Starting phenix.real_space_refine on Thu Mar 5 00:29:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3t_22032/03_2026/6x3t_22032.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3t_22032/03_2026/6x3t_22032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x3t_22032/03_2026/6x3t_22032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3t_22032/03_2026/6x3t_22032.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x3t_22032/03_2026/6x3t_22032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3t_22032/03_2026/6x3t_22032.map" } resolution = 2.55 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= 0.006 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 11248 2.51 5 N 2829 2.21 5 O 3241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 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: 17415 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2731 Classifications: {'peptide': 334} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'PFL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'PFL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.06, per 1000 atoms: 0.23 Number of scatterers: 17415 At special positions: 0 Unit cell: (117.99, 151.11, 130.41, 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 3241 8.00 N 2829 7.00 C 11248 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=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.04 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 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=2.04 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: 1.57 Conformation dependent library (CDL) restraints added in 657.8 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: 4018 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 34 sheets defined 32.7% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 239 removed outlier: 4.079A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 246 through 262 removed outlier: 3.579A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.694A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 339 removed outlier: 3.579A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.831A 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 removed outlier: 3.769A pdb=" N PHE B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 removed outlier: 3.617A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.564A pdb=" N SER B 92 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.830A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 251 through 275 Processing helix chain 'B' and resid 284 through 310 Processing helix chain 'B' and resid 314 through 347 removed outlier: 3.954A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.685A pdb=" N ASN B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 246 through 264 removed outlier: 3.998A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 270 removed outlier: 4.092A pdb=" N LEU C 268 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 340 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 87 through 94 removed outlier: 3.513A 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 230 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.787A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 274 Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 345 removed outlier: 3.699A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (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 85 through 88 Processing helix chain 'E' and resid 99 through 106 removed outlier: 3.893A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 3.754A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 5.144A 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 257 Processing helix chain 'E' and resid 261 through 285 Processing helix chain 'E' and resid 294 through 321 Processing helix chain 'E' and resid 324 through 356 removed outlier: 3.897A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.821A pdb=" N LEU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.672A pdb=" N THR J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.574A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.831A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.698A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 199 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A 205 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS A 197 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG A 207 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR A 195 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 209 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 193 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER A 211 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR A 191 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS A 213 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.680A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.235A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N VAL B 180 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.457A 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: 4.442A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLN B 204 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR B 210 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE B 202 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 212 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER B 200 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR B 214 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 198 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS B 216 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN B 196 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS B 218 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.423A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.495A pdb=" N ASP C 101 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA C 135 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.750A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 167 through 171 removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N VAL D 180 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 45 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.730A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.730A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.000A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 179 through 181 removed outlier: 9.048A pdb=" N VAL D 180 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 45 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 167 through 171 removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N VAL D 180 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 45 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.362A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN D 204 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR D 210 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE D 202 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 212 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER D 200 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR D 214 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL D 198 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS D 216 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN D 196 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS D 218 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.737A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU E 150 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER E 116 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.737A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU E 71 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL E 65 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR E 73 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE E 77 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL E 59 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA E 79 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N MET E 57 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR E 81 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR E 55 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N TYR E 83 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE E 53 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS E 184 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N MET E 57 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N SER E 186 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N VAL E 59 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N VAL E 188 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 11.790A pdb=" N SER E 61 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N VAL E 190 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 13.434A pdb=" N GLY E 63 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.543A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY E 218 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.653A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.653A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.697A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.992A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.510A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.510A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.202A pdb=" N LYS K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP K 47 " --> pdb=" O LYS K 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 11 removed outlier: 4.335A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2865 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: 3.35 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3864 1.33 - 1.45: 4357 1.45 - 1.58: 9461 1.58 - 1.70: 0 1.70 - 1.83: 167 Bond restraints: 17849 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE1 ABU A 405 " ideal model delta sigma weight residual 1.247 1.336 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" CD ABU C 405 " pdb=" OE2 ABU C 405 " ideal model delta sigma weight residual 1.250 1.336 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C1 MAN G 7 " pdb=" C2 MAN G 7 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" CD ABU A 405 " pdb=" OE2 ABU A 405 " ideal model delta sigma weight residual 1.250 1.206 0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" C1 PFL D 601 " pdb=" O1 PFL D 601 " ideal model delta sigma weight residual 1.355 1.398 -0.043 2.00e-02 2.50e+03 4.58e+00 ... (remaining 17844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 23600 1.63 - 3.26: 536 3.26 - 4.88: 97 4.88 - 6.51: 35 6.51 - 8.14: 4 Bond angle restraints: 24272 Sorted by residual: angle pdb=" C GLY A 170 " pdb=" N ASP A 171 " pdb=" CA ASP A 171 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.59e+00 angle pdb=" CA TYR C 299 " pdb=" CB TYR C 299 " pdb=" CG TYR C 299 " ideal model delta sigma weight residual 113.90 108.93 4.97 1.80e+00 3.09e-01 7.61e+00 angle pdb=" C GLY C 170 " pdb=" N ASP C 171 " pdb=" CA ASP C 171 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.07e+00 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 109.15 4.75 1.80e+00 3.09e-01 6.97e+00 angle pdb=" C3 MAN G 7 " pdb=" C2 MAN G 7 " pdb=" O2 MAN G 7 " ideal model delta sigma weight residual 111.77 104.29 7.48 3.00e+00 1.11e-01 6.21e+00 ... (remaining 24267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 10235 21.48 - 42.96: 424 42.96 - 64.44: 84 64.44 - 85.91: 45 85.91 - 107.39: 22 Dihedral angle restraints: 10810 sinusoidal: 4556 harmonic: 6254 Sorted by residual: dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA VAL B 64 " pdb=" C VAL B 64 " pdb=" N PHE B 65 " pdb=" CA PHE B 65 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ILE A 47 " pdb=" C ILE A 47 " pdb=" N ASP A 48 " pdb=" CA ASP A 48 " ideal model delta harmonic sigma weight residual -180.00 -155.17 -24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 10807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2189 0.053 - 0.106: 534 0.106 - 0.159: 76 0.159 - 0.212: 2 0.212 - 0.264: 5 Chirality restraints: 2806 Sorted by residual: chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+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 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 208 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2803 not shown) Planarity restraints: 2991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 242 " -0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO E 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 153 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO B 154 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " -0.017 2.00e-02 2.50e+03 1.05e-02 2.19e+00 pdb=" CG TYR A 299 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " -0.004 2.00e-02 2.50e+03 ... (remaining 2988 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 640 2.72 - 3.26: 16781 3.26 - 3.81: 29412 3.81 - 4.35: 37646 4.35 - 4.90: 63131 Nonbonded interactions: 147610 Sorted by model distance: nonbonded pdb=" OG1 THR B 122 " pdb=" OD1 ASP B 124 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASP B 63 " pdb=" OG1 THR B 134 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP D 10 " pdb=" OG1 THR D 12 " model vdw 2.185 3.040 nonbonded pdb=" OG SER L 65 " pdb=" OG1 THR L 72 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP C 101 " pdb=" OG SER C 104 " model vdw 2.219 3.040 ... (remaining 147605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 7 through 173 or (resid 174 and (name N or name CA or name \ C or name O )) or resid 175 through 405)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 16.550 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.005 0.089 17881 Z= 0.215 Angle : 0.674 8.142 24359 Z= 0.351 Chirality : 0.046 0.264 2806 Planarity : 0.004 0.040 2984 Dihedral : 14.711 107.393 6765 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.28 % Allowed : 7.65 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.78 (0.17), residues: 2103 helix: 0.51 (0.20), residues: 582 sheet: -0.37 (0.19), residues: 652 loop : -1.26 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 50 TYR 0.022 0.002 TYR A 299 PHE 0.015 0.002 PHE E 236 TRP 0.015 0.002 TRP K 103 HIS 0.003 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00470 (17849) covalent geometry : angle 0.66155 (24272) SS BOND : bond 0.00575 ( 9) SS BOND : angle 1.16419 ( 18) hydrogen bonds : bond 0.11902 ( 829) hydrogen bonds : angle 6.05350 ( 2865) link_ALPHA1-2 : bond 0.00693 ( 3) link_ALPHA1-2 : angle 1.32115 ( 9) link_ALPHA1-3 : bond 0.00578 ( 2) link_ALPHA1-3 : angle 3.30571 ( 6) link_ALPHA1-6 : bond 0.00433 ( 2) link_ALPHA1-6 : angle 2.13991 ( 6) link_BETA1-4 : bond 0.00228 ( 9) link_BETA1-4 : angle 2.41403 ( 27) link_NAG-ASN : bond 0.00473 ( 7) link_NAG-ASN : angle 2.60647 ( 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 368 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 0.488 Fit side-chains REVERT: A 14 GLU cc_start: 0.7180 (tt0) cc_final: 0.6679 (tp30) REVERT: A 318 ARG cc_start: 0.6230 (mtm110) cc_final: 0.5468 (ppt170) REVERT: A 323 PHE cc_start: 0.6019 (t80) cc_final: 0.5480 (m-80) REVERT: B 24 ASP cc_start: 0.6922 (t0) cc_final: 0.6524 (p0) REVERT: B 141 MET cc_start: 0.8444 (mtt) cc_final: 0.7962 (mtt) REVERT: B 204 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7921 (tp-100) REVERT: B 271 ILE cc_start: 0.7482 (mt) cc_final: 0.7259 (mm) REVERT: B 275 ASN cc_start: 0.5850 (m-40) cc_final: 0.5607 (m-40) REVERT: B 286 MET cc_start: 0.8281 (ttp) cc_final: 0.7824 (ttp) REVERT: B 317 ARG cc_start: 0.6685 (ttt180) cc_final: 0.6373 (ttt-90) REVERT: C 90 GLN cc_start: 0.8109 (mt0) cc_final: 0.7758 (mp10) REVERT: C 182 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6971 (tp30) REVERT: C 227 MET cc_start: 0.7395 (mmt) cc_final: 0.7148 (mmt) REVERT: C 286 MET cc_start: 0.8338 (mtt) cc_final: 0.8056 (mtt) REVERT: C 303 ASN cc_start: 0.8402 (t0) cc_final: 0.8100 (t0) REVERT: C 304 TYR cc_start: 0.8049 (t80) cc_final: 0.7717 (t80) REVERT: D 24 ASP cc_start: 0.7248 (t70) cc_final: 0.6907 (p0) REVERT: D 73 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: D 248 ASN cc_start: 0.6912 (t0) cc_final: 0.6648 (t0) REVERT: D 286 MET cc_start: 0.7738 (ttp) cc_final: 0.7535 (ttm) REVERT: D 320 LYS cc_start: 0.6816 (ttpt) cc_final: 0.6465 (ttmm) REVERT: D 324 LEU cc_start: 0.6874 (mt) cc_final: 0.6659 (mp) REVERT: E 66 ASN cc_start: 0.7678 (t0) cc_final: 0.7468 (t0) REVERT: E 168 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7487 (mt-10) REVERT: E 189 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7356 (mt-10) REVERT: E 236 PHE cc_start: 0.7911 (m-80) cc_final: 0.7645 (m-80) REVERT: I 61 ARG cc_start: 0.6766 (ptt-90) cc_final: 0.6522 (ptt90) REVERT: I 72 THR cc_start: 0.8285 (m) cc_final: 0.8061 (t) REVERT: J 19 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7015 (mttm) REVERT: J 114 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7169 (p) REVERT: L 21 LEU cc_start: 0.7874 (mp) cc_final: 0.7653 (mt) REVERT: L 24 LYS cc_start: 0.8364 (mttt) cc_final: 0.7968 (mttp) REVERT: L 82 ASP cc_start: 0.6323 (m-30) cc_final: 0.5739 (m-30) REVERT: K 25 SER cc_start: 0.7521 (m) cc_final: 0.7045 (t) REVERT: K 61 ASP cc_start: 0.7618 (t0) cc_final: 0.7371 (t0) outliers start: 43 outliers final: 21 residues processed: 358 average time/residue: 0.6585 time to fit residues: 260.1509 Evaluate side-chains 296 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 102 HIS B 190 GLN B 229 GLN C 224 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 258 ASN K 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106281 restraints weight = 21697.124| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.07 r_work: 0.3001 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17881 Z= 0.238 Angle : 0.685 8.579 24359 Z= 0.353 Chirality : 0.047 0.183 2806 Planarity : 0.006 0.062 2984 Dihedral : 10.155 81.504 2868 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.46 % Allowed : 11.90 % Favored : 83.64 % 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: 0.08 (0.18), residues: 2103 helix: 1.43 (0.21), residues: 589 sheet: -0.16 (0.19), residues: 666 loop : -0.64 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 274 TYR 0.036 0.002 TYR A 299 PHE 0.018 0.002 PHE E 236 TRP 0.018 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00546 (17849) covalent geometry : angle 0.67289 (24272) SS BOND : bond 0.00678 ( 9) SS BOND : angle 1.20622 ( 18) hydrogen bonds : bond 0.05191 ( 829) hydrogen bonds : angle 4.90419 ( 2865) link_ALPHA1-2 : bond 0.00852 ( 3) link_ALPHA1-2 : angle 1.19343 ( 9) link_ALPHA1-3 : bond 0.01070 ( 2) link_ALPHA1-3 : angle 2.44413 ( 6) link_ALPHA1-6 : bond 0.00634 ( 2) link_ALPHA1-6 : angle 2.75154 ( 6) link_BETA1-4 : bond 0.00285 ( 9) link_BETA1-4 : angle 2.70848 ( 27) link_NAG-ASN : bond 0.00539 ( 7) link_NAG-ASN : angle 2.53353 ( 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 358 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 274 time to evaluate : 0.732 Fit side-chains REVERT: A 14 GLU cc_start: 0.7911 (tt0) cc_final: 0.7060 (tp30) REVERT: A 21 LYS cc_start: 0.7238 (mttp) cc_final: 0.6829 (mttp) REVERT: A 40 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.7789 (mpt) REVERT: A 86 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7806 (mtm-85) REVERT: A 101 ASP cc_start: 0.8339 (p0) cc_final: 0.7967 (p0) REVERT: A 306 PHE cc_start: 0.5824 (t80) cc_final: 0.5452 (t80) REVERT: A 318 ARG cc_start: 0.6378 (mtm110) cc_final: 0.5505 (ppt170) REVERT: A 323 PHE cc_start: 0.6236 (t80) cc_final: 0.5584 (m-80) REVERT: B 24 ASP cc_start: 0.7454 (t0) cc_final: 0.6761 (p0) REVERT: B 141 MET cc_start: 0.8680 (mtt) cc_final: 0.8234 (mtt) REVERT: B 204 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8371 (tp-100) REVERT: B 271 ILE cc_start: 0.7586 (mt) cc_final: 0.7330 (mm) REVERT: B 275 ASN cc_start: 0.5959 (m-40) cc_final: 0.5691 (m-40) REVERT: B 286 MET cc_start: 0.8853 (ttp) cc_final: 0.8540 (ttp) REVERT: C 90 GLN cc_start: 0.8503 (mt0) cc_final: 0.8102 (mp10) REVERT: C 182 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7104 (tp30) REVERT: C 272 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7010 (mm) REVERT: C 283 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7783 (tpt) REVERT: C 286 MET cc_start: 0.8802 (mtt) cc_final: 0.8599 (mtt) REVERT: C 303 ASN cc_start: 0.8549 (t0) cc_final: 0.8282 (t0) REVERT: C 304 TYR cc_start: 0.8197 (t80) cc_final: 0.7857 (t80) REVERT: D 24 ASP cc_start: 0.7554 (t70) cc_final: 0.6953 (p0) REVERT: D 40 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: D 73 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: D 88 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6873 (p0) REVERT: D 141 MET cc_start: 0.8567 (mtt) cc_final: 0.8313 (mtp) REVERT: D 248 ASN cc_start: 0.7153 (t0) cc_final: 0.6831 (t0) REVERT: D 320 LYS cc_start: 0.7063 (ttpt) cc_final: 0.6638 (ttmm) REVERT: D 324 LEU cc_start: 0.7080 (mt) cc_final: 0.6823 (mp) REVERT: D 331 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7992 (tp) REVERT: E 233 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6076 (ttm) REVERT: E 236 PHE cc_start: 0.8175 (m-80) cc_final: 0.7924 (m-80) REVERT: E 282 ILE cc_start: 0.7896 (mm) cc_final: 0.7663 (OUTLIER) REVERT: E 331 MET cc_start: 0.7018 (ttm) cc_final: 0.6488 (ptp) REVERT: I 61 ARG cc_start: 0.6740 (ptt-90) cc_final: 0.6489 (ptt90) REVERT: I 72 THR cc_start: 0.8508 (m) cc_final: 0.8298 (t) REVERT: J 73 ASP cc_start: 0.7312 (t70) cc_final: 0.7111 (t70) REVERT: J 114 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7197 (p) REVERT: L 18 ARG cc_start: 0.6791 (mtp85) cc_final: 0.6445 (ttm-80) REVERT: L 24 LYS cc_start: 0.8724 (mttt) cc_final: 0.8371 (mttp) REVERT: L 61 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7137 (ptp90) REVERT: L 82 ASP cc_start: 0.6316 (m-30) cc_final: 0.5749 (m-30) REVERT: K 25 SER cc_start: 0.7640 (m) cc_final: 0.7110 (t) REVERT: K 61 ASP cc_start: 0.7950 (t0) cc_final: 0.7690 (t0) REVERT: K 89 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.5724 (pp20) outliers start: 84 outliers final: 44 residues processed: 333 average time/residue: 0.6499 time to fit residues: 239.8722 Evaluate side-chains 322 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 113 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 134 optimal weight: 0.0770 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 190 GLN C 185 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 258 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.133943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108488 restraints weight = 21880.642| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.10 r_work: 0.3040 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17881 Z= 0.136 Angle : 0.578 7.247 24359 Z= 0.297 Chirality : 0.043 0.162 2806 Planarity : 0.004 0.044 2984 Dihedral : 8.555 76.809 2860 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.04 % Allowed : 13.49 % Favored : 82.47 % 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: 0.61 (0.18), residues: 2103 helix: 2.00 (0.22), residues: 593 sheet: 0.12 (0.19), residues: 659 loop : -0.43 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 40 TYR 0.035 0.002 TYR A 299 PHE 0.014 0.002 PHE E 338 TRP 0.012 0.001 TRP K 103 HIS 0.006 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00297 (17849) covalent geometry : angle 0.56682 (24272) SS BOND : bond 0.00335 ( 9) SS BOND : angle 0.66794 ( 18) hydrogen bonds : bond 0.04117 ( 829) hydrogen bonds : angle 4.44833 ( 2865) link_ALPHA1-2 : bond 0.00702 ( 3) link_ALPHA1-2 : angle 1.21904 ( 9) link_ALPHA1-3 : bond 0.00947 ( 2) link_ALPHA1-3 : angle 1.87702 ( 6) link_ALPHA1-6 : bond 0.00515 ( 2) link_ALPHA1-6 : angle 2.04825 ( 6) link_BETA1-4 : bond 0.00285 ( 9) link_BETA1-4 : angle 2.45488 ( 27) link_NAG-ASN : bond 0.00340 ( 7) link_NAG-ASN : angle 2.28941 ( 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 358 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 282 time to evaluate : 0.711 Fit side-chains REVERT: A 14 GLU cc_start: 0.7911 (tt0) cc_final: 0.7054 (tp30) REVERT: A 21 LYS cc_start: 0.7169 (mttp) cc_final: 0.6808 (mttt) REVERT: A 40 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.7648 (mpt) REVERT: A 86 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7710 (mtm-85) REVERT: A 101 ASP cc_start: 0.8259 (p0) cc_final: 0.7858 (p0) REVERT: A 244 TYR cc_start: 0.6598 (p90) cc_final: 0.6339 (p90) REVERT: A 306 PHE cc_start: 0.5748 (t80) cc_final: 0.5490 (t80) REVERT: A 318 ARG cc_start: 0.6371 (mtm110) cc_final: 0.5484 (ppt170) REVERT: A 323 PHE cc_start: 0.6137 (t80) cc_final: 0.5653 (m-80) REVERT: B 24 ASP cc_start: 0.7338 (t0) cc_final: 0.6769 (p0) REVERT: B 141 MET cc_start: 0.8629 (mtt) cc_final: 0.8212 (mtt) REVERT: B 286 MET cc_start: 0.8775 (ttp) cc_final: 0.8473 (ttp) REVERT: C 90 GLN cc_start: 0.8409 (mt0) cc_final: 0.7988 (mp-120) REVERT: C 182 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7123 (tp30) REVERT: C 245 ASP cc_start: 0.6837 (p0) cc_final: 0.6381 (p0) REVERT: C 303 ASN cc_start: 0.8486 (t0) cc_final: 0.8241 (t0) REVERT: C 304 TYR cc_start: 0.8179 (t80) cc_final: 0.7855 (t80) REVERT: D 24 ASP cc_start: 0.7509 (t70) cc_final: 0.6886 (p0) REVERT: D 40 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: D 73 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: D 141 MET cc_start: 0.8488 (mtt) cc_final: 0.8217 (mtp) REVERT: D 248 ASN cc_start: 0.7228 (t0) cc_final: 0.6870 (t0) REVERT: D 320 LYS cc_start: 0.7061 (ttpt) cc_final: 0.6697 (ttmm) REVERT: D 331 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7957 (tp) REVERT: E 236 PHE cc_start: 0.8028 (m-80) cc_final: 0.7817 (m-80) REVERT: E 331 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6470 (ptp) REVERT: J 73 ASP cc_start: 0.7378 (t70) cc_final: 0.7145 (t70) REVERT: L 61 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7014 (ptp90) REVERT: L 82 ASP cc_start: 0.6405 (m-30) cc_final: 0.5947 (m-30) REVERT: K 61 ASP cc_start: 0.8013 (t0) cc_final: 0.7719 (t0) outliers start: 76 outliers final: 42 residues processed: 329 average time/residue: 0.6564 time to fit residues: 239.6265 Evaluate side-chains 320 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 138 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 176 optimal weight: 0.0000 chunk 100 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 187 optimal weight: 6.9990 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN B 190 GLN C 185 GLN C 243 ASN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN E 258 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.133278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107609 restraints weight = 21829.685| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.09 r_work: 0.3028 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17881 Z= 0.166 Angle : 0.603 7.836 24359 Z= 0.309 Chirality : 0.044 0.174 2806 Planarity : 0.005 0.057 2984 Dihedral : 8.012 74.554 2847 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.41 % Allowed : 14.45 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.18), residues: 2103 helix: 2.20 (0.22), residues: 589 sheet: 0.17 (0.19), residues: 662 loop : -0.35 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 50 TYR 0.036 0.002 TYR A 299 PHE 0.016 0.002 PHE E 236 TRP 0.014 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00375 (17849) covalent geometry : angle 0.59124 (24272) SS BOND : bond 0.00452 ( 9) SS BOND : angle 0.92333 ( 18) hydrogen bonds : bond 0.04311 ( 829) hydrogen bonds : angle 4.46455 ( 2865) link_ALPHA1-2 : bond 0.00772 ( 3) link_ALPHA1-2 : angle 1.16082 ( 9) link_ALPHA1-3 : bond 0.01009 ( 2) link_ALPHA1-3 : angle 2.13727 ( 6) link_ALPHA1-6 : bond 0.00448 ( 2) link_ALPHA1-6 : angle 2.30747 ( 6) link_BETA1-4 : bond 0.00243 ( 9) link_BETA1-4 : angle 2.46132 ( 27) link_NAG-ASN : bond 0.00404 ( 7) link_NAG-ASN : angle 2.38800 ( 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 361 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 278 time to evaluate : 0.636 Fit side-chains REVERT: A 14 GLU cc_start: 0.7911 (tt0) cc_final: 0.7057 (tp30) REVERT: A 21 LYS cc_start: 0.7148 (mttp) cc_final: 0.6858 (mttp) REVERT: A 40 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7713 (mpt) REVERT: A 86 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7721 (mtm-85) REVERT: A 101 ASP cc_start: 0.8304 (p0) cc_final: 0.7889 (p0) REVERT: A 244 TYR cc_start: 0.6652 (p90) cc_final: 0.6298 (p90) REVERT: A 306 PHE cc_start: 0.5725 (t80) cc_final: 0.5427 (t80) REVERT: A 318 ARG cc_start: 0.6343 (mtm110) cc_final: 0.5486 (ppt170) REVERT: A 323 PHE cc_start: 0.6127 (t80) cc_final: 0.5611 (m-80) REVERT: B 24 ASP cc_start: 0.7400 (t0) cc_final: 0.6857 (p0) REVERT: B 141 MET cc_start: 0.8627 (mtt) cc_final: 0.8202 (mtt) REVERT: B 286 MET cc_start: 0.8830 (ttp) cc_final: 0.8562 (ttp) REVERT: C 90 GLN cc_start: 0.8401 (mt0) cc_final: 0.7990 (mp-120) REVERT: C 182 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7120 (tp30) REVERT: C 272 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6997 (mm) REVERT: C 303 ASN cc_start: 0.8442 (t0) cc_final: 0.8214 (t0) REVERT: C 304 TYR cc_start: 0.8187 (t80) cc_final: 0.7883 (t80) REVERT: D 24 ASP cc_start: 0.7538 (t70) cc_final: 0.6910 (p0) REVERT: D 40 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: D 73 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: D 248 ASN cc_start: 0.7243 (t0) cc_final: 0.6873 (t0) REVERT: D 320 LYS cc_start: 0.7079 (ttpt) cc_final: 0.6749 (ttmm) REVERT: D 331 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7947 (tp) REVERT: E 233 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6144 (ttm) REVERT: E 236 PHE cc_start: 0.8002 (m-80) cc_final: 0.7793 (m-80) REVERT: E 313 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7714 (tm-30) REVERT: E 331 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6419 (ptp) REVERT: I 61 ARG cc_start: 0.6780 (ptt90) cc_final: 0.6529 (ptt90) REVERT: J 73 ASP cc_start: 0.7312 (t70) cc_final: 0.7105 (t70) REVERT: L 61 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6871 (ptp90) REVERT: L 82 ASP cc_start: 0.6474 (m-30) cc_final: 0.5989 (m-30) REVERT: K 61 ASP cc_start: 0.8022 (t0) cc_final: 0.7736 (t0) outliers start: 83 outliers final: 52 residues processed: 327 average time/residue: 0.6314 time to fit residues: 228.9630 Evaluate side-chains 327 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 267 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 159 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 139 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.133279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107853 restraints weight = 21674.966| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.99 r_work: 0.3036 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17881 Z= 0.181 Angle : 0.614 7.613 24359 Z= 0.315 Chirality : 0.045 0.180 2806 Planarity : 0.005 0.054 2984 Dihedral : 7.968 74.718 2847 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.31 % Allowed : 14.60 % Favored : 80.08 % 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: 0.81 (0.18), residues: 2103 helix: 2.24 (0.22), residues: 589 sheet: 0.20 (0.19), residues: 650 loop : -0.31 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 232 TYR 0.038 0.002 TYR A 299 PHE 0.017 0.002 PHE E 338 TRP 0.015 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00410 (17849) covalent geometry : angle 0.60259 (24272) SS BOND : bond 0.00483 ( 9) SS BOND : angle 1.02957 ( 18) hydrogen bonds : bond 0.04443 ( 829) hydrogen bonds : angle 4.49053 ( 2865) link_ALPHA1-2 : bond 0.00801 ( 3) link_ALPHA1-2 : angle 1.13336 ( 9) link_ALPHA1-3 : bond 0.00945 ( 2) link_ALPHA1-3 : angle 2.25384 ( 6) link_ALPHA1-6 : bond 0.00441 ( 2) link_ALPHA1-6 : angle 2.39046 ( 6) link_BETA1-4 : bond 0.00238 ( 9) link_BETA1-4 : angle 2.43512 ( 27) link_NAG-ASN : bond 0.00439 ( 7) link_NAG-ASN : angle 2.46257 ( 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 374 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 274 time to evaluate : 0.743 Fit side-chains REVERT: A 14 GLU cc_start: 0.7896 (tt0) cc_final: 0.7038 (tp30) REVERT: A 21 LYS cc_start: 0.7203 (mttp) cc_final: 0.6916 (mttp) REVERT: A 40 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.7698 (mpt) REVERT: A 86 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7717 (mtm-85) REVERT: A 101 ASP cc_start: 0.8288 (p0) cc_final: 0.7873 (p0) REVERT: A 244 TYR cc_start: 0.6594 (p90) cc_final: 0.6204 (p90) REVERT: A 306 PHE cc_start: 0.5768 (t80) cc_final: 0.5383 (t80) REVERT: A 318 ARG cc_start: 0.6356 (mtm110) cc_final: 0.5480 (ppt170) REVERT: A 323 PHE cc_start: 0.6034 (t80) cc_final: 0.5624 (m-80) REVERT: B 24 ASP cc_start: 0.7404 (t0) cc_final: 0.6849 (p0) REVERT: B 141 MET cc_start: 0.8611 (mtt) cc_final: 0.8191 (mtt) REVERT: B 286 MET cc_start: 0.8805 (ttp) cc_final: 0.8431 (ttp) REVERT: C 9 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6797 (mtt) REVERT: C 90 GLN cc_start: 0.8394 (mt0) cc_final: 0.7938 (mp10) REVERT: C 182 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7062 (tp30) REVERT: C 272 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7016 (mm) REVERT: C 303 ASN cc_start: 0.8431 (t0) cc_final: 0.8198 (t0) REVERT: C 304 TYR cc_start: 0.8148 (t80) cc_final: 0.7818 (t80) REVERT: D 24 ASP cc_start: 0.7491 (t70) cc_final: 0.6943 (p0) REVERT: D 40 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: D 73 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: D 141 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: D 248 ASN cc_start: 0.7227 (t0) cc_final: 0.6853 (t0) REVERT: D 320 LYS cc_start: 0.7025 (ttpt) cc_final: 0.6695 (ttmm) REVERT: D 331 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7959 (tp) REVERT: E 233 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6136 (ttm) REVERT: E 236 PHE cc_start: 0.8013 (m-80) cc_final: 0.7805 (m-80) REVERT: E 313 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7748 (tm-30) REVERT: E 331 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6398 (ptp) REVERT: J 30 LYS cc_start: 0.7525 (mmtp) cc_final: 0.7269 (mmtm) REVERT: L 61 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6901 (ptp90) REVERT: L 82 ASP cc_start: 0.6479 (m-30) cc_final: 0.6019 (m-30) REVERT: K 11 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6578 (tp) REVERT: K 61 ASP cc_start: 0.8011 (t0) cc_final: 0.7715 (t0) outliers start: 100 outliers final: 61 residues processed: 337 average time/residue: 0.6138 time to fit residues: 230.1444 Evaluate side-chains 342 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 270 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 24 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106785 restraints weight = 21575.749| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.03 r_work: 0.3003 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17881 Z= 0.240 Angle : 0.685 8.591 24359 Z= 0.351 Chirality : 0.048 0.196 2806 Planarity : 0.005 0.066 2984 Dihedral : 8.390 79.084 2847 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.83 % Allowed : 15.88 % Favored : 79.29 % 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: 0.66 (0.18), residues: 2103 helix: 2.06 (0.21), residues: 589 sheet: -0.00 (0.19), residues: 674 loop : -0.24 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 232 TYR 0.042 0.002 TYR A 299 PHE 0.019 0.002 PHE C 306 TRP 0.018 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00554 (17849) covalent geometry : angle 0.67200 (24272) SS BOND : bond 0.00658 ( 9) SS BOND : angle 1.17494 ( 18) hydrogen bonds : bond 0.05007 ( 829) hydrogen bonds : angle 4.70907 ( 2865) link_ALPHA1-2 : bond 0.00881 ( 3) link_ALPHA1-2 : angle 1.08948 ( 9) link_ALPHA1-3 : bond 0.00942 ( 2) link_ALPHA1-3 : angle 2.71246 ( 6) link_ALPHA1-6 : bond 0.00477 ( 2) link_ALPHA1-6 : angle 2.68924 ( 6) link_BETA1-4 : bond 0.00260 ( 9) link_BETA1-4 : angle 2.64138 ( 27) link_NAG-ASN : bond 0.00575 ( 7) link_NAG-ASN : angle 2.65486 ( 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 359 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 268 time to evaluate : 0.674 Fit side-chains REVERT: A 14 GLU cc_start: 0.7893 (tt0) cc_final: 0.6957 (tp30) REVERT: A 21 LYS cc_start: 0.7146 (mttp) cc_final: 0.6802 (mttp) REVERT: A 40 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.7798 (mpt) REVERT: A 86 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7813 (mtm-85) REVERT: A 101 ASP cc_start: 0.8299 (p0) cc_final: 0.7900 (p0) REVERT: A 244 TYR cc_start: 0.6602 (p90) cc_final: 0.6336 (p90) REVERT: A 245 ASP cc_start: 0.7311 (m-30) cc_final: 0.6959 (p0) REVERT: A 306 PHE cc_start: 0.5777 (t80) cc_final: 0.5374 (t80) REVERT: A 318 ARG cc_start: 0.6380 (mtm110) cc_final: 0.5516 (ppt170) REVERT: B 24 ASP cc_start: 0.7404 (t0) cc_final: 0.6817 (p0) REVERT: B 123 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8463 (pt0) REVERT: B 141 MET cc_start: 0.8625 (mtt) cc_final: 0.8177 (mtt) REVERT: B 286 MET cc_start: 0.8837 (ttp) cc_final: 0.8608 (ttp) REVERT: C 9 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6769 (mtt) REVERT: C 90 GLN cc_start: 0.8516 (mt0) cc_final: 0.8046 (mp10) REVERT: C 182 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7072 (tp30) REVERT: C 303 ASN cc_start: 0.8441 (t0) cc_final: 0.8222 (t0) REVERT: C 304 TYR cc_start: 0.8138 (t80) cc_final: 0.7822 (t80) REVERT: D 24 ASP cc_start: 0.7508 (t70) cc_final: 0.6924 (p0) REVERT: D 40 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: D 73 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: D 248 ASN cc_start: 0.7266 (t0) cc_final: 0.6909 (t0) REVERT: D 320 LYS cc_start: 0.7025 (ttpt) cc_final: 0.6703 (ttmm) REVERT: D 331 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7973 (tp) REVERT: E 150 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8248 (pt0) REVERT: E 236 PHE cc_start: 0.8121 (m-80) cc_final: 0.7893 (m-80) REVERT: E 313 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7753 (tm-30) REVERT: E 331 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6393 (ptp) REVERT: J 30 LYS cc_start: 0.7494 (mmtp) cc_final: 0.7245 (mmtm) REVERT: L 82 ASP cc_start: 0.6510 (m-30) cc_final: 0.5968 (m-30) REVERT: K 11 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6605 (tp) REVERT: K 25 SER cc_start: 0.7566 (m) cc_final: 0.6941 (t) REVERT: K 61 ASP cc_start: 0.7896 (t0) cc_final: 0.7567 (t0) outliers start: 91 outliers final: 63 residues processed: 326 average time/residue: 0.6331 time to fit residues: 229.3121 Evaluate side-chains 336 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 264 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 192 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 1 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107097 restraints weight = 21506.611| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.01 r_work: 0.3039 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17881 Z= 0.147 Angle : 0.588 7.497 24359 Z= 0.301 Chirality : 0.044 0.168 2806 Planarity : 0.004 0.047 2984 Dihedral : 7.874 75.414 2847 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.04 % Allowed : 16.68 % Favored : 79.29 % 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: 0.95 (0.18), residues: 2103 helix: 2.33 (0.22), residues: 589 sheet: 0.29 (0.19), residues: 651 loop : -0.23 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 40 TYR 0.038 0.002 TYR A 299 PHE 0.019 0.002 PHE E 338 TRP 0.013 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00327 (17849) covalent geometry : angle 0.57723 (24272) SS BOND : bond 0.00350 ( 9) SS BOND : angle 0.70564 ( 18) hydrogen bonds : bond 0.04118 ( 829) hydrogen bonds : angle 4.36950 ( 2865) link_ALPHA1-2 : bond 0.00759 ( 3) link_ALPHA1-2 : angle 1.20566 ( 9) link_ALPHA1-3 : bond 0.00934 ( 2) link_ALPHA1-3 : angle 1.90359 ( 6) link_ALPHA1-6 : bond 0.00462 ( 2) link_ALPHA1-6 : angle 2.17654 ( 6) link_BETA1-4 : bond 0.00237 ( 9) link_BETA1-4 : angle 2.30459 ( 27) link_NAG-ASN : bond 0.00376 ( 7) link_NAG-ASN : angle 2.39068 ( 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 352 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 276 time to evaluate : 0.655 Fit side-chains REVERT: A 14 GLU cc_start: 0.7802 (tt0) cc_final: 0.6910 (tp30) REVERT: A 21 LYS cc_start: 0.6996 (mttp) cc_final: 0.6671 (mttp) REVERT: A 40 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.7679 (mpt) REVERT: A 86 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7679 (mtm-85) REVERT: A 101 ASP cc_start: 0.8277 (p0) cc_final: 0.7812 (p0) REVERT: A 239 SER cc_start: 0.7760 (OUTLIER) cc_final: 0.7468 (t) REVERT: A 244 TYR cc_start: 0.6615 (p90) cc_final: 0.6321 (p90) REVERT: A 245 ASP cc_start: 0.7227 (m-30) cc_final: 0.6911 (p0) REVERT: A 306 PHE cc_start: 0.5721 (t80) cc_final: 0.5337 (t80) REVERT: A 318 ARG cc_start: 0.6348 (mtm110) cc_final: 0.5454 (ppt170) REVERT: A 323 PHE cc_start: 0.5401 (OUTLIER) cc_final: 0.4542 (t80) REVERT: B 24 ASP cc_start: 0.7383 (t0) cc_final: 0.6809 (p0) REVERT: B 141 MET cc_start: 0.8615 (mtt) cc_final: 0.8129 (mtt) REVERT: B 286 MET cc_start: 0.8791 (ttp) cc_final: 0.8546 (ttp) REVERT: C 9 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6712 (mtt) REVERT: C 90 GLN cc_start: 0.8341 (mt0) cc_final: 0.7887 (mp10) REVERT: C 180 LYS cc_start: 0.7714 (mtmt) cc_final: 0.7356 (mppt) REVERT: C 182 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7026 (tp30) REVERT: C 303 ASN cc_start: 0.8333 (t0) cc_final: 0.8108 (t0) REVERT: C 304 TYR cc_start: 0.8051 (t80) cc_final: 0.7718 (t80) REVERT: D 24 ASP cc_start: 0.7481 (t70) cc_final: 0.6864 (p0) REVERT: D 40 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: D 73 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: D 248 ASN cc_start: 0.7177 (t0) cc_final: 0.6798 (t0) REVERT: D 320 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6657 (ttmm) REVERT: D 331 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7913 (tp) REVERT: E 313 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7795 (tm-30) REVERT: E 331 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6427 (ptp) REVERT: J 30 LYS cc_start: 0.7564 (mmtp) cc_final: 0.7313 (mmtm) REVERT: L 82 ASP cc_start: 0.6387 (m-30) cc_final: 0.5935 (m-30) REVERT: K 11 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6578 (tp) REVERT: K 61 ASP cc_start: 0.7972 (t0) cc_final: 0.7674 (t0) outliers start: 76 outliers final: 53 residues processed: 323 average time/residue: 0.6551 time to fit residues: 234.7660 Evaluate side-chains 333 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104952 restraints weight = 21492.490| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.95 r_work: 0.3005 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17881 Z= 0.254 Angle : 0.697 8.668 24359 Z= 0.357 Chirality : 0.048 0.202 2806 Planarity : 0.006 0.058 2984 Dihedral : 8.304 78.919 2844 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.89 % Allowed : 15.99 % Favored : 79.13 % 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 (0.18), residues: 2103 helix: 2.07 (0.21), residues: 589 sheet: -0.05 (0.19), residues: 692 loop : -0.12 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 232 TYR 0.044 0.002 TYR A 299 PHE 0.020 0.003 PHE E 338 TRP 0.018 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00589 (17849) covalent geometry : angle 0.68415 (24272) SS BOND : bond 0.00697 ( 9) SS BOND : angle 1.20942 ( 18) hydrogen bonds : bond 0.05048 ( 829) hydrogen bonds : angle 4.71307 ( 2865) link_ALPHA1-2 : bond 0.00870 ( 3) link_ALPHA1-2 : angle 1.08730 ( 9) link_ALPHA1-3 : bond 0.00909 ( 2) link_ALPHA1-3 : angle 2.71232 ( 6) link_ALPHA1-6 : bond 0.00459 ( 2) link_ALPHA1-6 : angle 2.76850 ( 6) link_BETA1-4 : bond 0.00279 ( 9) link_BETA1-4 : angle 2.68742 ( 27) link_NAG-ASN : bond 0.00605 ( 7) link_NAG-ASN : angle 2.69060 ( 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 357 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 265 time to evaluate : 0.706 Fit side-chains REVERT: A 14 GLU cc_start: 0.7855 (tt0) cc_final: 0.6928 (tp30) REVERT: A 21 LYS cc_start: 0.7031 (mttp) cc_final: 0.6730 (mttp) REVERT: A 40 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.7813 (mpt) REVERT: A 86 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7785 (mtm-85) REVERT: A 101 ASP cc_start: 0.8340 (p0) cc_final: 0.7915 (p0) REVERT: A 245 ASP cc_start: 0.7294 (m-30) cc_final: 0.6963 (p0) REVERT: A 318 ARG cc_start: 0.6378 (mtm110) cc_final: 0.5519 (ppt170) REVERT: A 323 PHE cc_start: 0.5343 (OUTLIER) cc_final: 0.5035 (t80) REVERT: B 24 ASP cc_start: 0.7419 (t0) cc_final: 0.6819 (p0) REVERT: B 141 MET cc_start: 0.8629 (mtt) cc_final: 0.8220 (mtt) REVERT: B 286 MET cc_start: 0.8876 (ttp) cc_final: 0.8662 (ttp) REVERT: C 9 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6782 (mtt) REVERT: C 90 GLN cc_start: 0.8478 (mt0) cc_final: 0.8002 (mp10) REVERT: C 180 LYS cc_start: 0.7691 (mtmt) cc_final: 0.7383 (mppt) REVERT: C 182 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7037 (tp30) REVERT: C 303 ASN cc_start: 0.8395 (t0) cc_final: 0.8180 (t0) REVERT: C 304 TYR cc_start: 0.8096 (t80) cc_final: 0.7787 (t80) REVERT: D 24 ASP cc_start: 0.7576 (t70) cc_final: 0.6940 (p0) REVERT: D 40 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: D 73 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: D 248 ASN cc_start: 0.7220 (t0) cc_final: 0.6860 (t0) REVERT: D 320 LYS cc_start: 0.6990 (ttpt) cc_final: 0.6666 (ttmm) REVERT: D 331 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7956 (tp) REVERT: E 331 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6416 (ptp) REVERT: J 30 LYS cc_start: 0.7505 (mmtp) cc_final: 0.7250 (mmtm) REVERT: L 82 ASP cc_start: 0.6514 (m-30) cc_final: 0.6051 (m-30) REVERT: K 11 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6617 (tp) REVERT: K 61 ASP cc_start: 0.7883 (t0) cc_final: 0.7552 (t0) outliers start: 92 outliers final: 63 residues processed: 322 average time/residue: 0.6513 time to fit residues: 232.4138 Evaluate side-chains 332 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 261 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 35 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 134 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108709 restraints weight = 21531.175| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.02 r_work: 0.3067 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17881 Z= 0.122 Angle : 0.568 9.550 24359 Z= 0.290 Chirality : 0.043 0.157 2806 Planarity : 0.004 0.049 2984 Dihedral : 7.457 72.021 2844 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.45 % Allowed : 17.37 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.06 (0.18), residues: 2103 helix: 2.43 (0.21), residues: 591 sheet: 0.36 (0.19), residues: 637 loop : -0.16 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 40 TYR 0.036 0.001 TYR A 299 PHE 0.021 0.001 PHE E 338 TRP 0.011 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00266 (17849) covalent geometry : angle 0.55870 (24272) SS BOND : bond 0.00233 ( 9) SS BOND : angle 0.49613 ( 18) hydrogen bonds : bond 0.03728 ( 829) hydrogen bonds : angle 4.19949 ( 2865) link_ALPHA1-2 : bond 0.00680 ( 3) link_ALPHA1-2 : angle 1.29152 ( 9) link_ALPHA1-3 : bond 0.00934 ( 2) link_ALPHA1-3 : angle 1.56906 ( 6) link_ALPHA1-6 : bond 0.00494 ( 2) link_ALPHA1-6 : angle 1.94429 ( 6) link_BETA1-4 : bond 0.00268 ( 9) link_BETA1-4 : angle 2.14376 ( 27) link_NAG-ASN : bond 0.00339 ( 7) link_NAG-ASN : angle 2.24357 ( 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 343 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 278 time to evaluate : 0.596 Fit side-chains REVERT: A 14 GLU cc_start: 0.7776 (tt0) cc_final: 0.6907 (tp30) REVERT: A 21 LYS cc_start: 0.7158 (mttp) cc_final: 0.6662 (mttp) REVERT: A 40 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7608 (mpt) REVERT: A 70 LYS cc_start: 0.7322 (mppt) cc_final: 0.6965 (mttt) REVERT: A 86 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7638 (mtm-85) REVERT: A 101 ASP cc_start: 0.8316 (p0) cc_final: 0.7854 (p0) REVERT: A 243 ASN cc_start: 0.7182 (p0) cc_final: 0.6693 (p0) REVERT: A 245 ASP cc_start: 0.7064 (m-30) cc_final: 0.6741 (p0) REVERT: A 318 ARG cc_start: 0.6328 (mtm110) cc_final: 0.5481 (ppt170) REVERT: A 323 PHE cc_start: 0.5374 (OUTLIER) cc_final: 0.4490 (t80) REVERT: B 24 ASP cc_start: 0.7405 (t0) cc_final: 0.6822 (p0) REVERT: B 141 MET cc_start: 0.8622 (mtt) cc_final: 0.8118 (mtt) REVERT: B 286 MET cc_start: 0.8771 (ttp) cc_final: 0.8424 (ttp) REVERT: C 90 GLN cc_start: 0.8318 (mt0) cc_final: 0.7870 (mp10) REVERT: C 180 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7374 (mppt) REVERT: C 182 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6922 (tp30) REVERT: C 303 ASN cc_start: 0.8332 (t0) cc_final: 0.8116 (t0) REVERT: D 24 ASP cc_start: 0.7456 (t70) cc_final: 0.6886 (p0) REVERT: D 40 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: D 73 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: D 78 LYS cc_start: 0.7733 (mptt) cc_final: 0.7498 (mmtm) REVERT: D 248 ASN cc_start: 0.7212 (t0) cc_final: 0.6810 (t0) REVERT: D 320 LYS cc_start: 0.6818 (ttpt) cc_final: 0.6524 (ttmm) REVERT: D 331 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7890 (tp) REVERT: E 331 MET cc_start: 0.6976 (ttm) cc_final: 0.6444 (ptp) REVERT: J 30 LYS cc_start: 0.7556 (mmtp) cc_final: 0.7294 (mmtm) REVERT: L 24 LYS cc_start: 0.8683 (mttt) cc_final: 0.8002 (mmmt) REVERT: L 82 ASP cc_start: 0.6374 (m-30) cc_final: 0.5874 (m-30) REVERT: K 61 ASP cc_start: 0.7946 (t0) cc_final: 0.7652 (t0) outliers start: 65 outliers final: 39 residues processed: 316 average time/residue: 0.6419 time to fit residues: 224.6306 Evaluate side-chains 313 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 163 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 85 ASN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 258 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106249 restraints weight = 21350.205| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.98 r_work: 0.3034 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17881 Z= 0.185 Angle : 0.633 10.325 24359 Z= 0.323 Chirality : 0.045 0.183 2806 Planarity : 0.005 0.053 2984 Dihedral : 7.722 72.422 2842 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.03 % Allowed : 18.22 % Favored : 78.76 % 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: 0.95 (0.18), residues: 2103 helix: 2.34 (0.21), residues: 589 sheet: 0.14 (0.19), residues: 680 loop : -0.08 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 40 TYR 0.041 0.002 TYR A 299 PHE 0.031 0.002 PHE A 306 TRP 0.016 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00423 (17849) covalent geometry : angle 0.62139 (24272) SS BOND : bond 0.00471 ( 9) SS BOND : angle 0.85529 ( 18) hydrogen bonds : bond 0.04381 ( 829) hydrogen bonds : angle 4.43199 ( 2865) link_ALPHA1-2 : bond 0.00766 ( 3) link_ALPHA1-2 : angle 1.16948 ( 9) link_ALPHA1-3 : bond 0.00944 ( 2) link_ALPHA1-3 : angle 2.21061 ( 6) link_ALPHA1-6 : bond 0.00391 ( 2) link_ALPHA1-6 : angle 2.37934 ( 6) link_BETA1-4 : bond 0.00245 ( 9) link_BETA1-4 : angle 2.43597 ( 27) link_NAG-ASN : bond 0.00466 ( 7) link_NAG-ASN : angle 2.47668 ( 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 323 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 266 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7819 (tt0) cc_final: 0.6917 (tp30) REVERT: A 40 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.7696 (mpt) REVERT: A 86 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7695 (mtm-85) REVERT: A 101 ASP cc_start: 0.8277 (p0) cc_final: 0.7833 (p0) REVERT: A 318 ARG cc_start: 0.6338 (mtm110) cc_final: 0.5492 (ppt170) REVERT: A 323 PHE cc_start: 0.5320 (OUTLIER) cc_final: 0.4997 (t80) REVERT: B 24 ASP cc_start: 0.7416 (t0) cc_final: 0.6851 (p0) REVERT: B 141 MET cc_start: 0.8603 (mtt) cc_final: 0.8183 (mtt) REVERT: B 286 MET cc_start: 0.8838 (ttp) cc_final: 0.8491 (ttp) REVERT: C 9 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6788 (mtt) REVERT: C 90 GLN cc_start: 0.8388 (mt0) cc_final: 0.7922 (mp10) REVERT: C 180 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7513 (mppt) REVERT: C 182 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6957 (tp30) REVERT: C 303 ASN cc_start: 0.8353 (t0) cc_final: 0.8126 (t0) REVERT: D 24 ASP cc_start: 0.7524 (t70) cc_final: 0.6833 (p0) REVERT: D 73 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: D 78 LYS cc_start: 0.7769 (mptt) cc_final: 0.7520 (mmtm) REVERT: D 248 ASN cc_start: 0.7321 (t0) cc_final: 0.6932 (t0) REVERT: D 320 LYS cc_start: 0.6973 (ttpt) cc_final: 0.6615 (ttmm) REVERT: D 331 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7847 (tp) REVERT: E 313 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7603 (tm-30) REVERT: E 331 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6400 (ptp) REVERT: J 30 LYS cc_start: 0.7561 (mmtp) cc_final: 0.7301 (mmtm) REVERT: J 98 ARG cc_start: 0.8242 (ttp-170) cc_final: 0.7980 (ttp-170) REVERT: L 82 ASP cc_start: 0.6454 (m-30) cc_final: 0.5967 (m-30) REVERT: K 25 SER cc_start: 0.7682 (m) cc_final: 0.7389 (p) REVERT: K 61 ASP cc_start: 0.7854 (t0) cc_final: 0.7551 (t0) outliers start: 57 outliers final: 41 residues processed: 302 average time/residue: 0.6172 time to fit residues: 206.4752 Evaluate side-chains 314 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.0470 chunk 175 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 190 GLN C 85 ASN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109178 restraints weight = 21455.305| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.85 r_work: 0.3072 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17881 Z= 0.126 Angle : 0.574 10.362 24359 Z= 0.292 Chirality : 0.043 0.163 2806 Planarity : 0.004 0.046 2984 Dihedral : 7.298 67.613 2842 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.81 % Allowed : 18.64 % Favored : 78.54 % 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: 1.11 (0.18), residues: 2103 helix: 2.46 (0.21), residues: 593 sheet: 0.37 (0.19), residues: 637 loop : -0.11 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 40 TYR 0.036 0.002 TYR A 299 PHE 0.029 0.002 PHE A 306 TRP 0.012 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00278 (17849) covalent geometry : angle 0.56479 (24272) SS BOND : bond 0.00263 ( 9) SS BOND : angle 0.54642 ( 18) hydrogen bonds : bond 0.03770 ( 829) hydrogen bonds : angle 4.18371 ( 2865) link_ALPHA1-2 : bond 0.00674 ( 3) link_ALPHA1-2 : angle 1.23872 ( 9) link_ALPHA1-3 : bond 0.00997 ( 2) link_ALPHA1-3 : angle 1.68418 ( 6) link_ALPHA1-6 : bond 0.00454 ( 2) link_ALPHA1-6 : angle 2.04066 ( 6) link_BETA1-4 : bond 0.00254 ( 9) link_BETA1-4 : angle 2.16240 ( 27) link_NAG-ASN : bond 0.00342 ( 7) link_NAG-ASN : angle 2.25635 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7520.65 seconds wall clock time: 128 minutes 34.99 seconds (7714.99 seconds total)