Starting phenix.real_space_refine on Sat Jun 21 15:21:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9brz_44846/06_2025/9brz_44846.cif Found real_map, /net/cci-nas-00/data/ceres_data/9brz_44846/06_2025/9brz_44846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9brz_44846/06_2025/9brz_44846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9brz_44846/06_2025/9brz_44846.map" model { file = "/net/cci-nas-00/data/ceres_data/9brz_44846/06_2025/9brz_44846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9brz_44846/06_2025/9brz_44846.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.087 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 172 5.16 5 C 16502 2.51 5 N 4044 2.21 5 O 4486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25204 Number of models: 1 Model: "" Number of chains: 22 Chain: "c" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1642 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "d" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2833 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "f" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 666 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "s" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1671 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 203} Chain: "e" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "a" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 6039 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 31, 'TRANS': 711} Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 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: "C" 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: "D" 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: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 13.96, per 1000 atoms: 0.55 Number of scatterers: 25204 At special positions: 0 Unit cell: (132.209, 166.65, 152.207, 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 172 16.00 O 4486 8.00 N 4044 7.00 C 16502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " NAG A 3 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 1 " - " ASN c 351 " " NAG B 1 " - " ASN c 344 " " NAG C 1 " - " ASN c 290 " " NAG D 1 " - " ASN c 267 " " NAG c 501 " - " ASN c 297 " " NAG c 502 " - " ASN c 255 " " NAG c 503 " - " ASN c 399 " Time building additional restraints: 6.55 Conformation dependent library (CDL) restraints added in 3.1 seconds 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5924 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 9 sheets defined 76.7% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'c' and resid 280 through 283 Processing helix chain 'c' and resid 416 through 442 Processing helix chain 'b' and resid 5 through 30 removed outlier: 4.056A pdb=" N TYR b 9 " --> pdb=" O LEU b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 32 through 36 removed outlier: 3.580A pdb=" N ARG b 35 " --> pdb=" O LEU b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 45 removed outlier: 3.733A pdb=" N THR b 45 " --> pdb=" O PHE b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 82 removed outlier: 4.230A pdb=" N TRP b 50 " --> pdb=" O SER b 46 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE b 59 " --> pdb=" O ILE b 55 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER b 62 " --> pdb=" O ALA b 58 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER b 76 " --> pdb=" O ILE b 72 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL b 82 " --> pdb=" O ILE b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 88 removed outlier: 6.535A pdb=" N ARG b 86 " --> pdb=" O LYS b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 89 through 90 No H-bonds generated for 'chain 'b' and resid 89 through 90' Processing helix chain 'b' and resid 91 through 114 removed outlier: 4.444A pdb=" N ILE b 95 " --> pdb=" O ASN b 91 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL b 101 " --> pdb=" O PHE b 97 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA b 102 " --> pdb=" O CYS b 98 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN b 114 " --> pdb=" O ILE b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 168 removed outlier: 6.050A pdb=" N HIS b 129 " --> pdb=" O LYS b 125 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ARG b 130 " --> pdb=" O ALA b 126 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN b 131 " --> pdb=" O ILE b 127 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA b 168 " --> pdb=" O ALA b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 176 Processing helix chain 'b' and resid 177 through 200 removed outlier: 3.906A pdb=" N GLU b 181 " --> pdb=" O ILE b 177 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE b 187 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY b 188 " --> pdb=" O GLY b 184 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL b 192 " --> pdb=" O GLY b 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 16 removed outlier: 3.516A pdb=" N ASN d 15 " --> pdb=" O PHE d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 27 removed outlier: 3.813A pdb=" N ALA d 27 " --> pdb=" O ARG d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 39 Processing helix chain 'd' and resid 43 through 54 removed outlier: 3.811A pdb=" N SER d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR d 54 " --> pdb=" O HIS d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 89 removed outlier: 3.511A pdb=" N ILE d 72 " --> pdb=" O THR d 68 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 120 removed outlier: 4.291A pdb=" N SER d 105 " --> pdb=" O PHE d 101 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR d 106 " --> pdb=" O ILE d 102 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS d 120 " --> pdb=" O THR d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 131 Processing helix chain 'd' and resid 132 through 136 removed outlier: 3.510A pdb=" N SER d 136 " --> pdb=" O PRO d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 through 146 Processing helix chain 'd' and resid 148 through 157 Processing helix chain 'd' and resid 162 through 167 removed outlier: 3.544A pdb=" N PHE d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 178 through 203 removed outlier: 4.212A pdb=" N ILE d 182 " --> pdb=" O MET d 178 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 229 removed outlier: 3.705A pdb=" N ASP d 208 " --> pdb=" O GLY d 204 " (cutoff:3.500A) Proline residue: d 212 - end of helix Processing helix chain 'd' and resid 235 through 241 Processing helix chain 'd' and resid 249 through 256 removed outlier: 3.722A pdb=" N LEU d 254 " --> pdb=" O TYR d 250 " (cutoff:3.500A) Processing helix chain 'd' and resid 262 through 271 removed outlier: 3.544A pdb=" N VAL d 266 " --> pdb=" O ASP d 262 " (cutoff:3.500A) Processing helix chain 'd' and resid 273 through 283 Processing helix chain 'd' and resid 291 through 307 removed outlier: 3.546A pdb=" N ARG d 295 " --> pdb=" O THR d 291 " (cutoff:3.500A) Processing helix chain 'd' and resid 315 through 341 Processing helix chain 'd' and resid 345 through 349 removed outlier: 4.235A pdb=" N TYR d 349 " --> pdb=" O ILE d 346 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 11 Processing helix chain 'f' and resid 12 through 35 Processing helix chain 'f' and resid 54 through 68 removed outlier: 4.391A pdb=" N ILE f 58 " --> pdb=" O GLY f 54 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 89 removed outlier: 4.339A pdb=" N ALA f 72 " --> pdb=" O ASN f 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA f 73 " --> pdb=" O CYS f 69 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR f 76 " --> pdb=" O ALA f 72 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY f 81 " --> pdb=" O LEU f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 23 removed outlier: 4.303A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL g 16 " --> pdb=" O SER g 12 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA g 19 " --> pdb=" O GLY g 15 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 46 removed outlier: 4.004A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 55 removed outlier: 3.723A pdb=" N ILE g 52 " --> pdb=" O PRO g 49 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N MET g 53 " --> pdb=" O GLU g 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS g 54 " --> pdb=" O LEU g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 79 removed outlier: 3.653A pdb=" N VAL g 60 " --> pdb=" O ILE g 56 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE g 65 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 85 through 122 Processing helix chain 'g' and resid 126 through 152 removed outlier: 4.609A pdb=" N GLY g 130 " --> pdb=" O ARG g 126 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE g 137 " --> pdb=" O LEU g 133 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU g 141 " --> pdb=" O PHE g 137 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY g 142 " --> pdb=" O ALA g 138 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU g 143 " --> pdb=" O GLU g 139 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL g 148 " --> pdb=" O TYR g 144 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA g 149 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 10 No H-bonds generated for 'chain 'h' and resid 8 through 10' Processing helix chain 'h' and resid 11 through 48 removed outlier: 4.336A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET h 23 " --> pdb=" O ALA h 19 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER h 26 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA h 35 " --> pdb=" O ALA h 31 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS h 36 " --> pdb=" O TYR h 32 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER h 37 " --> pdb=" O GLY h 33 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA h 43 " --> pdb=" O THR h 39 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL h 46 " --> pdb=" O ALA h 42 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET h 47 " --> pdb=" O ALA h 43 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG h 48 " --> pdb=" O MET h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 49 through 52 removed outlier: 4.082A pdb=" N ILE h 52 " --> pdb=" O PRO h 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 49 through 52' Processing helix chain 'h' and resid 56 through 79 removed outlier: 3.596A pdb=" N VAL h 60 " --> pdb=" O ILE h 56 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER h 79 " --> pdb=" O LEU h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 124 removed outlier: 3.922A pdb=" N ARG h 119 " --> pdb=" O ASP h 115 " (cutoff:3.500A) Processing helix chain 'h' and resid 126 through 153 removed outlier: 4.370A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU h 133 " --> pdb=" O VAL h 129 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE h 134 " --> pdb=" O GLY h 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU h 141 " --> pdb=" O PHE h 137 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY h 142 " --> pdb=" O ALA h 138 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 46 removed outlier: 4.434A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 47 through 50 removed outlier: 6.731A pdb=" N GLU i 50 " --> pdb=" O MET i 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 47 through 50' Processing helix chain 'i' and resid 51 through 56 removed outlier: 3.601A pdb=" N ILE i 56 " --> pdb=" O ILE i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 56 through 79 removed outlier: 3.587A pdb=" N LEU i 75 " --> pdb=" O VAL i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 122 removed outlier: 3.816A pdb=" N SER i 89 " --> pdb=" O THR i 85 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA i 122 " --> pdb=" O VAL i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 126 removed outlier: 6.734A pdb=" N ARG i 126 " --> pdb=" O GLN i 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 123 through 126' Processing helix chain 'i' and resid 127 through 153 removed outlier: 4.565A pdb=" N LEU i 141 " --> pdb=" O PHE i 137 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY i 142 " --> pdb=" O ALA i 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 48 removed outlier: 4.225A pdb=" N GLY j 15 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA j 43 " --> pdb=" O THR j 39 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET j 47 " --> pdb=" O ALA j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 53 through 55 No H-bonds generated for 'chain 'j' and resid 53 through 55' Processing helix chain 'j' and resid 56 through 79 removed outlier: 4.174A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 85 through 122 Processing helix chain 'j' and resid 126 through 153 removed outlier: 4.265A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE j 132 " --> pdb=" O PHE j 128 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU j 133 " --> pdb=" O VAL j 129 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE j 134 " --> pdb=" O GLY j 130 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA j 149 " --> pdb=" O GLY j 145 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 43 removed outlier: 3.987A pdb=" N PHE k 13 " --> pdb=" O GLU k 9 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER k 26 " --> pdb=" O ALA k 22 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR k 39 " --> pdb=" O ALA k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 55 removed outlier: 4.214A pdb=" N LEU k 51 " --> pdb=" O ARG k 48 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE k 52 " --> pdb=" O PRO k 49 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N MET k 53 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER k 55 " --> pdb=" O ILE k 52 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 80 removed outlier: 4.678A pdb=" N ILE k 65 " --> pdb=" O MET k 61 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA k 66 " --> pdb=" O ALA k 62 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE k 67 " --> pdb=" O GLY k 63 " (cutoff:3.500A) Processing helix chain 'k' and resid 85 through 122 removed outlier: 3.872A pdb=" N ALA k 122 " --> pdb=" O VAL k 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 126 through 154 removed outlier: 4.476A pdb=" N GLY k 130 " --> pdb=" O ARG k 126 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE k 137 " --> pdb=" O LEU k 133 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY k 142 " --> pdb=" O ALA k 138 " (cutoff:3.500A) Processing helix chain 'l' and resid 10 through 45 removed outlier: 4.174A pdb=" N PHE l 14 " --> pdb=" O TYR l 10 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N MET l 23 " --> pdb=" O ALA l 19 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA l 27 " --> pdb=" O MET l 23 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 55 removed outlier: 4.197A pdb=" N LEU l 51 " --> pdb=" O ARG l 48 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N MET l 53 " --> pdb=" O GLU l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 79 removed outlier: 3.691A pdb=" N VAL l 60 " --> pdb=" O ILE l 56 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE l 65 " --> pdb=" O MET l 61 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA l 66 " --> pdb=" O ALA l 62 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 124 Processing helix chain 'l' and resid 126 through 154 removed outlier: 4.696A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 45 removed outlier: 4.450A pdb=" N PHE m 14 " --> pdb=" O TYR m 10 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY m 15 " --> pdb=" O SER m 11 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET m 23 " --> pdb=" O ALA m 19 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 47 No H-bonds generated for 'chain 'm' and resid 46 through 47' Processing helix chain 'm' and resid 48 through 50 No H-bonds generated for 'chain 'm' and resid 48 through 50' Processing helix chain 'm' and resid 51 through 56 Processing helix chain 'm' and resid 56 through 77 Processing helix chain 'm' and resid 85 through 124 removed outlier: 3.713A pdb=" N SER m 89 " --> pdb=" O THR m 85 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG m 119 " --> pdb=" O ASP m 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 127 through 153 removed outlier: 3.537A pdb=" N PHE m 137 " --> pdb=" O LEU m 133 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA m 138 " --> pdb=" O ILE m 134 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY m 142 " --> pdb=" O ALA m 138 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 46 removed outlier: 4.316A pdb=" N PHE n 14 " --> pdb=" O TYR n 10 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER n 26 " --> pdb=" O ALA n 22 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA n 43 " --> pdb=" O THR n 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL n 46 " --> pdb=" O ALA n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 55 removed outlier: 4.406A pdb=" N MET n 53 " --> pdb=" O GLU n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 80 removed outlier: 3.638A pdb=" N GLY n 69 " --> pdb=" O ILE n 65 " (cutoff:3.500A) Processing helix chain 'n' and resid 85 through 122 removed outlier: 3.894A pdb=" N ALA n 122 " --> pdb=" O VAL n 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 123 through 125 No H-bonds generated for 'chain 'n' and resid 123 through 125' Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.634A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU n 141 " --> pdb=" O PHE n 137 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY n 142 " --> pdb=" O ALA n 138 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 45 removed outlier: 4.456A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER o 26 " --> pdb=" O ALA o 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 47 No H-bonds generated for 'chain 'o' and resid 46 through 47' Processing helix chain 'o' and resid 48 through 55 removed outlier: 5.735A pdb=" N MET o 53 " --> pdb=" O GLU o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.856A pdb=" N ILE o 64 " --> pdb=" O VAL o 60 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE o 65 " --> pdb=" O MET o 61 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA o 66 " --> pdb=" O ALA o 62 " (cutoff:3.500A) Processing helix chain 'o' and resid 85 through 124 removed outlier: 3.958A pdb=" N ARG o 119 " --> pdb=" O ASP o 115 " (cutoff:3.500A) Processing helix chain 'o' and resid 126 through 154 removed outlier: 4.713A pdb=" N GLY o 130 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU o 141 " --> pdb=" O PHE o 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY o 142 " --> pdb=" O ALA o 138 " (cutoff:3.500A) Processing helix chain 'p' and resid 600 through 628 Processing helix chain 's' and resid 19 through 24 Processing helix chain 's' and resid 24 through 45 removed outlier: 3.718A pdb=" N PHE s 28 " --> pdb=" O GLU s 24 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA s 42 " --> pdb=" O ILE s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 128 removed outlier: 3.841A pdb=" N ALA s 105 " --> pdb=" O TYR s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 129 through 134 Processing helix chain 's' and resid 138 through 172 Processing helix chain 's' and resid 173 through 181 removed outlier: 3.661A pdb=" N ILE s 177 " --> pdb=" O ASP s 173 " (cutoff:3.500A) Processing helix chain 's' and resid 182 through 186 Processing helix chain 's' and resid 199 through 228 removed outlier: 4.005A pdb=" N GLY s 228 " --> pdb=" O PHE s 224 " (cutoff:3.500A) Processing helix chain 'e' and resid 6 through 28 Proline residue: e 25 - end of helix Processing helix chain 'e' and resid 33 through 60 removed outlier: 3.795A pdb=" N ILE e 37 " --> pdb=" O ASN e 33 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN e 59 " --> pdb=" O ALA e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 80 removed outlier: 4.299A pdb=" N PHE e 78 " --> pdb=" O TRP e 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP e 80 " --> pdb=" O VAL e 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 21 through 33 removed outlier: 3.683A pdb=" N CYS a 25 " --> pdb=" O ALA a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 75 removed outlier: 3.731A pdb=" N VAL a 55 " --> pdb=" O PHE a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 116 removed outlier: 3.961A pdb=" N ASP a 96 " --> pdb=" O ARG a 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE a 104 " --> pdb=" O ASN a 100 " (cutoff:3.500A) Processing helix chain 'a' and resid 116 through 130 removed outlier: 4.202A pdb=" N ARG a 120 " --> pdb=" O GLU a 116 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN a 121 " --> pdb=" O ALA a 117 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU a 127 " --> pdb=" O LEU a 123 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS a 129 " --> pdb=" O LEU a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'a' and resid 179 through 192 Processing helix chain 'a' and resid 226 through 238 removed outlier: 4.306A pdb=" N LYS a 234 " --> pdb=" O LYS a 230 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS a 235 " --> pdb=" O ASN a 231 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE a 236 " --> pdb=" O ARG a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 239 through 241 No H-bonds generated for 'chain 'a' and resid 239 through 241' Processing helix chain 'a' and resid 251 through 274 Processing helix chain 'a' and resid 275 through 285 removed outlier: 4.046A pdb=" N ARG a 279 " --> pdb=" O THR a 275 " (cutoff:3.500A) Processing helix chain 'a' and resid 286 through 289 removed outlier: 4.003A pdb=" N ASN a 289 " --> pdb=" O ALA a 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 286 through 289' Processing helix chain 'a' and resid 290 through 310 Processing helix chain 'a' and resid 314 through 318 removed outlier: 3.594A pdb=" N LYS a 317 " --> pdb=" O VAL a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 326 through 328 No H-bonds generated for 'chain 'a' and resid 326 through 328' Processing helix chain 'a' and resid 329 through 344 removed outlier: 3.798A pdb=" N HIS a 343 " --> pdb=" O ARG a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 371 through 382 Processing helix chain 'a' and resid 391 through 406 removed outlier: 4.290A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) Proline residue: a 400 - end of helix Processing helix chain 'a' and resid 409 through 426 removed outlier: 3.737A pdb=" N ARG a 426 " --> pdb=" O TRP a 422 " (cutoff:3.500A) Processing helix chain 'a' and resid 426 through 432 Processing helix chain 'a' and resid 437 through 446 Processing helix chain 'a' and resid 446 through 465 removed outlier: 3.617A pdb=" N TYR a 459 " --> pdb=" O LEU a 455 " (cutoff:3.500A) Processing helix chain 'a' and resid 481 through 488 Processing helix chain 'a' and resid 493 through 498 Processing helix chain 'a' and resid 520 through 525 removed outlier: 3.817A pdb=" N TRP a 523 " --> pdb=" O ASP a 520 " (cutoff:3.500A) Processing helix chain 'a' and resid 528 through 554 removed outlier: 3.993A pdb=" N PHE a 532 " --> pdb=" O ASN a 528 " (cutoff:3.500A) Processing helix chain 'a' and resid 555 through 564 removed outlier: 3.840A pdb=" N ASN a 559 " --> pdb=" O LEU a 555 " (cutoff:3.500A) Processing helix chain 'a' and resid 566 through 571 removed outlier: 3.856A pdb=" N PHE a 571 " --> pdb=" O LEU a 567 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 598 removed outlier: 3.757A pdb=" N GLU a 576 " --> pdb=" O GLY a 572 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU a 587 " --> pdb=" O LEU a 583 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR a 598 " --> pdb=" O LYS a 594 " (cutoff:3.500A) Processing helix chain 'a' and resid 599 through 603 Processing helix chain 'a' and resid 608 through 619 Processing helix chain 'a' and resid 632 through 667 removed outlier: 3.601A pdb=" N ILE a 636 " --> pdb=" O GLY a 632 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix removed outlier: 5.596A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Proline residue: a 656 - end of helix Processing helix chain 'a' and resid 713 through 738 Processing helix chain 'a' and resid 740 through 760 removed outlier: 4.219A pdb=" N VAL a 760 " --> pdb=" O LEU a 756 " (cutoff:3.500A) Processing helix chain 'a' and resid 761 through 765 Processing helix chain 'a' and resid 771 through 791 removed outlier: 3.896A pdb=" N GLY a 775 " --> pdb=" O ALA a 771 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE a 778 " --> pdb=" O LEU a 774 " (cutoff:3.500A) Processing helix chain 'a' and resid 793 through 813 removed outlier: 3.802A pdb=" N GLU a 810 " --> pdb=" O LEU a 806 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE a 811 " --> pdb=" O HIS a 807 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 252 through 253 removed outlier: 3.748A pdb=" N VAL c 270 " --> pdb=" O LYS c 277 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS c 277 " --> pdb=" O VAL c 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 252 through 253 removed outlier: 7.164A pdb=" N THR c 389 " --> pdb=" O SER c 369 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N SER c 369 " --> pdb=" O THR c 389 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N HIS c 391 " --> pdb=" O TYR c 367 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR c 367 " --> pdb=" O HIS c 391 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER c 362 " --> pdb=" O SER c 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 295 through 297 removed outlier: 5.811A pdb=" N ALA c 313 " --> pdb=" O PRO c 309 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG c 338 " --> pdb=" O ILE c 320 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA c 322 " --> pdb=" O MET c 336 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N MET c 336 " --> pdb=" O ALA c 322 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG c 324 " --> pdb=" O PHE c 334 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE c 334 " --> pdb=" O ARG c 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 295 through 297 removed outlier: 5.811A pdb=" N ALA c 313 " --> pdb=" O PRO c 309 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG c 338 " --> pdb=" O ILE c 320 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA c 322 " --> pdb=" O MET c 336 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N MET c 336 " --> pdb=" O ALA c 322 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG c 324 " --> pdb=" O PHE c 334 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE c 334 " --> pdb=" O ARG c 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 's' and resid 64 through 72 removed outlier: 4.124A pdb=" N LEU s 65 " --> pdb=" O VAL s 55 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL s 55 " --> pdb=" O LEU s 65 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER s 54 " --> pdb=" O GLU s 193 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU s 193 " --> pdb=" O SER s 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 's' and resid 81 through 85 Processing sheet with id=AA7, first strand: chain 'a' and resid 12 through 13 removed outlier: 3.564A pdb=" N GLU a 322 " --> pdb=" O ARG a 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 171 through 175 Processing sheet with id=AA9, first strand: chain 'a' and resid 206 through 207 1883 hydrogen bonds defined for protein. 5493 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: 8.77 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3935 1.28 - 1.42: 6778 1.42 - 1.56: 14722 1.56 - 1.69: 11 1.69 - 1.83: 303 Bond restraints: 25749 Sorted by residual: bond pdb=" CA TYR f 76 " pdb=" C TYR f 76 " ideal model delta sigma weight residual 1.524 1.408 0.115 1.37e-02 5.33e+03 7.05e+01 bond pdb=" C LEU f 78 " pdb=" O LEU f 78 " ideal model delta sigma weight residual 1.236 1.147 0.089 1.16e-02 7.43e+03 5.91e+01 bond pdb=" C TYR f 76 " pdb=" O TYR f 76 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.28e-02 6.10e+03 3.30e+01 bond pdb=" C SER p 635 " pdb=" N ILE p 636 " ideal model delta sigma weight residual 1.335 1.280 0.055 1.26e-02 6.30e+03 1.93e+01 bond pdb=" N SER p 635 " pdb=" CA SER p 635 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.15e-02 7.56e+03 1.73e+01 ... (remaining 25744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 33828 2.36 - 4.72: 919 4.72 - 7.08: 126 7.08 - 9.44: 26 9.44 - 11.80: 4 Bond angle restraints: 34903 Sorted by residual: angle pdb=" N CYS f 69 " pdb=" CA CYS f 69 " pdb=" C CYS f 69 " ideal model delta sigma weight residual 113.02 104.67 8.35 1.20e+00 6.94e-01 4.84e+01 angle pdb=" N LEU f 75 " pdb=" CA LEU f 75 " pdb=" C LEU f 75 " ideal model delta sigma weight residual 111.28 104.08 7.20 1.09e+00 8.42e-01 4.37e+01 angle pdb=" N TYR f 76 " pdb=" CA TYR f 76 " pdb=" C TYR f 76 " ideal model delta sigma weight residual 112.45 103.79 8.66 1.39e+00 5.18e-01 3.88e+01 angle pdb=" N LEU f 75 " pdb=" CA LEU f 75 " pdb=" CB LEU f 75 " ideal model delta sigma weight residual 110.12 117.30 -7.18 1.47e+00 4.63e-01 2.39e+01 angle pdb=" O ASN p 628 " pdb=" C ASN p 628 " pdb=" N MET p 629 " ideal model delta sigma weight residual 122.57 116.11 6.46 1.34e+00 5.57e-01 2.33e+01 ... (remaining 34898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12966 17.91 - 35.82: 1678 35.82 - 53.73: 451 53.73 - 71.64: 49 71.64 - 89.55: 21 Dihedral angle restraints: 15165 sinusoidal: 5862 harmonic: 9303 Sorted by residual: dihedral pdb=" CA SER l 20 " pdb=" C SER l 20 " pdb=" N SER l 21 " pdb=" CA SER l 21 " ideal model delta harmonic sigma weight residual 180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ALA c 397 " pdb=" C ALA c 397 " pdb=" N PHE c 398 " pdb=" CA PHE c 398 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA VAL l 24 " pdb=" C VAL l 24 " pdb=" N PHE l 25 " pdb=" CA PHE l 25 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 15162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3889 0.090 - 0.180: 196 0.180 - 0.270: 8 0.270 - 0.360: 2 0.360 - 0.449: 1 Chirality restraints: 4096 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.95e+00 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.27e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN c 344 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 4093 not shown) Planarity restraints: 4339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE h 13 " 0.029 2.00e-02 2.50e+03 2.31e-02 9.38e+00 pdb=" CG PHE h 13 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE h 13 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE h 13 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE h 13 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE h 13 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE h 13 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE h 13 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.05e+00 pdb=" C PHE h 13 " -0.052 2.00e-02 2.50e+03 pdb=" O PHE h 13 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE h 14 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 255 " -0.028 2.00e-02 2.50e+03 2.50e-02 7.84e+00 pdb=" CG ASN c 255 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN c 255 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN c 255 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG c 502 " -0.029 2.00e-02 2.50e+03 ... (remaining 4336 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 315 2.67 - 3.23: 27293 3.23 - 3.79: 39198 3.79 - 4.34: 49378 4.34 - 4.90: 78983 Nonbonded interactions: 195167 Sorted by model distance: nonbonded pdb=" OE2 GLU c 308 " pdb=" CG PRO c 309 " model vdw 2.117 3.440 nonbonded pdb=" O TYR f 76 " pdb=" C LEU f 77 " model vdw 2.161 3.270 nonbonded pdb=" OE2 GLU c 308 " pdb=" CD PRO c 309 " model vdw 2.221 3.440 nonbonded pdb=" CD GLU c 308 " pdb=" CD PRO c 309 " model vdw 2.347 3.670 nonbonded pdb=" O LEU k 51 " pdb=" CD1 LEU k 51 " model vdw 2.394 3.460 ... (remaining 195162 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 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.030 Extract box with map and model: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 54.270 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 25761 Z= 0.280 Angle : 0.941 11.800 34939 Z= 0.516 Chirality : 0.045 0.449 4096 Planarity : 0.007 0.090 4332 Dihedral : 16.829 89.547 9241 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 3.59 % Allowed : 27.45 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3239 helix: 0.55 (0.11), residues: 2197 sheet: -0.65 (0.50), residues: 116 loop : -1.58 (0.22), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP a 490 HIS 0.010 0.002 HIS s 78 PHE 0.052 0.002 PHE h 13 TYR 0.039 0.002 TYR d 104 ARG 0.007 0.001 ARG n 126 Details of bonding type rmsd link_NAG-ASN : bond 0.02909 ( 7) link_NAG-ASN : angle 6.20093 ( 21) link_BETA1-4 : bond 0.01265 ( 5) link_BETA1-4 : angle 4.34371 ( 15) hydrogen bonds : bond 0.17819 ( 1860) hydrogen bonds : angle 6.86657 ( 5493) covalent geometry : bond 0.00551 (25749) covalent geometry : angle 0.92432 (34903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 728 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 273 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7520 (mmtm) REVERT: c 294 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.7207 (m) REVERT: c 367 TYR cc_start: 0.8520 (m-80) cc_final: 0.8218 (m-80) REVERT: c 392 ASN cc_start: 0.8311 (t0) cc_final: 0.7659 (m110) REVERT: b 7 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8861 (tt) REVERT: b 138 MET cc_start: 0.8239 (ppp) cc_final: 0.7991 (ptt) REVERT: b 169 GLN cc_start: 0.8006 (mp10) cc_final: 0.7558 (mp10) REVERT: d 197 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8878 (ttmm) REVERT: d 308 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7706 (t80) REVERT: f 27 ILE cc_start: 0.7918 (mt) cc_final: 0.7493 (tp) REVERT: f 57 ASN cc_start: 0.8239 (m-40) cc_final: 0.7914 (t0) REVERT: f 58 ILE cc_start: 0.8261 (pt) cc_final: 0.7961 (pt) REVERT: g 23 MET cc_start: 0.8266 (tpp) cc_final: 0.7890 (mmm) REVERT: h 10 TYR cc_start: 0.7141 (p90) cc_final: 0.6933 (p90) REVERT: h 23 MET cc_start: 0.7199 (tpt) cc_final: 0.6812 (tpt) REVERT: h 108 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8171 (t80) REVERT: j 50 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8433 (pm20) REVERT: j 80 LEU cc_start: 0.7880 (mt) cc_final: 0.7183 (mt) REVERT: k 61 MET cc_start: 0.7791 (mmt) cc_final: 0.7525 (mmt) REVERT: m 23 MET cc_start: 0.7787 (tpp) cc_final: 0.7274 (tpt) REVERT: m 53 MET cc_start: 0.7048 (ppp) cc_final: 0.6623 (ppp) REVERT: m 54 LYS cc_start: 0.8635 (mmtp) cc_final: 0.8110 (mmtp) REVERT: m 119 ARG cc_start: 0.8500 (mpp80) cc_final: 0.8190 (mpp80) REVERT: n 51 LEU cc_start: 0.8962 (mm) cc_final: 0.8495 (tp) REVERT: n 155 LYS cc_start: 0.7196 (tttt) cc_final: 0.6465 (ttmt) REVERT: o 70 LEU cc_start: 0.9125 (tp) cc_final: 0.8878 (tt) REVERT: o 119 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.7778 (mtm-85) REVERT: o 131 MET cc_start: 0.8732 (ttp) cc_final: 0.8486 (ttm) REVERT: p 627 TRP cc_start: 0.7241 (t60) cc_final: 0.6192 (t60) REVERT: s 116 PHE cc_start: 0.4941 (t80) cc_final: 0.4679 (t80) REVERT: e 17 TRP cc_start: 0.4002 (m-10) cc_final: 0.3799 (m100) REVERT: e 50 LEU cc_start: 0.7879 (tp) cc_final: 0.7552 (tt) REVERT: a 34 LYS cc_start: 0.8864 (mmtm) cc_final: 0.8411 (mptt) REVERT: a 300 MET cc_start: 0.8225 (ppp) cc_final: 0.7966 (ppp) REVERT: a 311 ASN cc_start: 0.7148 (t0) cc_final: 0.6344 (t0) REVERT: a 338 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8501 (ptp-110) REVERT: a 457 SER cc_start: 0.7963 (m) cc_final: 0.7573 (m) REVERT: a 515 TYR cc_start: 0.5092 (t80) cc_final: 0.4707 (t80) REVERT: a 732 CYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6642 (p) outliers start: 95 outliers final: 73 residues processed: 781 average time/residue: 0.3460 time to fit residues: 433.3950 Evaluate side-chains 720 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 640 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 294 SER Chi-restraints excluded: chain c residue 316 THR Chi-restraints excluded: chain c residue 328 VAL Chi-restraints excluded: chain c residue 334 PHE Chi-restraints excluded: chain c residue 365 CYS Chi-restraints excluded: chain c residue 442 SER Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 96 ILE Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 181 GLU Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain d residue 197 LYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 225 ILE Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain i residue 11 SER Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 53 MET Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 50 GLU Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 131 MET Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain j residue 151 ILE Chi-restraints excluded: chain k residue 20 SER Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain m residue 64 ILE Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 84 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 132 ILE Chi-restraints excluded: chain o residue 141 LEU Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 181 MET Chi-restraints excluded: chain a residue 15 LEU Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 458 ILE Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 605 ASN Chi-restraints excluded: chain a residue 652 LEU Chi-restraints excluded: chain a residue 732 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 274 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 189 optimal weight: 0.0020 chunk 295 optimal weight: 0.0060 overall best weight: 2.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 304 ASN f 56 GLN j 92 GLN n 92 GLN s 18 GLN a 106 ASN a 502 GLN ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.142925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.122414 restraints weight = 58268.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.125030 restraints weight = 30317.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.126698 restraints weight = 18337.576| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25761 Z= 0.197 Angle : 0.727 14.361 34939 Z= 0.376 Chirality : 0.044 0.448 4096 Planarity : 0.004 0.055 4332 Dihedral : 7.407 58.214 3876 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.16 % Allowed : 25.87 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3239 helix: 1.44 (0.11), residues: 2181 sheet: -0.33 (0.51), residues: 117 loop : -1.37 (0.22), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP a 324 HIS 0.005 0.001 HIS d 313 PHE 0.028 0.002 PHE a 800 TYR 0.024 0.002 TYR b 71 ARG 0.012 0.001 ARG p 639 Details of bonding type rmsd link_NAG-ASN : bond 0.01115 ( 7) link_NAG-ASN : angle 5.57433 ( 21) link_BETA1-4 : bond 0.00495 ( 5) link_BETA1-4 : angle 2.92417 ( 15) hydrogen bonds : bond 0.08043 ( 1860) hydrogen bonds : angle 4.93058 ( 5493) covalent geometry : bond 0.00413 (25749) covalent geometry : angle 0.71199 (34903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 684 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 337 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7515 (tm-30) REVERT: c 432 ILE cc_start: 0.9480 (mm) cc_final: 0.9049 (mt) REVERT: b 7 LEU cc_start: 0.9144 (tp) cc_final: 0.8841 (tt) REVERT: b 138 MET cc_start: 0.8249 (ppp) cc_final: 0.7997 (ptp) REVERT: d 75 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8275 (mmmt) REVERT: d 197 LYS cc_start: 0.9274 (ttmm) cc_final: 0.8954 (ttmm) REVERT: d 265 GLN cc_start: 0.9011 (mt0) cc_final: 0.8765 (mt0) REVERT: d 308 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8079 (t80) REVERT: f 57 ASN cc_start: 0.8350 (m-40) cc_final: 0.7912 (t0) REVERT: f 58 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7870 (pt) REVERT: f 67 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.5030 (m-80) REVERT: g 23 MET cc_start: 0.8067 (tpp) cc_final: 0.7649 (tpt) REVERT: h 10 TYR cc_start: 0.7173 (p90) cc_final: 0.6926 (p90) REVERT: h 108 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8263 (t80) REVERT: h 118 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8080 (m) REVERT: i 28 MET cc_start: 0.8786 (mmm) cc_final: 0.8539 (mmt) REVERT: j 41 ILE cc_start: 0.8196 (tp) cc_final: 0.7835 (tp) REVERT: k 61 MET cc_start: 0.7695 (mmt) cc_final: 0.7433 (mmt) REVERT: l 23 MET cc_start: 0.7920 (tpt) cc_final: 0.7671 (tpt) REVERT: l 61 MET cc_start: 0.8666 (tpp) cc_final: 0.8354 (mmm) REVERT: n 51 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8602 (tt) REVERT: n 154 THR cc_start: 0.8199 (p) cc_final: 0.7941 (m) REVERT: n 155 LYS cc_start: 0.6700 (tttt) cc_final: 0.6182 (ttmt) REVERT: o 55 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8811 (t) REVERT: o 70 LEU cc_start: 0.9235 (tp) cc_final: 0.8915 (tt) REVERT: o 126 ARG cc_start: 0.8565 (tpp80) cc_final: 0.8302 (mmm-85) REVERT: p 627 TRP cc_start: 0.7062 (t60) cc_final: 0.6286 (t60) REVERT: s 170 MET cc_start: 0.7222 (tpt) cc_final: 0.6941 (tpt) REVERT: s 183 MET cc_start: 0.7385 (mmm) cc_final: 0.7150 (mmm) REVERT: e 17 TRP cc_start: 0.4572 (m-10) cc_final: 0.4088 (m100) REVERT: a 28 GLU cc_start: 0.8181 (mm-30) cc_final: 0.6939 (pp20) REVERT: a 90 PHE cc_start: 0.6626 (t80) cc_final: 0.6208 (t80) REVERT: a 119 LYS cc_start: 0.9296 (tppp) cc_final: 0.8885 (tppt) REVERT: a 311 ASN cc_start: 0.6702 (t0) cc_final: 0.6409 (t0) REVERT: a 338 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8201 (ttp-110) REVERT: a 457 SER cc_start: 0.8068 (m) cc_final: 0.7712 (m) REVERT: a 479 TRP cc_start: 0.7159 (m100) cc_final: 0.6763 (m100) REVERT: a 515 TYR cc_start: 0.5432 (t80) cc_final: 0.4732 (t80) REVERT: a 732 CYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7058 (p) REVERT: a 749 HIS cc_start: 0.5793 (OUTLIER) cc_final: 0.5441 (m170) outliers start: 163 outliers final: 107 residues processed: 780 average time/residue: 0.3342 time to fit residues: 424.6922 Evaluate side-chains 727 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 611 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 334 PHE Chi-restraints excluded: chain c residue 372 SER Chi-restraints excluded: chain c residue 437 LEU Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 225 ILE Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 313 HIS Chi-restraints excluded: chain d residue 337 CYS Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 32 PHE Chi-restraints excluded: chain f residue 43 ASP Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 67 TYR Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 118 VAL Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 37 SER Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain j residue 151 ILE Chi-restraints excluded: chain k residue 20 SER Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 98 SER Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain m residue 148 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 ILE Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 80 LEU Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 113 VAL Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 51 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 181 MET Chi-restraints excluded: chain s residue 199 THR Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 540 MET Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 617 PHE Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 653 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 732 CYS Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 802 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 135 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 295 optimal weight: 0.0370 chunk 54 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 349 HIS c 392 ASN d 167 GLN ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.142198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121703 restraints weight = 58678.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.124316 restraints weight = 30547.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.125914 restraints weight = 18459.129| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25761 Z= 0.177 Angle : 0.684 14.401 34939 Z= 0.349 Chirality : 0.042 0.442 4096 Planarity : 0.004 0.059 4332 Dihedral : 6.520 59.190 3795 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 8.08 % Allowed : 25.08 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 3239 helix: 1.58 (0.11), residues: 2257 sheet: 0.10 (0.53), residues: 106 loop : -1.60 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 324 HIS 0.006 0.001 HIS s 78 PHE 0.020 0.002 PHE a 800 TYR 0.020 0.002 TYR a 562 ARG 0.010 0.001 ARG a 387 Details of bonding type rmsd link_NAG-ASN : bond 0.01018 ( 7) link_NAG-ASN : angle 5.27883 ( 21) link_BETA1-4 : bond 0.00584 ( 5) link_BETA1-4 : angle 2.65790 ( 15) hydrogen bonds : bond 0.07091 ( 1860) hydrogen bonds : angle 4.60379 ( 5493) covalent geometry : bond 0.00379 (25749) covalent geometry : angle 0.66961 (34903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 653 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 337 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7497 (tm-30) REVERT: c 392 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7508 (m110) REVERT: b 7 LEU cc_start: 0.9069 (tp) cc_final: 0.8775 (tt) REVERT: b 138 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7891 (ptp) REVERT: d 75 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8287 (mmmt) REVERT: d 197 LYS cc_start: 0.9263 (ttmm) cc_final: 0.8868 (ttmm) REVERT: d 215 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7984 (mm-30) REVERT: d 308 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.7973 (t80) REVERT: f 57 ASN cc_start: 0.8287 (m-40) cc_final: 0.7920 (t0) REVERT: f 58 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7948 (pt) REVERT: f 67 TYR cc_start: 0.6393 (OUTLIER) cc_final: 0.5223 (m-80) REVERT: f 82 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7787 (t80) REVERT: f 86 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7866 (mm110) REVERT: f 88 ARG cc_start: 0.8156 (tmm-80) cc_final: 0.7652 (tmm-80) REVERT: g 23 MET cc_start: 0.8038 (tpp) cc_final: 0.7709 (tpt) REVERT: g 36 LYS cc_start: 0.8705 (tptt) cc_final: 0.8473 (tptt) REVERT: g 47 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6517 (ttp) REVERT: h 108 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8336 (t80) REVERT: h 128 PHE cc_start: 0.7959 (t80) cc_final: 0.7545 (t80) REVERT: i 28 MET cc_start: 0.8818 (mmm) cc_final: 0.8526 (mmt) REVERT: i 92 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: i 97 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7664 (mp) REVERT: i 139 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6181 (tm-30) REVERT: j 41 ILE cc_start: 0.8242 (tp) cc_final: 0.7921 (tp) REVERT: j 80 LEU cc_start: 0.7726 (mt) cc_final: 0.7372 (mt) REVERT: k 23 MET cc_start: 0.8497 (tpt) cc_final: 0.7844 (tpp) REVERT: k 51 LEU cc_start: 0.7889 (mm) cc_final: 0.7532 (tp) REVERT: k 87 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7208 (t80) REVERT: m 23 MET cc_start: 0.7619 (tpt) cc_final: 0.7254 (tpp) REVERT: m 48 ARG cc_start: 0.8786 (mmt180) cc_final: 0.8426 (mmt90) REVERT: m 53 MET cc_start: 0.7016 (ppp) cc_final: 0.6655 (ppp) REVERT: m 54 LYS cc_start: 0.8706 (mmtp) cc_final: 0.8060 (mmtp) REVERT: m 87 TYR cc_start: 0.7788 (t80) cc_final: 0.7564 (t80) REVERT: m 92 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7419 (mm-40) REVERT: m 115 ASP cc_start: 0.8169 (t70) cc_final: 0.7665 (t0) REVERT: m 131 MET cc_start: 0.8854 (ttp) cc_final: 0.8204 (ttt) REVERT: m 136 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8362 (tt) REVERT: n 51 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8609 (tp) REVERT: n 131 MET cc_start: 0.8621 (tmm) cc_final: 0.8347 (ttt) REVERT: n 132 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9134 (pt) REVERT: n 155 LYS cc_start: 0.6968 (tttt) cc_final: 0.6454 (ttmt) REVERT: o 55 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.8533 (t) REVERT: o 70 LEU cc_start: 0.9243 (tp) cc_final: 0.8955 (tt) REVERT: o 76 ILE cc_start: 0.9272 (tp) cc_final: 0.8320 (tp) REVERT: o 131 MET cc_start: 0.8238 (ttp) cc_final: 0.7922 (ttm) REVERT: p 627 TRP cc_start: 0.7235 (t60) cc_final: 0.6348 (t60) REVERT: s 170 MET cc_start: 0.7256 (tpt) cc_final: 0.6977 (tpt) REVERT: e 17 TRP cc_start: 0.5042 (m-10) cc_final: 0.4508 (m100) REVERT: a 34 LYS cc_start: 0.8859 (mttp) cc_final: 0.8499 (mttm) REVERT: a 90 PHE cc_start: 0.6741 (t80) cc_final: 0.6337 (t80) REVERT: a 311 ASN cc_start: 0.7018 (t0) cc_final: 0.6796 (t0) REVERT: a 338 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8359 (ptp-110) REVERT: a 515 TYR cc_start: 0.5470 (t80) cc_final: 0.4588 (t80) REVERT: a 749 HIS cc_start: 0.5718 (OUTLIER) cc_final: 0.5367 (m170) outliers start: 214 outliers final: 140 residues processed: 778 average time/residue: 0.3447 time to fit residues: 441.2585 Evaluate side-chains 773 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 616 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 334 PHE Chi-restraints excluded: chain c residue 392 ASN Chi-restraints excluded: chain c residue 437 LEU Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 138 MET Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 279 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 313 HIS Chi-restraints excluded: chain d residue 337 CYS Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 32 PHE Chi-restraints excluded: chain f residue 43 ASP Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 67 TYR Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 47 MET Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 101 LEU Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 37 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 131 MET Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 97 LEU Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 154 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 98 SER Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain m residue 136 ILE Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain m residue 148 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 ILE Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 80 LEU Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 113 VAL Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 51 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 152 LEU Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain s residue 47 TYR Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 181 MET Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 329 ASP Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 450 ILE Chi-restraints excluded: chain a residue 458 ILE Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 540 MET Chi-restraints excluded: chain a residue 553 VAL Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 580 MET Chi-restraints excluded: chain a residue 590 LEU Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 647 CYS Chi-restraints excluded: chain a residue 652 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 802 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 249 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 chunk 78 optimal weight: 0.3980 chunk 169 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 433 GLN a 435 HIS ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.139461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.118674 restraints weight = 59413.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.121317 restraints weight = 30493.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.122937 restraints weight = 18259.779| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25761 Z= 0.189 Angle : 0.705 14.540 34939 Z= 0.359 Chirality : 0.043 0.436 4096 Planarity : 0.004 0.057 4332 Dihedral : 6.285 59.065 3776 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 8.91 % Allowed : 25.08 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3239 helix: 1.62 (0.11), residues: 2261 sheet: 0.08 (0.51), residues: 106 loop : -1.68 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 324 HIS 0.007 0.001 HIS a 435 PHE 0.026 0.002 PHE a 101 TYR 0.032 0.002 TYR k 144 ARG 0.007 0.000 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00931 ( 7) link_NAG-ASN : angle 4.99849 ( 21) link_BETA1-4 : bond 0.00493 ( 5) link_BETA1-4 : angle 2.60771 ( 15) hydrogen bonds : bond 0.06881 ( 1860) hydrogen bonds : angle 4.54796 ( 5493) covalent geometry : bond 0.00418 (25749) covalent geometry : angle 0.69248 (34903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 628 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 337 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7506 (tm-30) REVERT: b 7 LEU cc_start: 0.9144 (tp) cc_final: 0.8838 (tt) REVERT: b 101 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8002 (p) REVERT: d 75 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8317 (mmmt) REVERT: d 87 MET cc_start: 0.9091 (tpp) cc_final: 0.8860 (tpp) REVERT: d 197 LYS cc_start: 0.9280 (ttmm) cc_final: 0.8909 (ttmm) REVERT: d 210 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8168 (mmm) REVERT: d 308 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.7969 (t80) REVERT: f 57 ASN cc_start: 0.8332 (m-40) cc_final: 0.7960 (t0) REVERT: f 58 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7999 (pt) REVERT: f 67 TYR cc_start: 0.6272 (OUTLIER) cc_final: 0.5078 (m-80) REVERT: f 82 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7740 (t80) REVERT: f 86 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7944 (mm-40) REVERT: g 23 MET cc_start: 0.8165 (tpp) cc_final: 0.7420 (tpt) REVERT: g 47 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6709 (ttp) REVERT: h 128 PHE cc_start: 0.7992 (t80) cc_final: 0.7654 (t80) REVERT: i 28 MET cc_start: 0.8921 (mmm) cc_final: 0.8654 (mmt) REVERT: i 51 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7642 (pp) REVERT: i 92 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7884 (mt0) REVERT: i 97 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7802 (mp) REVERT: i 139 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6318 (tm-30) REVERT: j 26 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.7760 (t) REVERT: j 41 ILE cc_start: 0.8345 (tp) cc_final: 0.8013 (tp) REVERT: j 151 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7159 (tp) REVERT: k 23 MET cc_start: 0.8459 (tpt) cc_final: 0.7908 (tpp) REVERT: k 51 LEU cc_start: 0.7963 (mm) cc_final: 0.7516 (tp) REVERT: k 87 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7388 (t80) REVERT: l 23 MET cc_start: 0.7841 (tpt) cc_final: 0.7384 (tpt) REVERT: m 23 MET cc_start: 0.7568 (tpt) cc_final: 0.7236 (tpp) REVERT: m 48 ARG cc_start: 0.8810 (mmt180) cc_final: 0.8505 (mmt90) REVERT: m 53 MET cc_start: 0.6998 (ppp) cc_final: 0.6603 (ppp) REVERT: m 54 LYS cc_start: 0.8698 (mmtp) cc_final: 0.7987 (mmtp) REVERT: m 115 ASP cc_start: 0.8159 (t70) cc_final: 0.7675 (t0) REVERT: m 131 MET cc_start: 0.8809 (ttp) cc_final: 0.8412 (ttt) REVERT: n 51 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8625 (tp) REVERT: n 132 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9072 (pt) REVERT: n 155 LYS cc_start: 0.7225 (tttt) cc_final: 0.6708 (ttmt) REVERT: o 53 MET cc_start: 0.7733 (ppp) cc_final: 0.7532 (ppp) REVERT: o 55 SER cc_start: 0.9345 (OUTLIER) cc_final: 0.8676 (t) REVERT: o 70 LEU cc_start: 0.9267 (tp) cc_final: 0.8984 (tt) REVERT: o 139 GLU cc_start: 0.8692 (tp30) cc_final: 0.8109 (tm-30) REVERT: s 170 MET cc_start: 0.7407 (tpt) cc_final: 0.7154 (tpt) REVERT: s 181 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7070 (tpp) REVERT: e 17 TRP cc_start: 0.5307 (m-10) cc_final: 0.4737 (m100) REVERT: a 90 PHE cc_start: 0.6870 (t80) cc_final: 0.6568 (t80) REVERT: a 125 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8073 (pp) REVERT: a 311 ASN cc_start: 0.7212 (t0) cc_final: 0.6965 (t0) REVERT: a 338 ARG cc_start: 0.8664 (ttm-80) cc_final: 0.8373 (ptp-110) REVERT: a 515 TYR cc_start: 0.5483 (t80) cc_final: 0.4435 (t80) REVERT: a 749 HIS cc_start: 0.5827 (OUTLIER) cc_final: 0.5614 (m170) REVERT: a 800 PHE cc_start: 0.8010 (t80) cc_final: 0.7716 (t80) REVERT: a 827 SER cc_start: 0.8989 (m) cc_final: 0.8716 (p) outliers start: 236 outliers final: 171 residues processed: 759 average time/residue: 0.3260 time to fit residues: 405.7768 Evaluate side-chains 782 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 591 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 328 VAL Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 206 THR Chi-restraints excluded: chain d residue 210 MET Chi-restraints excluded: chain d residue 279 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 313 HIS Chi-restraints excluded: chain d residue 332 VAL Chi-restraints excluded: chain d residue 337 CYS Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 32 PHE Chi-restraints excluded: chain f residue 39 VAL Chi-restraints excluded: chain f residue 43 ASP Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 67 TYR Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain h residue 150 LEU Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 47 MET Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 101 LEU Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 128 PHE Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 37 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 131 MET Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain j residue 151 ILE Chi-restraints excluded: chain k residue 20 SER Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 97 LEU Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 VAL Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 143 LEU Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 154 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 98 SER Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain m residue 148 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 ILE Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 113 VAL Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 51 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 152 LEU Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 608 VAL Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain s residue 33 GLN Chi-restraints excluded: chain s residue 47 TYR Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 181 MET Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 215 VAL Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 329 ASP Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 450 ILE Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 540 MET Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 580 MET Chi-restraints excluded: chain a residue 590 LEU Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 617 PHE Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 647 CYS Chi-restraints excluded: chain a residue 652 LEU Chi-restraints excluded: chain a residue 653 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 719 VAL Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 802 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 78 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 0.0980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 304 ASN ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 334 GLN ** a 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 749 HIS ** 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 = 0.4031 r_free = 0.4031 target = 0.141627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.121124 restraints weight = 58599.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.123808 restraints weight = 29503.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.125472 restraints weight = 17551.107| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25761 Z= 0.161 Angle : 0.678 14.777 34939 Z= 0.342 Chirality : 0.043 0.437 4096 Planarity : 0.004 0.056 4332 Dihedral : 6.033 58.528 3772 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 8.23 % Allowed : 26.17 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.15), residues: 3239 helix: 1.77 (0.11), residues: 2262 sheet: 0.13 (0.52), residues: 106 loop : -1.73 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP a 324 HIS 0.004 0.001 HIS s 78 PHE 0.019 0.001 PHE h 108 TYR 0.026 0.002 TYR b 71 ARG 0.006 0.000 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00799 ( 7) link_NAG-ASN : angle 4.42127 ( 21) link_BETA1-4 : bond 0.00406 ( 5) link_BETA1-4 : angle 2.57048 ( 15) hydrogen bonds : bond 0.06386 ( 1860) hydrogen bonds : angle 4.33257 ( 5493) covalent geometry : bond 0.00346 (25749) covalent geometry : angle 0.66773 (34903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 632 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 337 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7395 (tm-30) REVERT: b 7 LEU cc_start: 0.9081 (tp) cc_final: 0.8783 (tt) REVERT: b 101 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7907 (p) REVERT: d 75 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8299 (mmmt) REVERT: d 87 MET cc_start: 0.8984 (tpp) cc_final: 0.8729 (tpp) REVERT: d 197 LYS cc_start: 0.9270 (ttmm) cc_final: 0.8925 (ttmm) REVERT: d 210 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8261 (mmm) REVERT: d 215 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8029 (mm-30) REVERT: d 308 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7972 (t80) REVERT: f 36 HIS cc_start: 0.5547 (OUTLIER) cc_final: 0.5040 (m-70) REVERT: f 57 ASN cc_start: 0.8306 (m-40) cc_final: 0.7901 (t0) REVERT: f 58 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7912 (pt) REVERT: f 67 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: f 82 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7640 (t80) REVERT: f 88 ARG cc_start: 0.8118 (tmm-80) cc_final: 0.7570 (tmm-80) REVERT: g 23 MET cc_start: 0.7991 (tpp) cc_final: 0.7191 (tpt) REVERT: g 47 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6699 (ttp) REVERT: g 139 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7155 (tm-30) REVERT: h 128 PHE cc_start: 0.7847 (t80) cc_final: 0.7567 (t80) REVERT: i 9 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5525 (pm20) REVERT: i 51 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7703 (pp) REVERT: i 97 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7681 (mp) REVERT: i 139 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: j 41 ILE cc_start: 0.8343 (tp) cc_final: 0.8016 (tp) REVERT: j 151 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7262 (tp) REVERT: k 51 LEU cc_start: 0.7961 (mm) cc_final: 0.7469 (tt) REVERT: k 87 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7142 (t80) REVERT: l 23 MET cc_start: 0.7750 (tpt) cc_final: 0.7341 (tpt) REVERT: l 61 MET cc_start: 0.8914 (mmm) cc_final: 0.8655 (mmm) REVERT: m 23 MET cc_start: 0.7557 (tpt) cc_final: 0.7219 (tpp) REVERT: m 48 ARG cc_start: 0.8811 (mmt180) cc_final: 0.8370 (mmt90) REVERT: m 115 ASP cc_start: 0.8248 (t70) cc_final: 0.7764 (t0) REVERT: m 131 MET cc_start: 0.8716 (ttp) cc_final: 0.7989 (ttm) REVERT: n 51 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8646 (tt) REVERT: n 132 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9048 (pt) REVERT: n 155 LYS cc_start: 0.7161 (tttt) cc_final: 0.6633 (ttmt) REVERT: o 55 SER cc_start: 0.9330 (OUTLIER) cc_final: 0.8796 (t) REVERT: o 70 LEU cc_start: 0.9221 (tp) cc_final: 0.8909 (tt) REVERT: o 139 GLU cc_start: 0.8680 (tp30) cc_final: 0.8204 (tm-30) REVERT: s 181 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6786 (tmm) REVERT: e 17 TRP cc_start: 0.5477 (m-10) cc_final: 0.4992 (m100) REVERT: a 34 LYS cc_start: 0.8784 (mttp) cc_final: 0.8478 (mttp) REVERT: a 90 PHE cc_start: 0.6883 (t80) cc_final: 0.6594 (t80) REVERT: a 338 ARG cc_start: 0.8664 (ttm-80) cc_final: 0.8170 (ttp-110) REVERT: a 479 TRP cc_start: 0.7236 (m100) cc_final: 0.6902 (m100) REVERT: a 515 TYR cc_start: 0.5563 (t80) cc_final: 0.4496 (t80) REVERT: a 740 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7412 (mt) REVERT: a 749 HIS cc_start: 0.5734 (OUTLIER) cc_final: 0.5476 (m170) REVERT: a 819 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8226 (t) REVERT: a 827 SER cc_start: 0.8980 (m) cc_final: 0.8718 (p) outliers start: 218 outliers final: 151 residues processed: 756 average time/residue: 0.3232 time to fit residues: 400.3223 Evaluate side-chains 759 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 587 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 328 VAL Chi-restraints excluded: chain c residue 334 PHE Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 206 THR Chi-restraints excluded: chain d residue 210 MET Chi-restraints excluded: chain d residue 279 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 313 HIS Chi-restraints excluded: chain d residue 320 PHE Chi-restraints excluded: chain d residue 337 CYS Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 18 LEU Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 32 PHE Chi-restraints excluded: chain f residue 36 HIS Chi-restraints excluded: chain f residue 43 ASP Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 67 TYR Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain h residue 150 LEU Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 9 GLU Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 128 PHE Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 37 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 131 MET Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain j residue 151 ILE Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 97 LEU Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 154 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 98 SER Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 ILE Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 113 VAL Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 51 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 152 LEU Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain s residue 33 GLN Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 181 MET Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 329 ASP Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 435 HIS Chi-restraints excluded: chain a residue 450 ILE Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 540 MET Chi-restraints excluded: chain a residue 553 VAL Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 580 MET Chi-restraints excluded: chain a residue 590 LEU Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 617 PHE Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 647 CYS Chi-restraints excluded: chain a residue 652 LEU Chi-restraints excluded: chain a residue 653 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 802 HIS Chi-restraints excluded: chain a residue 819 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 133 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 201 optimal weight: 0.9980 chunk 206 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 0.0000 chunk 220 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 HIS ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 304 ASN s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 59 GLN ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 762 HIS ** a 766 HIS ** 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 = 0.3978 r_free = 0.3978 target = 0.137495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.117192 restraints weight = 59083.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.119688 restraints weight = 30437.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.121233 restraints weight = 18357.443| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25761 Z= 0.214 Angle : 0.728 14.577 34939 Z= 0.374 Chirality : 0.044 0.431 4096 Planarity : 0.004 0.066 4332 Dihedral : 6.078 58.911 3766 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 8.80 % Allowed : 26.44 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 3239 helix: 1.60 (0.11), residues: 2263 sheet: 0.18 (0.52), residues: 106 loop : -1.87 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP a 324 HIS 0.005 0.001 HIS a 762 PHE 0.025 0.002 PHE h 108 TYR 0.040 0.002 TYR s 47 ARG 0.019 0.001 ARG a 387 Details of bonding type rmsd link_NAG-ASN : bond 0.00677 ( 7) link_NAG-ASN : angle 4.35230 ( 21) link_BETA1-4 : bond 0.00582 ( 5) link_BETA1-4 : angle 2.60568 ( 15) hydrogen bonds : bond 0.06915 ( 1860) hydrogen bonds : angle 4.54938 ( 5493) covalent geometry : bond 0.00483 (25749) covalent geometry : angle 0.71865 (34903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 585 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 337 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7522 (tm-30) REVERT: c 382 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8608 (p) REVERT: b 7 LEU cc_start: 0.9122 (tp) cc_final: 0.8827 (tt) REVERT: d 75 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8337 (mmmt) REVERT: d 197 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8915 (ttmm) REVERT: d 215 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8012 (mm-30) REVERT: d 308 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8095 (t80) REVERT: f 36 HIS cc_start: 0.5747 (OUTLIER) cc_final: 0.5117 (m-70) REVERT: f 43 ASP cc_start: 0.6091 (OUTLIER) cc_final: 0.5886 (t70) REVERT: f 57 ASN cc_start: 0.8386 (m-40) cc_final: 0.7965 (t0) REVERT: f 58 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7748 (pt) REVERT: f 67 TYR cc_start: 0.6388 (OUTLIER) cc_final: 0.5182 (m-80) REVERT: f 82 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7662 (t80) REVERT: f 86 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7767 (mm-40) REVERT: g 23 MET cc_start: 0.8157 (tpp) cc_final: 0.7545 (tpt) REVERT: g 47 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6628 (ttp) REVERT: g 139 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7012 (tm-30) REVERT: h 17 MET cc_start: 0.8370 (tpp) cc_final: 0.8122 (mmp) REVERT: i 51 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7385 (pp) REVERT: i 97 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7886 (mp) REVERT: i 139 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6284 (tm-30) REVERT: j 26 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.7885 (t) REVERT: j 41 ILE cc_start: 0.8356 (tp) cc_final: 0.7988 (tp) REVERT: j 151 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7344 (tp) REVERT: k 23 MET cc_start: 0.8383 (tpt) cc_final: 0.8145 (tpt) REVERT: k 51 LEU cc_start: 0.7929 (mm) cc_final: 0.7447 (tp) REVERT: k 87 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7472 (t80) REVERT: l 23 MET cc_start: 0.7913 (tpt) cc_final: 0.7598 (tpt) REVERT: l 28 MET cc_start: 0.8490 (mmm) cc_final: 0.8289 (mmp) REVERT: m 23 MET cc_start: 0.7721 (tpt) cc_final: 0.7362 (tpp) REVERT: m 48 ARG cc_start: 0.8750 (mmt180) cc_final: 0.8522 (mmt90) REVERT: m 54 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8284 (mmtp) REVERT: m 115 ASP cc_start: 0.8267 (t70) cc_final: 0.7693 (t0) REVERT: m 131 MET cc_start: 0.8723 (ttp) cc_final: 0.8447 (ttt) REVERT: n 51 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8624 (tt) REVERT: n 132 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9109 (pt) REVERT: n 155 LYS cc_start: 0.7390 (tttt) cc_final: 0.6959 (ttmt) REVERT: o 55 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.8603 (t) REVERT: o 70 LEU cc_start: 0.9292 (tp) cc_final: 0.9027 (tt) REVERT: o 139 GLU cc_start: 0.8637 (tp30) cc_final: 0.8099 (tm-30) REVERT: s 181 MET cc_start: 0.7662 (tpp) cc_final: 0.6755 (tmm) REVERT: a 34 LYS cc_start: 0.8818 (mttp) cc_final: 0.8521 (mttp) REVERT: a 90 PHE cc_start: 0.7018 (t80) cc_final: 0.6741 (t80) REVERT: a 338 ARG cc_start: 0.8663 (ttm-80) cc_final: 0.8434 (ptp-110) REVERT: a 458 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7744 (tt) REVERT: a 515 TYR cc_start: 0.5637 (t80) cc_final: 0.4338 (t80) REVERT: a 570 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.7060 (m-10) REVERT: a 650 TRP cc_start: 0.6246 (m100) cc_final: 0.5396 (m100) REVERT: a 740 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7761 (mt) REVERT: a 806 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7770 (tp) REVERT: a 827 SER cc_start: 0.9004 (m) cc_final: 0.8756 (p) outliers start: 233 outliers final: 178 residues processed: 725 average time/residue: 0.3326 time to fit residues: 396.4968 Evaluate side-chains 760 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 560 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 328 VAL Chi-restraints excluded: chain c residue 368 VAL Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain b residue 12 ILE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 119 PHE Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain d residue 105 SER Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 197 LYS Chi-restraints excluded: chain d residue 206 THR Chi-restraints excluded: chain d residue 210 MET Chi-restraints excluded: chain d residue 279 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 320 PHE Chi-restraints excluded: chain d residue 332 VAL Chi-restraints excluded: chain d residue 337 CYS Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 18 LEU Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 32 PHE Chi-restraints excluded: chain f residue 36 HIS Chi-restraints excluded: chain f residue 43 ASP Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 67 TYR Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain h residue 150 LEU Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 128 PHE Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 37 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 131 MET Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain j residue 151 ILE Chi-restraints excluded: chain k residue 20 SER Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 VAL Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 154 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 37 SER Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 ILE Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 80 LEU Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 113 VAL Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 51 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 152 LEU Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 608 VAL Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 215 VAL Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 329 ASP Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 435 HIS Chi-restraints excluded: chain a residue 450 ILE Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 458 ILE Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 540 MET Chi-restraints excluded: chain a residue 553 VAL Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 570 TYR Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 580 MET Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 617 PHE Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 647 CYS Chi-restraints excluded: chain a residue 652 LEU Chi-restraints excluded: chain a residue 653 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 719 VAL Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 802 HIS Chi-restraints excluded: chain a residue 806 LEU Chi-restraints excluded: chain a residue 823 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 278 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 277 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 304 ASN s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.143029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.123029 restraints weight = 58402.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.125619 restraints weight = 30369.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.127188 restraints weight = 18255.018| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25761 Z= 0.153 Angle : 0.685 14.337 34939 Z= 0.347 Chirality : 0.042 0.430 4096 Planarity : 0.004 0.055 4332 Dihedral : 5.889 59.199 3763 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.31 % Allowed : 29.38 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3239 helix: 1.77 (0.11), residues: 2269 sheet: 0.27 (0.51), residues: 105 loop : -1.97 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP e 17 HIS 0.015 0.001 HIS a 749 PHE 0.024 0.001 PHE h 108 TYR 0.026 0.001 TYR k 144 ARG 0.009 0.000 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 7) link_NAG-ASN : angle 4.17446 ( 21) link_BETA1-4 : bond 0.00589 ( 5) link_BETA1-4 : angle 2.38355 ( 15) hydrogen bonds : bond 0.06177 ( 1860) hydrogen bonds : angle 4.25702 ( 5493) covalent geometry : bond 0.00318 (25749) covalent geometry : angle 0.67566 (34903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 616 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 7 LEU cc_start: 0.8918 (tp) cc_final: 0.8673 (tt) REVERT: b 101 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8016 (p) REVERT: d 75 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8264 (mmmt) REVERT: d 197 LYS cc_start: 0.9214 (ttmm) cc_final: 0.8909 (ttmm) REVERT: d 215 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7828 (mm-30) REVERT: d 308 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.7835 (t80) REVERT: f 36 HIS cc_start: 0.5733 (OUTLIER) cc_final: 0.5114 (m-70) REVERT: f 57 ASN cc_start: 0.8363 (m-40) cc_final: 0.7991 (t0) REVERT: f 58 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7755 (pt) REVERT: f 82 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7589 (t80) REVERT: f 86 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7777 (mm-40) REVERT: g 23 MET cc_start: 0.7845 (tpp) cc_final: 0.7136 (tpt) REVERT: g 47 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6463 (ttp) REVERT: g 61 MET cc_start: 0.6947 (mtp) cc_final: 0.6643 (mtm) REVERT: g 139 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7104 (tm-30) REVERT: h 36 LYS cc_start: 0.8180 (ptmm) cc_final: 0.7803 (ptmm) REVERT: i 51 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7195 (pp) REVERT: i 97 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7797 (mp) REVERT: i 139 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6188 (tm-30) REVERT: j 26 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.7799 (t) REVERT: j 41 ILE cc_start: 0.8407 (tp) cc_final: 0.8065 (tp) REVERT: k 51 LEU cc_start: 0.7979 (mm) cc_final: 0.7559 (tp) REVERT: k 61 MET cc_start: 0.7865 (mmt) cc_final: 0.7404 (mtp) REVERT: k 87 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7059 (t80) REVERT: l 23 MET cc_start: 0.7666 (tpt) cc_final: 0.7348 (tpt) REVERT: l 28 MET cc_start: 0.8304 (mmm) cc_final: 0.8069 (mmp) REVERT: m 23 MET cc_start: 0.7486 (tpt) cc_final: 0.7156 (tpp) REVERT: m 54 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8158 (mmtp) REVERT: m 115 ASP cc_start: 0.8194 (t70) cc_final: 0.7610 (t0) REVERT: m 131 MET cc_start: 0.8589 (ttp) cc_final: 0.8125 (ttt) REVERT: n 51 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8670 (tt) REVERT: n 132 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9141 (pt) REVERT: n 155 LYS cc_start: 0.7012 (tttt) cc_final: 0.6589 (ttmt) REVERT: o 139 GLU cc_start: 0.8494 (tp30) cc_final: 0.8177 (tm-30) REVERT: s 97 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7715 (tt) REVERT: s 181 MET cc_start: 0.7679 (tpp) cc_final: 0.6744 (tmm) REVERT: e 17 TRP cc_start: 0.5815 (OUTLIER) cc_final: 0.5125 (m100) REVERT: a 34 LYS cc_start: 0.8735 (mttp) cc_final: 0.8492 (mttp) REVERT: a 90 PHE cc_start: 0.6939 (t80) cc_final: 0.6714 (t80) REVERT: a 515 TYR cc_start: 0.5220 (t80) cc_final: 0.4246 (t80) REVERT: a 570 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.7007 (m-10) REVERT: a 590 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8039 (tp) REVERT: a 650 TRP cc_start: 0.6046 (m100) cc_final: 0.5305 (m100) REVERT: a 740 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7333 (mt) REVERT: a 827 SER cc_start: 0.8956 (m) cc_final: 0.8680 (p) outliers start: 167 outliers final: 124 residues processed: 721 average time/residue: 0.3346 time to fit residues: 396.3012 Evaluate side-chains 727 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 585 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 328 VAL Chi-restraints excluded: chain c residue 334 PHE Chi-restraints excluded: chain c residue 368 VAL Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain d residue 105 SER Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 206 THR Chi-restraints excluded: chain d residue 210 MET Chi-restraints excluded: chain d residue 279 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 320 PHE Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 32 PHE Chi-restraints excluded: chain f residue 36 HIS Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain h residue 150 LEU Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 128 PHE Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 154 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 37 SER Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 113 VAL Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 51 LEU Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 152 LEU Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 17 TRP Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 329 ASP Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 435 HIS Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 540 MET Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 570 TYR Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 580 MET Chi-restraints excluded: chain a residue 590 LEU Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 617 PHE Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 653 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 802 HIS Chi-restraints excluded: chain a residue 823 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 233 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 118 optimal weight: 0.0470 chunk 71 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 281 optimal weight: 0.0470 chunk 59 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 299 HIS d 304 ASN ** d 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 59 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.145054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.124978 restraints weight = 58174.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.127533 restraints weight = 30667.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.129199 restraints weight = 18510.275| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25761 Z= 0.148 Angle : 0.690 14.123 34939 Z= 0.347 Chirality : 0.042 0.417 4096 Planarity : 0.004 0.049 4332 Dihedral : 5.743 59.319 3761 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.55 % Allowed : 30.59 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.15), residues: 3239 helix: 1.85 (0.11), residues: 2262 sheet: 0.11 (0.52), residues: 97 loop : -1.97 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP e 17 HIS 0.007 0.001 HIS a 749 PHE 0.020 0.001 PHE o 128 TYR 0.027 0.001 TYR k 144 ARG 0.008 0.000 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 7) link_NAG-ASN : angle 4.06265 ( 21) link_BETA1-4 : bond 0.00546 ( 5) link_BETA1-4 : angle 2.28421 ( 15) hydrogen bonds : bond 0.05707 ( 1860) hydrogen bonds : angle 4.16152 ( 5493) covalent geometry : bond 0.00307 (25749) covalent geometry : angle 0.68136 (34903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 636 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 101 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.7992 (p) REVERT: d 75 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8267 (mmmt) REVERT: d 197 LYS cc_start: 0.9211 (ttmm) cc_final: 0.8842 (ttmm) REVERT: d 215 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7822 (mm-30) REVERT: d 308 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.7882 (t80) REVERT: d 346 ILE cc_start: 0.9142 (tt) cc_final: 0.8890 (tt) REVERT: f 27 ILE cc_start: 0.8000 (mt) cc_final: 0.7400 (tp) REVERT: f 36 HIS cc_start: 0.5531 (OUTLIER) cc_final: 0.4937 (m-70) REVERT: f 57 ASN cc_start: 0.8388 (m-40) cc_final: 0.7997 (t0) REVERT: f 58 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7915 (pt) REVERT: f 82 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7570 (t80) REVERT: f 86 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7837 (mm-40) REVERT: f 88 ARG cc_start: 0.8134 (tmm-80) cc_final: 0.7541 (tmm-80) REVERT: g 23 MET cc_start: 0.7787 (tpp) cc_final: 0.7082 (tpt) REVERT: g 47 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6586 (ttp) REVERT: g 61 MET cc_start: 0.6810 (mtp) cc_final: 0.6575 (mtm) REVERT: g 139 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7084 (tm-30) REVERT: h 44 MET cc_start: 0.7448 (tpp) cc_final: 0.7112 (tpp) REVERT: i 51 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7159 (pp) REVERT: i 61 MET cc_start: 0.6732 (mmm) cc_final: 0.6500 (mmm) REVERT: i 97 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7792 (mp) REVERT: j 41 ILE cc_start: 0.8336 (tp) cc_final: 0.7985 (tp) REVERT: j 151 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7302 (tp) REVERT: k 51 LEU cc_start: 0.8021 (mm) cc_final: 0.7607 (tp) REVERT: k 61 MET cc_start: 0.7781 (mmt) cc_final: 0.7391 (mtp) REVERT: k 87 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6865 (t80) REVERT: k 144 TYR cc_start: 0.7979 (m-80) cc_final: 0.7765 (m-80) REVERT: l 23 MET cc_start: 0.7636 (tpt) cc_final: 0.7158 (tpt) REVERT: m 48 ARG cc_start: 0.8585 (mmt90) cc_final: 0.8282 (mmt90) REVERT: m 54 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8253 (mmtp) REVERT: m 61 MET cc_start: 0.7861 (mmt) cc_final: 0.7486 (mmt) REVERT: m 115 ASP cc_start: 0.8210 (t70) cc_final: 0.7619 (t0) REVERT: m 131 MET cc_start: 0.8507 (ttp) cc_final: 0.8206 (ttp) REVERT: m 139 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8627 (mm-30) REVERT: n 51 LEU cc_start: 0.8979 (mm) cc_final: 0.8703 (tt) REVERT: n 132 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9084 (pt) REVERT: n 155 LYS cc_start: 0.6867 (tttt) cc_final: 0.6554 (ttmt) REVERT: o 7 ASN cc_start: 0.8371 (p0) cc_final: 0.8095 (p0) REVERT: o 92 GLN cc_start: 0.8039 (mt0) cc_final: 0.7720 (mt0) REVERT: o 139 GLU cc_start: 0.8452 (tp30) cc_final: 0.8099 (tm-30) REVERT: s 97 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7783 (tt) REVERT: s 181 MET cc_start: 0.7665 (tpp) cc_final: 0.6788 (tmm) REVERT: e 17 TRP cc_start: 0.5813 (m-10) cc_final: 0.5202 (m100) REVERT: a 10 MET cc_start: 0.3931 (tpp) cc_final: 0.3675 (tmm) REVERT: a 90 PHE cc_start: 0.6949 (t80) cc_final: 0.6711 (t80) REVERT: a 515 TYR cc_start: 0.5068 (t80) cc_final: 0.4138 (t80) REVERT: a 574 ILE cc_start: 0.7577 (mt) cc_final: 0.7362 (mm) REVERT: a 590 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8041 (tp) REVERT: a 650 TRP cc_start: 0.6088 (m100) cc_final: 0.5271 (m100) REVERT: a 740 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7445 (mt) REVERT: a 827 SER cc_start: 0.8919 (m) cc_final: 0.8642 (p) outliers start: 147 outliers final: 111 residues processed: 731 average time/residue: 0.3286 time to fit residues: 398.7611 Evaluate side-chains 725 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 600 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 328 VAL Chi-restraints excluded: chain c residue 334 PHE Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 210 MET Chi-restraints excluded: chain d residue 279 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 320 PHE Chi-restraints excluded: chain d residue 332 VAL Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain f residue 32 PHE Chi-restraints excluded: chain f residue 36 HIS Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 52 ILE Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 128 PHE Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain j residue 151 ILE Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 128 PHE Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 154 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 113 VAL Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 51 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain s residue 33 GLN Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 215 VAL Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 329 ASP Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 435 HIS Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 580 MET Chi-restraints excluded: chain a residue 590 LEU Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 617 PHE Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 653 LEU Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 823 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 238 optimal weight: 0.0870 chunk 310 optimal weight: 9.9990 chunk 52 optimal weight: 0.2980 chunk 273 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 227 optimal weight: 50.0000 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 59 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.144876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.124393 restraints weight = 58960.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.127183 restraints weight = 29936.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.128905 restraints weight = 17646.493| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25761 Z= 0.146 Angle : 0.701 14.112 34939 Z= 0.348 Chirality : 0.042 0.414 4096 Planarity : 0.004 0.049 4332 Dihedral : 5.636 59.347 3760 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.51 % Allowed : 31.12 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3239 helix: 1.86 (0.11), residues: 2262 sheet: 0.15 (0.53), residues: 97 loop : -1.97 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP a 324 HIS 0.007 0.001 HIS a 412 PHE 0.028 0.001 PHE a 714 TYR 0.037 0.001 TYR h 32 ARG 0.011 0.000 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 7) link_NAG-ASN : angle 4.02010 ( 21) link_BETA1-4 : bond 0.00542 ( 5) link_BETA1-4 : angle 2.23148 ( 15) hydrogen bonds : bond 0.05534 ( 1860) hydrogen bonds : angle 4.12868 ( 5493) covalent geometry : bond 0.00311 (25749) covalent geometry : angle 0.69251 (34903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 618 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 101 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7919 (p) REVERT: d 75 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8321 (mmmt) REVERT: d 197 LYS cc_start: 0.9250 (ttmm) cc_final: 0.8895 (ttmm) REVERT: d 215 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7946 (mm-30) REVERT: d 308 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.7852 (t80) REVERT: d 346 ILE cc_start: 0.9101 (tt) cc_final: 0.8870 (tt) REVERT: f 27 ILE cc_start: 0.8002 (mt) cc_final: 0.7446 (tp) REVERT: f 57 ASN cc_start: 0.8451 (m-40) cc_final: 0.7967 (t0) REVERT: f 58 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7743 (pt) REVERT: f 82 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7740 (t80) REVERT: f 86 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7891 (mm-40) REVERT: g 23 MET cc_start: 0.7933 (tpp) cc_final: 0.7208 (tpt) REVERT: g 47 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6825 (ttp) REVERT: g 61 MET cc_start: 0.6995 (mtp) cc_final: 0.6724 (mtm) REVERT: g 139 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7100 (tm-30) REVERT: i 51 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7108 (pp) REVERT: i 61 MET cc_start: 0.7160 (mmm) cc_final: 0.6721 (mmm) REVERT: i 92 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: i 97 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7814 (mp) REVERT: j 41 ILE cc_start: 0.8234 (tp) cc_final: 0.7901 (tp) REVERT: j 151 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7249 (tp) REVERT: k 51 LEU cc_start: 0.8150 (mm) cc_final: 0.7592 (tp) REVERT: k 61 MET cc_start: 0.7785 (mmt) cc_final: 0.7482 (mtp) REVERT: k 87 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6893 (t80) REVERT: k 144 TYR cc_start: 0.8037 (m-80) cc_final: 0.7750 (m-80) REVERT: l 23 MET cc_start: 0.7622 (tpt) cc_final: 0.7181 (tpt) REVERT: l 61 MET cc_start: 0.8897 (mmm) cc_final: 0.8671 (mmm) REVERT: m 48 ARG cc_start: 0.8804 (mmt90) cc_final: 0.8481 (mmt90) REVERT: m 54 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8376 (mmtp) REVERT: m 61 MET cc_start: 0.7982 (mmt) cc_final: 0.7700 (mmt) REVERT: m 115 ASP cc_start: 0.8341 (t70) cc_final: 0.7753 (t0) REVERT: m 131 MET cc_start: 0.8381 (ttp) cc_final: 0.8113 (ttp) REVERT: n 51 LEU cc_start: 0.9129 (mm) cc_final: 0.8710 (tt) REVERT: n 132 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8953 (pt) REVERT: n 155 LYS cc_start: 0.7213 (tttt) cc_final: 0.6602 (ttmt) REVERT: o 55 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.8891 (t) REVERT: o 92 GLN cc_start: 0.8173 (mt0) cc_final: 0.7858 (mt0) REVERT: o 139 GLU cc_start: 0.8565 (tp30) cc_final: 0.8130 (tm-30) REVERT: s 97 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7714 (tt) REVERT: s 181 MET cc_start: 0.7521 (tpp) cc_final: 0.6674 (tmm) REVERT: e 17 TRP cc_start: 0.5947 (m-10) cc_final: 0.5352 (m100) REVERT: e 59 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: a 10 MET cc_start: 0.4195 (tpp) cc_final: 0.3987 (tmm) REVERT: a 34 LYS cc_start: 0.8690 (mttp) cc_final: 0.8370 (mttp) REVERT: a 90 PHE cc_start: 0.6956 (t80) cc_final: 0.6635 (t80) REVERT: a 515 TYR cc_start: 0.5354 (t80) cc_final: 0.4218 (t80) REVERT: a 570 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7162 (m-10) REVERT: a 650 TRP cc_start: 0.6253 (m100) cc_final: 0.5410 (m100) REVERT: a 740 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7576 (mt) REVERT: a 827 SER cc_start: 0.8968 (m) cc_final: 0.8764 (p) outliers start: 146 outliers final: 115 residues processed: 713 average time/residue: 0.3152 time to fit residues: 368.1145 Evaluate side-chains 731 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 600 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 328 VAL Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 210 MET Chi-restraints excluded: chain d residue 279 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 320 PHE Chi-restraints excluded: chain d residue 332 VAL Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain f residue 32 PHE Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 36 LYS Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain h residue 150 LEU Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 128 PHE Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 11 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain j residue 151 ILE Chi-restraints excluded: chain k residue 20 SER Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 113 VAL Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 51 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain s residue 18 GLN Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 215 VAL Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 329 ASP Chi-restraints excluded: chain a residue 435 HIS Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 570 TYR Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 580 MET Chi-restraints excluded: chain a residue 590 LEU Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 617 PHE Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 653 LEU Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 823 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 29 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN s 78 HIS s 79 GLN e 59 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.143570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.123204 restraints weight = 59909.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125873 restraints weight = 30714.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.127534 restraints weight = 18311.101| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25761 Z= 0.148 Angle : 0.716 14.086 34939 Z= 0.356 Chirality : 0.042 0.414 4096 Planarity : 0.004 0.050 4332 Dihedral : 5.556 59.408 3759 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.98 % Allowed : 31.34 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.15), residues: 3239 helix: 1.84 (0.11), residues: 2261 sheet: 0.32 (0.54), residues: 95 loop : -1.95 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP a 324 HIS 0.005 0.001 HIS a 749 PHE 0.028 0.001 PHE s 116 TYR 0.045 0.001 TYR h 32 ARG 0.008 0.000 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 7) link_NAG-ASN : angle 3.99184 ( 21) link_BETA1-4 : bond 0.00553 ( 5) link_BETA1-4 : angle 2.19235 ( 15) hydrogen bonds : bond 0.05455 ( 1860) hydrogen bonds : angle 4.11507 ( 5493) covalent geometry : bond 0.00321 (25749) covalent geometry : angle 0.70857 (34903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 610 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 341 ILE cc_start: 0.9227 (mm) cc_final: 0.8953 (mm) REVERT: b 101 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7929 (p) REVERT: d 75 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8326 (mmmt) REVERT: d 197 LYS cc_start: 0.9258 (ttmm) cc_final: 0.8896 (ttmm) REVERT: d 215 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7965 (mm-30) REVERT: d 308 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.7845 (t80) REVERT: d 346 ILE cc_start: 0.9086 (tt) cc_final: 0.8840 (tt) REVERT: f 57 ASN cc_start: 0.8441 (m-40) cc_final: 0.7993 (t0) REVERT: f 58 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7725 (pt) REVERT: f 82 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7645 (t80) REVERT: f 86 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7826 (mm-40) REVERT: g 23 MET cc_start: 0.7960 (tpp) cc_final: 0.7260 (tpt) REVERT: g 47 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6838 (ttp) REVERT: g 61 MET cc_start: 0.7008 (mtp) cc_final: 0.6739 (mtm) REVERT: g 139 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7050 (tm-30) REVERT: i 51 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7146 (pp) REVERT: i 61 MET cc_start: 0.7223 (mmm) cc_final: 0.6773 (mmm) REVERT: i 92 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: i 97 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7807 (mp) REVERT: j 41 ILE cc_start: 0.8243 (tp) cc_final: 0.7910 (tp) REVERT: j 151 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7253 (tp) REVERT: k 51 LEU cc_start: 0.8132 (mm) cc_final: 0.7557 (tp) REVERT: k 61 MET cc_start: 0.7689 (mmt) cc_final: 0.6841 (mtm) REVERT: k 87 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.6785 (t80) REVERT: k 144 TYR cc_start: 0.7949 (m-80) cc_final: 0.7652 (m-80) REVERT: l 23 MET cc_start: 0.7617 (tpt) cc_final: 0.7185 (tpt) REVERT: l 61 MET cc_start: 0.8934 (mmm) cc_final: 0.8651 (mmm) REVERT: m 23 MET cc_start: 0.7878 (tpp) cc_final: 0.7568 (tpt) REVERT: m 48 ARG cc_start: 0.8817 (mmt90) cc_final: 0.8368 (mmt90) REVERT: m 61 MET cc_start: 0.8013 (mmt) cc_final: 0.7730 (mmt) REVERT: m 115 ASP cc_start: 0.8363 (t70) cc_final: 0.7771 (t0) REVERT: m 131 MET cc_start: 0.8336 (ttp) cc_final: 0.8081 (ttp) REVERT: n 51 LEU cc_start: 0.9145 (mm) cc_final: 0.8694 (tt) REVERT: n 132 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8972 (pt) REVERT: n 155 LYS cc_start: 0.7250 (tttt) cc_final: 0.6702 (ttmt) REVERT: o 92 GLN cc_start: 0.8141 (mt0) cc_final: 0.7853 (mt0) REVERT: o 119 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.7546 (mtm-85) REVERT: o 139 GLU cc_start: 0.8573 (tp30) cc_final: 0.8107 (tm-30) REVERT: s 97 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7702 (tt) REVERT: s 181 MET cc_start: 0.7468 (tpp) cc_final: 0.6644 (tmm) REVERT: e 17 TRP cc_start: 0.5963 (m-10) cc_final: 0.5381 (m100) REVERT: a 34 LYS cc_start: 0.8658 (mttp) cc_final: 0.8364 (mttp) REVERT: a 90 PHE cc_start: 0.6965 (t80) cc_final: 0.6648 (t80) REVERT: a 515 TYR cc_start: 0.5334 (t80) cc_final: 0.4227 (t80) REVERT: a 570 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.7175 (m-10) REVERT: a 650 TRP cc_start: 0.6350 (m100) cc_final: 0.5486 (m100) REVERT: a 740 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7559 (mt) REVERT: a 827 SER cc_start: 0.8969 (m) cc_final: 0.8767 (p) outliers start: 132 outliers final: 109 residues processed: 691 average time/residue: 0.3292 time to fit residues: 376.5485 Evaluate side-chains 718 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 595 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 328 VAL Chi-restraints excluded: chain c residue 334 PHE Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 210 MET Chi-restraints excluded: chain d residue 279 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 320 PHE Chi-restraints excluded: chain d residue 332 VAL Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain h residue 150 LEU Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 128 PHE Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain j residue 151 ILE Chi-restraints excluded: chain k residue 20 SER Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 37 SER Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 113 VAL Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 51 LEU Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 215 VAL Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 329 ASP Chi-restraints excluded: chain a residue 435 HIS Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 570 TYR Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 580 MET Chi-restraints excluded: chain a residue 590 LEU Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 617 PHE Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 653 LEU Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 823 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 151 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 279 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 394 GLN ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN e 59 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 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 = 0.4030 r_free = 0.4030 target = 0.141440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.121552 restraints weight = 58571.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124084 restraints weight = 30411.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.125593 restraints weight = 18494.683| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25761 Z= 0.192 Angle : 0.752 14.333 34939 Z= 0.379 Chirality : 0.044 0.415 4096 Planarity : 0.004 0.050 4332 Dihedral : 5.732 59.495 3759 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.66 % Allowed : 30.70 % Favored : 63.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 3239 helix: 1.69 (0.11), residues: 2271 sheet: 0.41 (0.55), residues: 93 loop : -2.00 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP a 324 HIS 0.006 0.001 HIS d 86 PHE 0.025 0.002 PHE a 714 TYR 0.028 0.002 TYR k 144 ARG 0.011 0.001 ARG a 387 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 7) link_NAG-ASN : angle 4.10567 ( 21) link_BETA1-4 : bond 0.00522 ( 5) link_BETA1-4 : angle 2.30713 ( 15) hydrogen bonds : bond 0.06155 ( 1860) hydrogen bonds : angle 4.32221 ( 5493) covalent geometry : bond 0.00435 (25749) covalent geometry : angle 0.74430 (34903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9705.82 seconds wall clock time: 168 minutes 2.88 seconds (10082.88 seconds total)