angle 0.53922 (24288) SS BOND : bond 0.00136 ( 9) SS BOND : angle 1.89420 ( 18) hydrogen bonds : bond 0.03491 ( 749) hydrogen bonds : angle 4.44136 ( 2325) link_ALPHA1-2 : bond 0.00365 ( 3) link_ALPHA1-2 : angle 1.63757 ( 9) link_ALPHA1-3 : bond 0.01347 ( 2) link_ALPHA1-3 : angle 0.98718 ( 6) link_ALPHA1-6 : bond 0.00285 ( 2) link_ALPHA1-6 : angle 1.78102 ( 6) link_BETA1-4 : bond 0.00448 ( 9) link_BETA1-4 : angle 1.56199 ( 27) link_NAG-ASN : bond 0.00179 ( 7) link_NAG-ASN : angle 1.45356 ( 21) *********************** 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 332 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 257 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8261 (tpp) cc_final: 0.8053 (tpp) REVERT: A 99 LEU cc_start: 0.8927 (tp) cc_final: 0.8639 (tp) REVERT: A 132 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8491 (p) REVERT: A 304 TYR cc_start: 0.8623 (t80) cc_final: 0.8227 (t80) REVERT: B 308 ASN cc_start: 0.8582 (t0) cc_final: 0.8039 (t0) REVERT: C 164 ILE cc_start: 0.9506 (tt) cc_final: 0.9305 (tt) REVERT: C 265 ASN cc_start: 0.8615 (t0) cc_final: 0.8207 (t0) REVERT: C 321 ARG cc_start: 0.8319 (mtm180) cc_final: 0.7839 (mtt180) REVERT: D 338 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7018 (mp) REVERT: E 197 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.8365 (ttp-110) REVERT: E 223 MET cc_start: 0.8128 (mmm) cc_final: 0.7473 (mmm) REVERT: E 338 PHE cc_start: 0.7205 (t80) cc_final: 0.6936 (t80) REVERT: I 45 LYS cc_start: 0.8525 (mmmt) cc_final: 0.7985 (mtpt) REVERT: I 48 ILE cc_start: 0.9055 (mm) cc_final: 0.8833 (mt) REVERT: K 5 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7530 (mm110) outliers start: 75 outliers final: 61 residues processed: 307 average time/residue: 0.1306 time to fit residues: 60.5519 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 : 0.595 ------------------------------------------------------------------------------- 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 222 ILE 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 107 SER Chi-restraints excluded: chain B residue 118 LEU 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 59 LEU 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 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 269 ARG Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 MET 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 267 THR Chi-restraints excluded: chain D residue 311 THR 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 253 VAL 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 96 CYS Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 34 SER 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 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 35 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 B 275 ASN B 308 ASN L 79 GLN ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.096661 restraints weight = 21606.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.099783 restraints weight = 12563.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.101830 restraints weight = 9013.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.103109 restraints weight = 7292.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103923 restraints weight = 6401.466| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17894 Z= 0.109 Angle : 0.519 8.225 24375 Z= 0.260 Chirality : 0.042 0.176 2809 Planarity : 0.003 0.042 2988 Dihedral : 5.888 59.300 2850 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.14 % Allowed : 18.00 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 2103 helix: 2.51 (0.21), residues: 565 sheet: -1.52 (0.19), residues: 691 loop : -1.08 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 274 TYR 0.033 0.001 TYR L 49 PHE 0.016 0.001 PHE E 158 TRP 0.008 0.001 TRP K 103 HIS 0.003 0.000 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00243 (17862) covalent geometry : angle 0.51243 (24288) SS BOND : bond 0.00350 ( 9) SS BOND : angle 1.63335 ( 18) hydrogen bonds : bond 0.03164 ( 749) hydrogen bonds : angle 4.28033 ( 2325) link_ALPHA1-2 : bond 0.00354 ( 3) link_ALPHA1-2 : angle 1.57350 ( 9) link_ALPHA1-3 : bond 0.01372 ( 2) link_ALPHA1-3 : angle 1.04014 ( 6) link_ALPHA1-6 : bond 0.00350 ( 2) link_ALPHA1-6 : angle 1.72771 ( 6) link_BETA1-4 : bond 0.00438 ( 9) link_BETA1-4 : angle 1.46285 ( 27) link_NAG-ASN : bond 0.00225 ( 7) link_NAG-ASN : angle 1.34589 ( 21) *********************** 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 329 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 251 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8416 (p) REVERT: B 308 ASN cc_start: 0.8415 (t0) cc_final: 0.7984 (t0) REVERT: C 164 ILE cc_start: 0.9479 (tt) cc_final: 0.9259 (tt) REVERT: C 265 ASN cc_start: 0.8553 (t0) cc_final: 0.8329 (t0) REVERT: C 321 ARG cc_start: 0.8273 (mtm180) cc_final: 0.7774 (mtt180) REVERT: D 338 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6976 (mp) REVERT: E 223 MET cc_start: 0.8088 (mmm) cc_final: 0.7407 (mmm) REVERT: E 338 PHE cc_start: 0.7205 (t80) cc_final: 0.6933 (t80) REVERT: I 45 LYS cc_start: 0.8486 (mmmt) cc_final: 0.7963 (mtpt) REVERT: I 79 GLN cc_start: 0.8370 (mp10) cc_final: 0.8169 (mp10) REVERT: K 5 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7546 (mm110) outliers start: 78 outliers final: 57 residues processed: 303 average time/residue: 0.1288 time to fit residues: 58.7489 Evaluate side-chains 300 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 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 255 ILE 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 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 B residue 338 LEU Chi-restraints excluded: chain C residue 53 VAL 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 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 MET 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 267 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 311 THR 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 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 321 VAL 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 I residue 101 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 34 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 107 optimal weight: 0.7980 chunk 73 optimal weight: 0.0870 chunk 195 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.094910 restraints weight = 21884.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098000 restraints weight = 12720.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.099992 restraints weight = 9114.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101240 restraints weight = 7415.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101977 restraints weight = 6499.464| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17894 Z= 0.160 Angle : 0.550 7.915 24375 Z= 0.276 Chirality : 0.044 0.186 2809 Planarity : 0.004 0.040 2988 Dihedral : 5.817 58.307 2850 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.20 % Allowed : 18.53 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 2103 helix: 2.50 (0.21), residues: 563 sheet: -1.46 (0.19), residues: 676 loop : -1.07 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.037 0.001 TYR L 49 PHE 0.014 0.001 PHE E 158 TRP 0.008 0.001 TRP K 103 HIS 0.003 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00379 (17862) covalent geometry : angle 0.54354 (24288) SS BOND : bond 0.00128 ( 9) SS BOND : angle 1.72514 ( 18) hydrogen bonds : bond 0.03352 ( 749) hydrogen bonds : angle 4.31180 ( 2325) link_ALPHA1-2 : bond 0.00321 ( 3) link_ALPHA1-2 : angle 1.68809 ( 9) link_ALPHA1-3 : bond 0.01330 ( 2) link_ALPHA1-3 : angle 1.10592 ( 6) link_ALPHA1-6 : bond 0.00168 ( 2) link_ALPHA1-6 : angle 1.84471 ( 6) link_BETA1-4 : bond 0.00470 ( 9) link_BETA1-4 : angle 1.48779 ( 27) link_NAG-ASN : bond 0.00161 ( 7) link_NAG-ASN : angle 1.39779 ( 21) *********************** 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 328 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 249 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8924 (tp) cc_final: 0.8666 (tp) REVERT: A 145 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8271 (mt) REVERT: B 308 ASN cc_start: 0.8426 (t0) cc_final: 0.8034 (t0) REVERT: C 164 ILE cc_start: 0.9499 (tt) cc_final: 0.9276 (tt) REVERT: C 265 ASN cc_start: 0.8573 (t0) cc_final: 0.8346 (t0) REVERT: C 321 ARG cc_start: 0.8284 (mtm180) cc_final: 0.7772 (mtt180) REVERT: E 223 MET cc_start: 0.8159 (mmm) cc_final: 0.7485 (mmm) REVERT: E 338 PHE cc_start: 0.7191 (t80) cc_final: 0.6917 (t80) REVERT: I 45 LYS cc_start: 0.8465 (mmmt) cc_final: 0.7965 (mtpt) REVERT: I 79 GLN cc_start: 0.8395 (mp10) cc_final: 0.8178 (mp10) REVERT: K 5 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7555 (mm110) REVERT: K 34 MET cc_start: 0.9265 (mmm) cc_final: 0.9012 (tpt) outliers start: 79 outliers final: 66 residues processed: 303 average time/residue: 0.1255 time to fit residues: 57.6549 Evaluate side-chains 314 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 246 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 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 55 ASP Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 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 232 LEU 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 76 VAL 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 294 MET 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 D residue 324 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 293 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 110 GLN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 34 SER 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 178 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.092768 restraints weight = 21995.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.095545 restraints weight = 13486.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.097398 restraints weight = 9961.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098435 restraints weight = 8213.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.099293 restraints weight = 7291.911| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17894 Z= 0.207 Angle : 0.588 7.912 24375 Z= 0.294 Chirality : 0.045 0.193 2809 Planarity : 0.004 0.039 2988 Dihedral : 5.903 57.281 2850 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.20 % Allowed : 18.85 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 2103 helix: 2.40 (0.21), residues: 563 sheet: -1.51 (0.19), residues: 678 loop : -1.09 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 221 TYR 0.036 0.002 TYR L 49 PHE 0.016 0.002 PHE A 306 TRP 0.008 0.001 TRP K 103 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00497 (17862) covalent geometry : angle 0.58048 (24288) SS BOND : bond 0.00144 ( 9) SS BOND : angle 1.89854 ( 18) hydrogen bonds : bond 0.03636 ( 749) hydrogen bonds : angle 4.40111 ( 2325) link_ALPHA1-2 : bond 0.00290 ( 3) link_ALPHA1-2 : angle 1.78674 ( 9) link_ALPHA1-3 : bond 0.01330 ( 2) link_ALPHA1-3 : angle 1.16077 ( 6) link_ALPHA1-6 : bond 0.00111 ( 2) link_ALPHA1-6 : angle 1.95711 ( 6) link_BETA1-4 : bond 0.00509 ( 9) link_BETA1-4 : angle 1.57304 ( 27) link_NAG-ASN : bond 0.00148 ( 7) link_NAG-ASN : angle 1.45706 ( 21) *********************** 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 342 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 263 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8980 (tp) cc_final: 0.8700 (tp) REVERT: A 145 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8278 (mt) REVERT: A 244 TYR cc_start: 0.7783 (p90) cc_final: 0.7519 (p90) REVERT: B 308 ASN cc_start: 0.8442 (t0) cc_final: 0.8064 (t0) REVERT: C 164 ILE cc_start: 0.9453 (tt) cc_final: 0.9222 (tt) REVERT: C 265 ASN cc_start: 0.8586 (t0) cc_final: 0.8203 (t0) REVERT: C 321 ARG cc_start: 0.8301 (mtm180) cc_final: 0.7770 (mtt180) REVERT: D 111 ASN cc_start: 0.9087 (t0) cc_final: 0.8634 (t0) REVERT: D 141 MET cc_start: 0.8291 (mtt) cc_final: 0.8038 (mtt) REVERT: E 223 MET cc_start: 0.8243 (mmm) cc_final: 0.7581 (mmm) REVERT: E 338 PHE cc_start: 0.7177 (t80) cc_final: 0.6879 (t80) REVERT: I 45 LYS cc_start: 0.8448 (mmmt) cc_final: 0.7937 (mtpt) REVERT: I 79 GLN cc_start: 0.8411 (mp10) cc_final: 0.8167 (mp10) REVERT: K 5 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7530 (mm110) outliers start: 79 outliers final: 71 residues processed: 318 average time/residue: 0.1293 time to fit residues: 61.8407 Evaluate side-chains 332 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 259 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 116 ILE 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 222 ILE 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 55 ASP Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 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 232 LEU 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 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 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 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 294 MET 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 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 253 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 293 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 83 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 34 SER 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 2 optimal weight: 3.9990 chunk 114 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 202 optimal weight: 0.3980 chunk 193 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.123627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.102374 restraints weight = 21534.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.102723 restraints weight = 17472.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.102846 restraints weight = 14481.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.102966 restraints weight = 14059.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103021 restraints weight = 13876.143| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17894 Z= 0.119 Angle : 0.534 7.780 24375 Z= 0.266 Chirality : 0.043 0.181 2809 Planarity : 0.003 0.041 2988 Dihedral : 5.627 53.806 2850 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.40 % Allowed : 19.76 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 2103 helix: 2.53 (0.21), residues: 565 sheet: -1.38 (0.19), residues: 676 loop : -0.93 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 54 TYR 0.035 0.001 TYR L 49 PHE 0.018 0.001 PHE E 308 TRP 0.008 0.001 TRP K 103 HIS 0.002 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00272 (17862) covalent geometry : angle 0.52767 (24288) SS BOND : bond 0.00120 ( 9) SS BOND : angle 1.59399 ( 18) hydrogen bonds : bond 0.03217 ( 749) hydrogen bonds : angle 4.25829 ( 2325) link_ALPHA1-2 : bond 0.00344 ( 3) link_ALPHA1-2 : angle 1.58501 ( 9) link_ALPHA1-3 : bond 0.01337 ( 2) link_ALPHA1-3 : angle 1.01431 ( 6) link_ALPHA1-6 : bond 0.00271 ( 2) link_ALPHA1-6 : angle 1.77009 ( 6) link_BETA1-4 : bond 0.00505 ( 9) link_BETA1-4 : angle 1.46787 ( 27) link_NAG-ASN : bond 0.00201 ( 7) link_NAG-ASN : angle 1.30943 ( 21) *********************** 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 318 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 254 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8424 (tpp) cc_final: 0.8044 (tpp) REVERT: A 132 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8439 (p) REVERT: B 308 ASN cc_start: 0.8380 (t0) cc_final: 0.8021 (t0) REVERT: C 321 ARG cc_start: 0.8233 (mtm180) cc_final: 0.7686 (mtt180) REVERT: D 141 MET cc_start: 0.8300 (mtt) cc_final: 0.8063 (mtt) REVERT: D 213 MET cc_start: 0.8435 (mmm) cc_final: 0.7186 (mmm) REVERT: E 223 MET cc_start: 0.8099 (mmm) cc_final: 0.7431 (mmm) REVERT: E 338 PHE cc_start: 0.7300 (t80) cc_final: 0.7024 (t80) REVERT: I 45 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8086 (mtpt) REVERT: I 79 GLN cc_start: 0.8422 (mp10) cc_final: 0.8207 (mp10) outliers start: 64 outliers final: 54 residues processed: 297 average time/residue: 0.1348 time to fit residues: 59.6931 Evaluate side-chains 301 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 255 ILE 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 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 B residue 338 LEU Chi-restraints excluded: chain C residue 53 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 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 MET 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 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 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 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 J residue 115 THR 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 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 198 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 146 optimal weight: 0.0030 chunk 181 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099048 restraints weight = 21495.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100882 restraints weight = 15480.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.102184 restraints weight = 12489.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103001 restraints weight = 10885.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.103627 restraints weight = 9900.631| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17894 Z= 0.106 Angle : 0.534 8.669 24375 Z= 0.264 Chirality : 0.042 0.183 2809 Planarity : 0.003 0.045 2988 Dihedral : 5.472 53.118 2850 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.08 % Allowed : 20.45 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.19), residues: 2103 helix: 2.62 (0.21), residues: 565 sheet: -1.29 (0.19), residues: 675 loop : -0.83 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 54 TYR 0.034 0.001 TYR L 49 PHE 0.021 0.001 PHE C 306 TRP 0.008 0.001 TRP C 67 HIS 0.002 0.000 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00239 (17862) covalent geometry : angle 0.52773 (24288) SS BOND : bond 0.00129 ( 9) SS BOND : angle 1.43909 ( 18) hydrogen bonds : bond 0.03044 ( 749) hydrogen bonds : angle 4.17966 ( 2325) link_ALPHA1-2 : bond 0.00323 ( 3) link_ALPHA1-2 : angle 1.59146 ( 9) link_ALPHA1-3 : bond 0.01310 ( 2) link_ALPHA1-3 : angle 1.05821 ( 6) link_ALPHA1-6 : bond 0.00256 ( 2) link_ALPHA1-6 : angle 1.75567 ( 6) link_BETA1-4 : bond 0.00467 ( 9) link_BETA1-4 : angle 1.45192 ( 27) link_NAG-ASN : bond 0.00216 ( 7) link_NAG-ASN : angle 1.24714 ( 21) ********************** 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 304 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 246 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8364 (p) REVERT: A 145 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8221 (mt) REVERT: B 308 ASN cc_start: 0.8284 (t0) cc_final: 0.7980 (t0) REVERT: C 261 MET cc_start: 0.8308 (mmm) cc_final: 0.7864 (mmm) REVERT: C 321 ARG cc_start: 0.8186 (mtm180) cc_final: 0.7660 (mtt180) REVERT: D 213 MET cc_start: 0.8444 (mmm) cc_final: 0.7120 (mmm) REVERT: E 223 MET cc_start: 0.8102 (mmm) cc_final: 0.7382 (mmm) REVERT: E 338 PHE cc_start: 0.7222 (t80) cc_final: 0.6939 (t80) REVERT: I 45 LYS cc_start: 0.8481 (mmmt) cc_final: 0.7993 (mtpt) REVERT: I 79 GLN cc_start: 0.8493 (mp10) cc_final: 0.8277 (mp10) REVERT: K 34 MET cc_start: 0.9280 (tpt) cc_final: 0.9019 (tpt) outliers start: 58 outliers final: 52 residues processed: 285 average time/residue: 0.1323 time to fit residues: 56.5137 Evaluate side-chains 299 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 245 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 255 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 107 SER 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 B residue 338 LEU Chi-restraints excluded: chain C residue 53 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 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 263 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 MET 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 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 273 VAL Chi-restraints excluded: chain E residue 293 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 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 J residue 115 THR 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 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 142 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS D 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.093275 restraints weight = 22001.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.096012 restraints weight = 13534.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097818 restraints weight = 9984.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.099008 restraints weight = 8267.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.099683 restraints weight = 7294.200| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 17894 Z= 0.178 Angle : 0.578 8.475 24375 Z= 0.286 Chirality : 0.044 0.191 2809 Planarity : 0.004 0.043 2988 Dihedral : 5.589 56.056 2850 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.19 % Allowed : 20.29 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 2103 helix: 2.52 (0.21), residues: 565 sheet: -1.32 (0.19), residues: 675 loop : -0.89 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 54 TYR 0.035 0.001 TYR L 49 PHE 0.022 0.001 PHE C 306 TRP 0.008 0.001 TRP J 108 HIS 0.002 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00428 (17862) covalent geometry : angle 0.57191 (24288) SS BOND : bond 0.00139 ( 9) SS BOND : angle 1.69740 ( 18) hydrogen bonds : bond 0.03360 ( 749) hydrogen bonds : angle 4.27896 ( 2325) link_ALPHA1-2 : bond 0.00301 ( 3) link_ALPHA1-2 : angle 1.75433 ( 9) link_ALPHA1-3 : bond 0.01169 ( 2) link_ALPHA1-3 : angle 1.10174 ( 6) link_ALPHA1-6 : bond 0.00133 ( 2) link_ALPHA1-6 : angle 1.90335 ( 6) link_BETA1-4 : bond 0.00475 ( 9) link_BETA1-4 : angle 1.51436 ( 27) link_NAG-ASN : bond 0.00154 ( 7) link_NAG-ASN : angle 1.30842 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2786.23 seconds wall clock time: 48 minutes 58.39 seconds (2938.39 seconds total)