Starting phenix.real_space_refine on Sat May 24 02:53:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9brz_44846/05_2025/9brz_44846.cif Found real_map, /net/cci-nas-00/data/ceres_data/9brz_44846/05_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_44846/05_2025/9brz_44846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9brz_44846/05_2025/9brz_44846.map" model { file = "/net/cci-nas-00/data/ceres_data/9brz_44846/05_2025/9brz_44846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9brz_44846/05_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-5687/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: 13.57, per 1000 atoms: 0.54 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: 6.64 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: 2.35 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: 9.59 Time building geometry restraints manager: 7.63 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 55.150 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.160 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.570 ------------------------------------------------------------------------------- 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 : 2.706 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: 0.3309 time to fit residues: 411.8692 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 : 2.736 ------------------------------------------------------------------------------- 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 = 0.142927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.122547 restraints weight = 58268.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.125093 restraints weight = 30089.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.126710 restraints weight = 18274.809| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 2.659 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: 0.7742 (mt-10) cc_final: 0.7510 (tm-30) REVERT: c 432 ILE cc_start: 0.9480 (mm) cc_final: 0.9049 (mt) REVERT: b 7 LEU cc_start: 0.9145 (tp) cc_final: 0.8841 (tt) REVERT: b 138 MET cc_start: 0.8249 (ppp) cc_final: 0.7994 (ptp) REVERT: d 75 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8273 (mmmt) REVERT: d 197 LYS cc_start: 0.9274 (ttmm) cc_final: 0.8956 (ttmm) REVERT: d 265 GLN cc_start: 0.9008 (mt0) cc_final: 0.8763 (mt0) REVERT: d 308 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8080 (t80) REVERT: f 57 ASN cc_start: 0.8347 (m-40) cc_final: 0.7915 (t0) REVERT: f 58 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7871 (pt) REVERT: f 67 TYR cc_start: 0.6238 (OUTLIER) cc_final: 0.5029 (m-80) REVERT: g 23 MET cc_start: 0.8065 (tpp) cc_final: 0.7649 (tpt) REVERT: h 10 TYR cc_start: 0.7173 (p90) cc_final: 0.6925 (p90) REVERT: h 108 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8259 (t80) REVERT: h 118 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8089 (m) REVERT: i 28 MET cc_start: 0.8786 (mmm) cc_final: 0.8538 (mmt) REVERT: j 41 ILE cc_start: 0.8197 (tp) cc_final: 0.7835 (tp) REVERT: k 61 MET cc_start: 0.7696 (mmt) cc_final: 0.7433 (mmt) REVERT: l 23 MET cc_start: 0.7917 (tpt) cc_final: 0.7667 (tpt) REVERT: l 61 MET cc_start: 0.8664 (tpp) cc_final: 0.8354 (mmm) REVERT: n 51 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8602 (tt) REVERT: n 154 THR cc_start: 0.8193 (p) cc_final: 0.7934 (m) REVERT: n 155 LYS cc_start: 0.6688 (tttt) cc_final: 0.6179 (ttmt) REVERT: o 55 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8810 (t) REVERT: o 70 LEU cc_start: 0.9235 (tp) cc_final: 0.8916 (tt) REVERT: o 126 ARG cc_start: 0.8567 (tpp80) cc_final: 0.8304 (mmm-85) REVERT: p 627 TRP cc_start: 0.7061 (t60) cc_final: 0.6288 (t60) REVERT: s 170 MET cc_start: 0.7221 (tpt) cc_final: 0.6937 (tpt) REVERT: s 183 MET cc_start: 0.7401 (mmm) cc_final: 0.7168 (mmm) REVERT: e 17 TRP cc_start: 0.4573 (m-10) cc_final: 0.4088 (m100) REVERT: a 28 GLU cc_start: 0.8181 (mm-30) cc_final: 0.6933 (pp20) REVERT: a 90 PHE cc_start: 0.6619 (t80) cc_final: 0.6201 (t80) REVERT: a 119 LYS cc_start: 0.9300 (tppp) cc_final: 0.8884 (tppt) REVERT: a 311 ASN cc_start: 0.6705 (t0) cc_final: 0.6407 (t0) REVERT: a 338 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8200 (ttp-110) REVERT: a 457 SER cc_start: 0.8071 (m) cc_final: 0.7716 (m) REVERT: a 479 TRP cc_start: 0.7160 (m100) cc_final: 0.6764 (m100) REVERT: a 515 TYR cc_start: 0.5424 (t80) cc_final: 0.4729 (t80) REVERT: a 732 CYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7057 (p) REVERT: a 749 HIS cc_start: 0.5789 (OUTLIER) cc_final: 0.5440 (m170) outliers start: 163 outliers final: 107 residues processed: 780 average time/residue: 0.3219 time to fit residues: 407.0199 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 : 2.630 ------------------------------------------------------------------------------- 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: 8.9990 chunk 197 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 295 optimal weight: 0.0470 chunk 54 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.1884 ------------------------------------------------------------------------------- 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 637 GLN ** a 749 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 = 0.4047 r_free = 0.4047 target = 0.142202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121766 restraints weight = 58813.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.124377 restraints weight = 30546.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.125975 restraints weight = 18444.675| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25761 Z= 0.178 Angle : 0.685 14.413 34939 Z= 0.350 Chirality : 0.043 0.442 4096 Planarity : 0.004 0.082 4332 Dihedral : 6.516 58.686 3795 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 8.23 % Allowed : 24.58 % Favored : 67.18 % 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: 1.59 (0.11), residues: 2257 sheet: 0.11 (0.53), residues: 106 loop : -1.61 (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 0.021 0.002 PHE a 584 TYR 0.022 0.002 TYR a 562 ARG 0.019 0.001 ARG a 387 Details of bonding type rmsd link_NAG-ASN : bond 0.01003 ( 7) link_NAG-ASN : angle 5.23363 ( 21) link_BETA1-4 : bond 0.00493 ( 5) link_BETA1-4 : angle 2.59211 ( 15) hydrogen bonds : bond 0.07007 ( 1860) hydrogen bonds : angle 4.57805 ( 5493) covalent geometry : bond 0.00377 (25749) covalent geometry : angle 0.67112 (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 878 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 660 time to evaluate : 2.647 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: c 337 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7495 (tm-30) REVERT: c 392 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7511 (m110) REVERT: b 7 LEU cc_start: 0.9065 (tp) cc_final: 0.8772 (tt) REVERT: b 101 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.7994 (p) REVERT: b 138 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7915 (ptp) REVERT: d 75 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8287 (mmmt) REVERT: d 197 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8848 (ttmm) REVERT: d 215 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7991 (mm-30) REVERT: d 308 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8001 (t80) REVERT: f 57 ASN cc_start: 0.8293 (m-40) cc_final: 0.7927 (t0) REVERT: f 58 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7990 (pt) REVERT: f 67 TYR cc_start: 0.6391 (OUTLIER) cc_final: 0.5222 (m-80) REVERT: f 82 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7708 (t80) REVERT: f 86 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7888 (mm-40) REVERT: f 88 ARG cc_start: 0.8154 (tmm-80) cc_final: 0.7641 (tmm-80) REVERT: g 23 MET cc_start: 0.8029 (tpp) cc_final: 0.7232 (tpt) REVERT: g 47 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6473 (ttp) REVERT: h 108 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8328 (t80) REVERT: h 128 PHE cc_start: 0.7916 (t80) cc_final: 0.7564 (t80) REVERT: i 28 MET cc_start: 0.8818 (mmm) cc_final: 0.8540 (mmt) REVERT: i 92 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: i 97 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7665 (mp) REVERT: i 139 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6169 (tm-30) REVERT: j 41 ILE cc_start: 0.8235 (tp) cc_final: 0.7917 (tp) REVERT: j 80 LEU cc_start: 0.7743 (mt) cc_final: 0.6980 (tp) REVERT: k 23 MET cc_start: 0.8479 (tpt) cc_final: 0.7833 (tpp) REVERT: k 51 LEU cc_start: 0.7864 (mm) cc_final: 0.7540 (tp) REVERT: k 87 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7239 (t80) REVERT: m 23 MET cc_start: 0.7557 (tpt) cc_final: 0.7216 (tpp) REVERT: m 48 ARG cc_start: 0.8810 (mmt180) cc_final: 0.8427 (mmt90) REVERT: m 53 MET cc_start: 0.6985 (ppp) cc_final: 0.6629 (ppp) REVERT: m 54 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8071 (mmtp) REVERT: m 61 MET cc_start: 0.7748 (mmt) cc_final: 0.7479 (mmt) REVERT: m 87 TYR cc_start: 0.7777 (t80) cc_final: 0.7552 (t80) REVERT: m 92 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7430 (mm-40) REVERT: m 115 ASP cc_start: 0.8183 (t70) cc_final: 0.7680 (t0) REVERT: m 131 MET cc_start: 0.8878 (ttp) cc_final: 0.8483 (ttt) REVERT: m 136 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8369 (tt) REVERT: m 139 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8605 (mm-30) REVERT: n 51 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8618 (tp) REVERT: n 132 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9138 (pt) REVERT: n 155 LYS cc_start: 0.7003 (tttt) cc_final: 0.6518 (ttmt) REVERT: o 55 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.8541 (t) REVERT: o 70 LEU cc_start: 0.9242 (tp) cc_final: 0.8948 (tt) REVERT: o 76 ILE cc_start: 0.9275 (tp) cc_final: 0.8317 (tp) REVERT: o 131 MET cc_start: 0.8240 (ttp) cc_final: 0.7959 (ttm) REVERT: s 170 MET cc_start: 0.7290 (tpt) cc_final: 0.7010 (tpt) REVERT: e 17 TRP cc_start: 0.5059 (m-10) cc_final: 0.4516 (m100) REVERT: a 34 LYS cc_start: 0.8873 (mttp) cc_final: 0.8480 (mttm) REVERT: a 90 PHE cc_start: 0.6846 (t80) cc_final: 0.6438 (t80) REVERT: a 311 ASN cc_start: 0.7015 (t0) cc_final: 0.6794 (t0) REVERT: a 338 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8359 (ptp-110) REVERT: a 515 TYR cc_start: 0.5478 (t80) cc_final: 0.4585 (t80) REVERT: a 749 HIS cc_start: 0.5778 (OUTLIER) cc_final: 0.5483 (m170) outliers start: 218 outliers final: 141 residues processed: 788 average time/residue: 0.3140 time to fit residues: 402.6448 Evaluate side-chains 770 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 611 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 328 VAL 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 75 SER Chi-restraints excluded: chain b residue 101 VAL 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 127 LEU Chi-restraints excluded: chain j residue 131 MET 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 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 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 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 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 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 123 LEU 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 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: 9.9990 chunk 240 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 75 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 chunk 169 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 268 optimal weight: 20.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 144 ASN ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 313 HIS ** 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 = 0.139515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119388 restraints weight = 59243.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.121750 restraints weight = 30930.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.123314 restraints weight = 18917.254| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2559 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= 0.188 Angle : 0.704 14.597 34939 Z= 0.356 Chirality : 0.043 0.433 4096 Planarity : 0.004 0.057 4332 Dihedral : 6.260 58.159 3776 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 8.69 % Allowed : 25.57 % Favored : 65.75 % 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: 1.08 (0.15), residues: 3239 helix: 1.64 (0.11), residues: 2261 sheet: 0.03 (0.52), residues: 105 loop : -1.69 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 595 HIS 0.007 0.001 HIS a 435 PHE 0.028 0.002 PHE a 101 TYR 0.034 0.002 TYR k 144 ARG 0.006 0.000 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00837 ( 7) link_NAG-ASN : angle 4.92405 ( 21) link_BETA1-4 : bond 0.00635 ( 5) link_BETA1-4 : angle 2.69764 ( 15) hydrogen bonds : bond 0.06818 ( 1860) hydrogen bonds : angle 4.52050 ( 5493) covalent geometry : bond 0.00414 (25749) covalent geometry : angle 0.69129 (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 861 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 631 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 7 LEU cc_start: 0.9037 (tp) cc_final: 0.8764 (tt) REVERT: d 75 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8279 (mmmt) REVERT: d 87 MET cc_start: 0.8931 (tpp) cc_final: 0.8660 (tpp) REVERT: d 197 LYS cc_start: 0.9249 (ttmm) cc_final: 0.8924 (ttmm) REVERT: d 215 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7811 (mm-30) REVERT: d 308 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8057 (t80) REVERT: f 57 ASN cc_start: 0.8290 (m-40) cc_final: 0.8011 (t0) REVERT: f 58 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8015 (pt) REVERT: f 67 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5116 (m-80) REVERT: f 82 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7543 (t80) REVERT: g 23 MET cc_start: 0.8038 (tpp) cc_final: 0.7321 (tpt) REVERT: g 47 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6577 (ttp) REVERT: g 139 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7056 (tm-30) REVERT: i 28 MET cc_start: 0.8824 (mmm) cc_final: 0.8550 (mmt) REVERT: i 92 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: i 97 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7897 (mp) REVERT: i 139 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6145 (tm-30) REVERT: j 26 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.7770 (t) REVERT: j 41 ILE cc_start: 0.8412 (tp) cc_final: 0.8056 (tp) REVERT: j 151 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7328 (tp) REVERT: k 23 MET cc_start: 0.8436 (tpt) cc_final: 0.7865 (tpp) REVERT: k 51 LEU cc_start: 0.7800 (mm) cc_final: 0.7474 (tp) REVERT: k 87 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.7279 (t80) REVERT: l 23 MET cc_start: 0.7772 (tpt) cc_final: 0.7310 (tpt) REVERT: m 23 MET cc_start: 0.7443 (tpt) cc_final: 0.7146 (tpp) REVERT: m 48 ARG cc_start: 0.8659 (mmt180) cc_final: 0.8255 (mmt90) REVERT: m 115 ASP cc_start: 0.8046 (t70) cc_final: 0.7526 (t0) REVERT: m 131 MET cc_start: 0.8848 (ttp) cc_final: 0.8477 (ttt) REVERT: n 51 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8613 (tp) REVERT: n 132 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9170 (pt) REVERT: n 155 LYS cc_start: 0.6853 (tttt) cc_final: 0.6493 (ttmt) REVERT: o 55 SER cc_start: 0.9315 (OUTLIER) cc_final: 0.8496 (t) REVERT: o 70 LEU cc_start: 0.9260 (tp) cc_final: 0.9000 (tt) REVERT: o 139 GLU cc_start: 0.8565 (tp30) cc_final: 0.8060 (tm-30) REVERT: s 170 MET cc_start: 0.7479 (tpt) cc_final: 0.7216 (tpt) REVERT: s 181 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6532 (tmm) REVERT: e 17 TRP cc_start: 0.5410 (m-10) cc_final: 0.4904 (m100) REVERT: a 90 PHE cc_start: 0.6843 (t80) cc_final: 0.6616 (t80) REVERT: a 515 TYR cc_start: 0.5487 (t80) cc_final: 0.4429 (t80) REVERT: a 749 HIS cc_start: 0.5719 (OUTLIER) cc_final: 0.5512 (m170) REVERT: a 800 PHE cc_start: 0.7890 (t80) cc_final: 0.7588 (t80) REVERT: a 819 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8155 (t) REVERT: a 827 SER cc_start: 0.8948 (m) cc_final: 0.8625 (p) outliers start: 230 outliers final: 165 residues processed: 762 average time/residue: 0.3143 time to fit residues: 391.3109 Evaluate side-chains 774 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 592 time to evaluate : 2.620 ------------------------------------------------------------------------------- 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 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 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 34 THR 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 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 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 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 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 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 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 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 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 Chi-restraints excluded: chain a residue 819 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 ** d 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** 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 = 0.4002 r_free = 0.4002 target = 0.139292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.119169 restraints weight = 58979.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121550 restraints weight = 30782.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.123086 restraints weight = 18786.920| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25761 Z= 0.189 Angle : 0.700 14.907 34939 Z= 0.356 Chirality : 0.043 0.434 4096 Planarity : 0.004 0.055 4332 Dihedral : 6.143 58.910 3772 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 8.91 % Allowed : 26.06 % Favored : 65.03 % 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: 1.09 (0.15), residues: 3239 helix: 1.65 (0.11), residues: 2263 sheet: 0.18 (0.52), residues: 106 loop : -1.75 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 595 HIS 0.004 0.001 HIS d 86 PHE 0.021 0.002 PHE a 101 TYR 0.025 0.002 TYR k 144 ARG 0.007 0.000 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 7) link_NAG-ASN : angle 4.46515 ( 21) link_BETA1-4 : bond 0.00514 ( 5) link_BETA1-4 : angle 2.65013 ( 15) hydrogen bonds : bond 0.06778 ( 1860) hydrogen bonds : angle 4.46825 ( 5493) covalent geometry : bond 0.00422 (25749) covalent geometry : angle 0.68983 (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 837 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 601 time to evaluate : 2.914 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 382 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8623 (p) REVERT: b 7 LEU cc_start: 0.9026 (tp) cc_final: 0.8756 (tt) REVERT: d 75 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8287 (mmmt) REVERT: d 87 MET cc_start: 0.8861 (tpp) cc_final: 0.8649 (tpp) REVERT: d 197 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8941 (ttmm) REVERT: d 215 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7802 (mm-30) REVERT: d 308 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8030 (t80) REVERT: f 36 HIS cc_start: 0.5726 (OUTLIER) cc_final: 0.5148 (m-70) REVERT: f 57 ASN cc_start: 0.8300 (m-40) cc_final: 0.7929 (t0) REVERT: f 58 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7807 (pt) REVERT: f 67 TYR cc_start: 0.6396 (OUTLIER) cc_final: 0.5177 (m-80) REVERT: f 82 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7573 (t80) REVERT: f 86 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7773 (mm-40) REVERT: g 23 MET cc_start: 0.8017 (tpp) cc_final: 0.7333 (tpt) REVERT: g 47 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6519 (ttp) REVERT: g 139 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7063 (tm-30) REVERT: i 9 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5620 (pm20) REVERT: i 97 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7886 (mp) REVERT: i 139 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6229 (tm-30) REVERT: j 26 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.7867 (t) REVERT: j 41 ILE cc_start: 0.8387 (tp) cc_final: 0.8024 (tp) REVERT: j 151 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7395 (tp) REVERT: k 23 MET cc_start: 0.8431 (tpt) cc_final: 0.7953 (tpp) REVERT: k 51 LEU cc_start: 0.7767 (mm) cc_final: 0.7396 (tt) REVERT: k 61 MET cc_start: 0.7561 (mmt) cc_final: 0.7092 (mmt) REVERT: k 87 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7260 (t80) REVERT: l 23 MET cc_start: 0.7843 (tpt) cc_final: 0.7439 (tpt) REVERT: m 23 MET cc_start: 0.7578 (tpt) cc_final: 0.7248 (tpp) REVERT: m 48 ARG cc_start: 0.8592 (mmt180) cc_final: 0.8232 (mmt90) REVERT: m 54 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8102 (mmtp) REVERT: m 115 ASP cc_start: 0.8178 (t70) cc_final: 0.7628 (t0) REVERT: m 131 MET cc_start: 0.8775 (ttp) cc_final: 0.8065 (ttm) REVERT: n 51 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8639 (tt) REVERT: n 132 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9164 (pt) REVERT: n 155 LYS cc_start: 0.6927 (tttt) cc_final: 0.6565 (ttmt) REVERT: o 55 SER cc_start: 0.9363 (OUTLIER) cc_final: 0.8576 (t) REVERT: o 70 LEU cc_start: 0.9273 (tp) cc_final: 0.9042 (tt) REVERT: o 76 ILE cc_start: 0.9296 (tp) cc_final: 0.8480 (tp) REVERT: o 92 GLN cc_start: 0.8549 (mt0) cc_final: 0.8310 (mm-40) REVERT: o 139 GLU cc_start: 0.8541 (tp30) cc_final: 0.8053 (tm-30) REVERT: s 181 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.6989 (tmm) REVERT: e 17 TRP cc_start: 0.5796 (m-10) cc_final: 0.5266 (m100) REVERT: a 34 LYS cc_start: 0.8818 (mttp) cc_final: 0.8539 (mttp) REVERT: a 90 PHE cc_start: 0.6833 (t80) cc_final: 0.6601 (t80) REVERT: a 311 ASN cc_start: 0.6693 (t0) cc_final: 0.6460 (t0) REVERT: a 458 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7763 (tt) REVERT: a 515 TYR cc_start: 0.5472 (t80) cc_final: 0.4447 (t80) REVERT: a 718 MET cc_start: 0.6351 (ptm) cc_final: 0.5889 (ptt) REVERT: a 740 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7569 (mt) REVERT: a 749 HIS cc_start: 0.5678 (OUTLIER) cc_final: 0.5412 (m170) REVERT: a 806 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7596 (tp) REVERT: a 819 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8136 (t) REVERT: a 827 SER cc_start: 0.8958 (m) cc_final: 0.8673 (p) outliers start: 236 outliers final: 174 residues processed: 741 average time/residue: 0.3124 time to fit residues: 379.4038 Evaluate side-chains 781 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 584 time to evaluate : 2.911 ------------------------------------------------------------------------------- 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 382 VAL Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 404 GLN 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 75 SER 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 112 ILE Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 197 LYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 206 THR 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 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 39 VAL 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 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 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 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 121 THR Chi-restraints excluded: chain h residue 129 VAL 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 47 MET 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 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 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 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 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 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 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 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 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 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 136 ILE 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 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 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 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 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 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 740 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 790 ILE Chi-restraints excluded: chain a residue 802 HIS Chi-restraints excluded: chain a residue 806 LEU 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: 5.9990 chunk 93 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 315 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 265 GLN ** 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** e 59 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.136658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.116639 restraints weight = 59039.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.118961 restraints weight = 30783.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.120460 restraints weight = 18830.651| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25761 Z= 0.220 Angle : 0.736 14.618 34939 Z= 0.379 Chirality : 0.044 0.431 4096 Planarity : 0.004 0.056 4332 Dihedral : 6.169 59.684 3766 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 9.59 % Allowed : 26.36 % Favored : 64.05 % 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: 0.90 (0.15), residues: 3239 helix: 1.54 (0.11), residues: 2252 sheet: 0.17 (0.52), residues: 106 loop : -1.87 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP a 595 HIS 0.010 0.001 HIS a 762 PHE 0.027 0.002 PHE a 780 TYR 0.038 0.002 TYR s 47 ARG 0.008 0.001 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 7) link_NAG-ASN : angle 4.36376 ( 21) link_BETA1-4 : bond 0.00614 ( 5) link_BETA1-4 : angle 2.62855 ( 15) hydrogen bonds : bond 0.07116 ( 1860) hydrogen bonds : angle 4.60929 ( 5493) covalent geometry : bond 0.00496 (25749) covalent geometry : angle 0.72691 (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 831 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 577 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: c 382 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8583 (p) REVERT: b 7 LEU cc_start: 0.9069 (tp) cc_final: 0.8794 (tt) REVERT: d 75 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8317 (mmmt) REVERT: d 197 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8954 (ttmm) REVERT: d 215 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7819 (mm-30) REVERT: d 308 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8086 (t80) REVERT: f 36 HIS cc_start: 0.5835 (OUTLIER) cc_final: 0.5063 (m-70) REVERT: f 57 ASN cc_start: 0.8365 (m-40) cc_final: 0.7985 (t0) REVERT: f 58 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7922 (pt) REVERT: f 67 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.5230 (m-80) REVERT: f 82 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7551 (t80) REVERT: f 86 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7914 (mm-40) REVERT: g 23 MET cc_start: 0.8064 (tpp) cc_final: 0.7486 (tpt) REVERT: g 47 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6688 (ttp) REVERT: h 17 MET cc_start: 0.8335 (tpp) cc_final: 0.8085 (mmp) REVERT: i 39 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.7647 (p) REVERT: i 97 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7953 (mp) REVERT: i 139 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6269 (tm-30) REVERT: j 26 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.7916 (t) REVERT: j 41 ILE cc_start: 0.8392 (tp) cc_final: 0.8020 (tp) REVERT: j 151 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7429 (tp) REVERT: k 23 MET cc_start: 0.8231 (tpt) cc_final: 0.7853 (tpp) REVERT: k 51 LEU cc_start: 0.7795 (mm) cc_final: 0.7363 (tp) REVERT: k 87 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7486 (t80) REVERT: l 23 MET cc_start: 0.7895 (tpt) cc_final: 0.7586 (tpt) REVERT: m 23 MET cc_start: 0.7721 (tpt) cc_final: 0.7347 (tpp) REVERT: m 54 LYS cc_start: 0.8748 (mmtp) cc_final: 0.8257 (mmtp) REVERT: m 115 ASP cc_start: 0.8234 (t70) cc_final: 0.7628 (t0) REVERT: m 131 MET cc_start: 0.8695 (ttp) cc_final: 0.8399 (ttt) REVERT: n 51 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8642 (tt) REVERT: n 132 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9167 (pt) REVERT: n 155 LYS cc_start: 0.7220 (tttt) cc_final: 0.6848 (ttmt) REVERT: o 55 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.8630 (t) REVERT: s 120 MET cc_start: 0.3378 (mmm) cc_final: 0.3171 (mmm) REVERT: s 181 MET cc_start: 0.7777 (tpp) cc_final: 0.6837 (tmm) REVERT: a 34 LYS cc_start: 0.8836 (mttp) cc_final: 0.8518 (mttp) REVERT: a 90 PHE cc_start: 0.7037 (t80) cc_final: 0.6787 (t80) REVERT: a 458 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7779 (tt) REVERT: a 515 TYR cc_start: 0.5336 (t80) cc_final: 0.4170 (t80) REVERT: a 570 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.7011 (m-10) REVERT: a 590 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8149 (tp) REVERT: a 650 TRP cc_start: 0.6183 (m100) cc_final: 0.5360 (m100) REVERT: a 740 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7694 (mt) REVERT: a 806 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7647 (tp) REVERT: a 827 SER cc_start: 0.8969 (m) cc_final: 0.8722 (p) outliers start: 254 outliers final: 190 residues processed: 733 average time/residue: 0.3084 time to fit residues: 369.5103 Evaluate side-chains 759 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 547 time to evaluate : 2.733 ------------------------------------------------------------------------------- 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 382 VAL Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 404 GLN 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 b residue 202 VAL Chi-restraints excluded: chain d residue 105 SER 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 197 LYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 206 THR Chi-restraints excluded: chain d residue 279 LEU Chi-restraints excluded: chain d residue 300 GLU 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 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 39 VAL Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 67 TYR 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 39 THR Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 113 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 129 VAL 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 67 ILE 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 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 28 MET 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 112 ILE 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 112 ILE 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 56 ILE Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 86 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 m residue 148 VAL 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 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 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 282 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 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 740 LEU Chi-restraints excluded: chain a residue 802 HIS Chi-restraints excluded: chain a residue 806 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 278 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 277 optimal weight: 0.1980 chunk 237 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 375 GLN ** a 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** 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 = 0.4011 r_free = 0.4011 target = 0.140037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.120235 restraints weight = 58808.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.122696 restraints weight = 30567.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.124218 restraints weight = 18588.532| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25761 Z= 0.168 Angle : 0.703 14.544 34939 Z= 0.358 Chirality : 0.043 0.428 4096 Planarity : 0.004 0.054 4332 Dihedral : 6.034 59.841 3763 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 7.97 % Allowed : 27.76 % Favored : 64.27 % 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: 1.01 (0.15), residues: 3239 helix: 1.65 (0.11), residues: 2270 sheet: 0.17 (0.51), residues: 106 loop : -2.00 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP e 17 HIS 0.010 0.001 HIS a 749 PHE 0.025 0.001 PHE h 108 TYR 0.027 0.002 TYR k 144 ARG 0.010 0.000 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 7) link_NAG-ASN : angle 4.25856 ( 21) link_BETA1-4 : bond 0.00563 ( 5) link_BETA1-4 : angle 2.49358 ( 15) hydrogen bonds : bond 0.06598 ( 1860) hydrogen bonds : angle 4.38369 ( 5493) covalent geometry : bond 0.00363 (25749) covalent geometry : angle 0.69353 (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 803 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 592 time to evaluate : 2.739 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: b 7 LEU cc_start: 0.8976 (tp) cc_final: 0.8728 (tt) REVERT: d 75 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8284 (mmmt) REVERT: d 197 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8952 (ttmm) REVERT: d 215 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7754 (mm-30) REVERT: d 308 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.7959 (t80) REVERT: f 36 HIS cc_start: 0.5817 (OUTLIER) cc_final: 0.5096 (m-70) REVERT: f 57 ASN cc_start: 0.8364 (m-40) cc_final: 0.7945 (t0) REVERT: f 58 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7848 (pt) REVERT: f 67 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.5168 (m-80) REVERT: f 82 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7600 (t80) REVERT: f 86 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7835 (mm-40) REVERT: g 23 MET cc_start: 0.7947 (tpp) cc_final: 0.7327 (tpt) REVERT: g 47 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6627 (ttp) REVERT: g 61 MET cc_start: 0.7169 (mtp) cc_final: 0.6891 (mtm) REVERT: h 36 LYS cc_start: 0.8117 (ptmm) cc_final: 0.7741 (ptmm) REVERT: h 131 MET cc_start: 0.7267 (tmm) cc_final: 0.6941 (tmm) REVERT: i 97 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7940 (mp) REVERT: i 139 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6257 (tm-30) REVERT: j 26 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.7868 (t) REVERT: j 41 ILE cc_start: 0.8443 (tp) cc_final: 0.8122 (tp) REVERT: k 51 LEU cc_start: 0.7876 (mm) cc_final: 0.7441 (tp) REVERT: k 87 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7230 (t80) REVERT: l 26 SER cc_start: 0.8874 (p) cc_final: 0.8667 (t) REVERT: m 23 MET cc_start: 0.7605 (tpt) cc_final: 0.7251 (tpp) REVERT: m 54 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8195 (mmtp) REVERT: m 115 ASP cc_start: 0.8269 (t70) cc_final: 0.7655 (t0) REVERT: m 131 MET cc_start: 0.8648 (ttp) cc_final: 0.8142 (ttt) REVERT: n 51 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8683 (tt) REVERT: n 132 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9181 (pt) REVERT: n 155 LYS cc_start: 0.7041 (tttt) cc_final: 0.6695 (ttmt) REVERT: o 7 ASN cc_start: 0.8246 (p0) cc_final: 0.7974 (p0) REVERT: o 55 SER cc_start: 0.9324 (OUTLIER) cc_final: 0.8645 (t) REVERT: o 139 GLU cc_start: 0.8642 (tp30) cc_final: 0.8231 (tm-30) REVERT: s 76 ARG cc_start: 0.5311 (OUTLIER) cc_final: 0.4936 (pmt-80) REVERT: s 97 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7880 (tt) REVERT: s 120 MET cc_start: 0.3774 (mmm) cc_final: 0.3569 (mmm) REVERT: s 181 MET cc_start: 0.7789 (tpp) cc_final: 0.6764 (tmm) REVERT: a 34 LYS cc_start: 0.8795 (mttp) cc_final: 0.8499 (mttp) REVERT: a 458 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7786 (tt) REVERT: a 515 TYR cc_start: 0.5189 (t80) cc_final: 0.4108 (t80) REVERT: a 570 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.7044 (m-10) REVERT: a 590 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8051 (tp) REVERT: a 650 TRP cc_start: 0.6182 (m100) cc_final: 0.5417 (m100) REVERT: a 740 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7550 (mt) REVERT: a 827 SER cc_start: 0.9005 (m) cc_final: 0.8734 (p) outliers start: 211 outliers final: 161 residues processed: 723 average time/residue: 0.3349 time to fit residues: 396.9055 Evaluate side-chains 741 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 561 time to evaluate : 2.774 ------------------------------------------------------------------------------- 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 368 VAL 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 61 LEU Chi-restraints excluded: chain b residue 75 SER 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 49 LEU Chi-restraints excluded: chain d residue 105 SER 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 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 51 PHE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 67 TYR 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 74 VAL 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 141 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 i residue 39 THR Chi-restraints excluded: chain i residue 41 ILE 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 134 ILE 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 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 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 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 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 65 ILE Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 86 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 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 51 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 70 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 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 619 VAL Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 76 ARG Chi-restraints excluded: chain s residue 88 VAL 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 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 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 218 SER 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 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 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 763 ILE Chi-restraints excluded: chain a residue 802 HIS 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: 1.9990 chunk 72 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 118 optimal weight: 0.0070 chunk 71 optimal weight: 0.7980 chunk 312 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 281 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- 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** ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN s 78 HIS ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** 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 = 0.4060 r_free = 0.4060 target = 0.143792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.123983 restraints weight = 57734.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.126504 restraints weight = 29778.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.128064 restraints weight = 17826.779| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3530 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= 0.153 Angle : 0.698 14.259 34939 Z= 0.351 Chirality : 0.042 0.417 4096 Planarity : 0.004 0.054 4332 Dihedral : 5.880 58.979 3763 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 6.57 % Allowed : 29.68 % Favored : 63.75 % 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: 1.13 (0.15), residues: 3239 helix: 1.76 (0.11), residues: 2270 sheet: 0.10 (0.53), residues: 97 loop : -1.99 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP e 17 HIS 0.008 0.001 HIS a 412 PHE 0.019 0.001 PHE a 584 TYR 0.028 0.001 TYR h 32 ARG 0.007 0.000 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 7) link_NAG-ASN : angle 4.10710 ( 21) link_BETA1-4 : bond 0.00561 ( 5) link_BETA1-4 : angle 2.36419 ( 15) hydrogen bonds : bond 0.06027 ( 1860) hydrogen bonds : angle 4.22745 ( 5493) covalent geometry : bond 0.00320 (25749) covalent geometry : angle 0.68952 (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: 174 poor density : 609 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 108 MET cc_start: 0.8712 (tpp) cc_final: 0.8486 (tpp) REVERT: d 75 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8263 (mmmt) REVERT: d 197 LYS cc_start: 0.9233 (ttmm) cc_final: 0.8923 (ttmm) REVERT: d 215 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7795 (mm-30) REVERT: d 278 LEU cc_start: 0.9512 (tp) cc_final: 0.9288 (pp) REVERT: d 308 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8045 (t80) REVERT: f 36 HIS cc_start: 0.5450 (OUTLIER) cc_final: 0.4758 (m-70) REVERT: f 57 ASN cc_start: 0.8272 (m-40) cc_final: 0.7953 (t0) REVERT: f 58 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7800 (pt) REVERT: f 82 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7484 (t80) REVERT: f 86 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7826 (mm-40) REVERT: g 23 MET cc_start: 0.7839 (tpp) cc_final: 0.7202 (tpt) REVERT: g 47 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6607 (ttp) REVERT: g 139 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6924 (tm-30) REVERT: h 36 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7860 (ptmm) REVERT: h 108 PHE cc_start: 0.8107 (m-80) cc_final: 0.7899 (m-80) REVERT: i 51 LEU cc_start: 0.7129 (pt) cc_final: 0.6650 (pp) REVERT: i 97 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7845 (mp) REVERT: i 139 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6159 (tm-30) REVERT: j 41 ILE cc_start: 0.8345 (tp) cc_final: 0.8001 (tp) REVERT: j 151 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7418 (tp) REVERT: k 51 LEU cc_start: 0.7934 (mm) cc_final: 0.7525 (tp) REVERT: k 61 MET cc_start: 0.7834 (mmt) cc_final: 0.7373 (mtp) REVERT: k 87 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.7106 (t80) REVERT: k 144 TYR cc_start: 0.7974 (m-80) cc_final: 0.7774 (m-80) REVERT: m 23 MET cc_start: 0.7481 (tpt) cc_final: 0.7158 (tpp) REVERT: m 48 ARG cc_start: 0.8655 (mmt90) cc_final: 0.8266 (mmt90) REVERT: m 54 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8312 (mmtp) REVERT: m 115 ASP cc_start: 0.8217 (t70) cc_final: 0.7559 (t0) REVERT: m 131 MET cc_start: 0.8556 (ttp) cc_final: 0.8225 (ttp) REVERT: n 51 LEU cc_start: 0.8996 (mm) cc_final: 0.8706 (tt) REVERT: n 132 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9188 (pt) REVERT: n 155 LYS cc_start: 0.6938 (tttt) cc_final: 0.6622 (ttmt) REVERT: o 7 ASN cc_start: 0.8368 (p0) cc_final: 0.8086 (p0) REVERT: o 55 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8753 (t) REVERT: o 92 GLN cc_start: 0.8111 (mt0) cc_final: 0.7783 (mt0) REVERT: s 181 MET cc_start: 0.7737 (tpp) cc_final: 0.6726 (tmm) REVERT: e 17 TRP cc_start: 0.5457 (m-10) cc_final: 0.5196 (m100) REVERT: a 515 TYR cc_start: 0.5142 (t80) cc_final: 0.4109 (t80) REVERT: a 570 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6982 (m-10) REVERT: a 574 ILE cc_start: 0.7541 (mt) cc_final: 0.7334 (mm) REVERT: a 650 TRP cc_start: 0.6142 (m100) cc_final: 0.5328 (m100) REVERT: a 740 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7432 (mt) REVERT: a 827 SER cc_start: 0.8975 (m) cc_final: 0.8689 (p) outliers start: 174 outliers final: 133 residues processed: 710 average time/residue: 0.3151 time to fit residues: 365.4715 Evaluate side-chains 727 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 581 time to evaluate : 2.730 ------------------------------------------------------------------------------- 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 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 61 LEU Chi-restraints excluded: chain b residue 75 SER 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 49 LEU 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 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 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 17 MET 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 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 121 THR 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 41 ILE 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 134 ILE 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 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 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 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 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 74 VAL 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 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 51 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 70 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 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 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 15 LEU 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 218 SER 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 567 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 652 LEU Chi-restraints excluded: chain a residue 653 LEU Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 802 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 238 optimal weight: 0.8980 chunk 310 optimal weight: 9.9990 chunk 52 optimal weight: 0.0050 chunk 273 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 227 optimal weight: 50.0000 chunk 131 optimal weight: 0.3980 chunk 141 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 315 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.0596 ------------------------------------------------------------------------------- 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 299 HIS d 304 ASN ** d 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** 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 = 0.4065 r_free = 0.4065 target = 0.144128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.124025 restraints weight = 58908.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.126569 restraints weight = 29960.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.128352 restraints weight = 18263.391| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25761 Z= 0.151 Angle : 0.710 14.127 34939 Z= 0.354 Chirality : 0.042 0.413 4096 Planarity : 0.004 0.053 4332 Dihedral : 5.743 58.850 3762 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.85 % Allowed : 30.44 % Favored : 63.71 % 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: 1.19 (0.15), residues: 3239 helix: 1.81 (0.11), residues: 2271 sheet: 0.12 (0.53), residues: 97 loop : -1.97 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP e 17 HIS 0.004 0.001 HIS a 762 PHE 0.020 0.001 PHE a 101 TYR 0.026 0.001 TYR k 144 ARG 0.011 0.001 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 7) link_NAG-ASN : angle 4.03745 ( 21) link_BETA1-4 : bond 0.00599 ( 5) link_BETA1-4 : angle 2.29055 ( 15) hydrogen bonds : bond 0.05736 ( 1860) hydrogen bonds : angle 4.16516 ( 5493) covalent geometry : bond 0.00317 (25749) covalent geometry : angle 0.70228 (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 760 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 605 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 108 MET cc_start: 0.8860 (tpp) cc_final: 0.8650 (tpp) REVERT: d 75 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8300 (mmmt) REVERT: d 197 LYS cc_start: 0.9261 (ttmm) cc_final: 0.8914 (ttmm) REVERT: d 215 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7864 (mm-30) REVERT: d 278 LEU cc_start: 0.9525 (tp) cc_final: 0.9267 (pp) REVERT: d 308 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.7986 (t80) REVERT: d 346 ILE cc_start: 0.9171 (tt) cc_final: 0.8894 (tt) REVERT: f 57 ASN cc_start: 0.8446 (m-40) cc_final: 0.7964 (t0) REVERT: f 58 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7871 (pt) REVERT: f 82 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7506 (t80) REVERT: f 86 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7841 (mm-40) REVERT: g 23 MET cc_start: 0.7903 (tpp) cc_final: 0.7231 (tpt) REVERT: g 47 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6735 (ttp) REVERT: g 61 MET cc_start: 0.7068 (mtp) cc_final: 0.6793 (mtm) REVERT: g 139 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6862 (tm-30) REVERT: i 51 LEU cc_start: 0.7367 (pt) cc_final: 0.6905 (pp) REVERT: i 61 MET cc_start: 0.7003 (mmm) cc_final: 0.6682 (mmm) REVERT: i 97 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7895 (mp) REVERT: i 139 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6066 (tm-30) REVERT: j 41 ILE cc_start: 0.8349 (tp) cc_final: 0.8037 (tp) REVERT: j 151 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7346 (tp) REVERT: k 23 MET cc_start: 0.7948 (tpt) cc_final: 0.7725 (tpt) REVERT: k 51 LEU cc_start: 0.8086 (mm) cc_final: 0.7575 (tp) REVERT: k 61 MET cc_start: 0.7824 (mmt) cc_final: 0.7480 (mtp) REVERT: k 87 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.6915 (t80) REVERT: k 144 TYR cc_start: 0.8046 (m-80) cc_final: 0.7772 (m-80) REVERT: m 48 ARG cc_start: 0.8746 (mmt90) cc_final: 0.8320 (mmt90) REVERT: m 115 ASP cc_start: 0.8309 (t70) cc_final: 0.7698 (t0) REVERT: m 131 MET cc_start: 0.8405 (ttp) cc_final: 0.8179 (ttp) REVERT: n 51 LEU cc_start: 0.9083 (mm) cc_final: 0.8727 (tt) REVERT: n 132 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9108 (pt) REVERT: n 155 LYS cc_start: 0.7165 (tttt) cc_final: 0.6792 (ttmt) REVERT: o 50 GLU cc_start: 0.8586 (pm20) cc_final: 0.8365 (pm20) REVERT: o 92 GLN cc_start: 0.8146 (mt0) cc_final: 0.7856 (mt0) REVERT: s 181 MET cc_start: 0.7480 (tpp) cc_final: 0.6545 (tmm) REVERT: e 17 TRP cc_start: 0.5570 (m-10) cc_final: 0.5285 (m100) REVERT: a 34 LYS cc_start: 0.8731 (mttp) cc_final: 0.8405 (mttp) REVERT: a 515 TYR cc_start: 0.5259 (t80) cc_final: 0.4160 (t80) REVERT: a 570 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.6980 (m-10) REVERT: a 650 TRP cc_start: 0.6216 (m100) cc_final: 0.5403 (m100) REVERT: a 740 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7478 (mt) REVERT: a 827 SER cc_start: 0.8973 (m) cc_final: 0.8724 (p) outliers start: 155 outliers final: 128 residues processed: 697 average time/residue: 0.3183 time to fit residues: 364.4664 Evaluate side-chains 727 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 588 time to evaluate : 2.798 ------------------------------------------------------------------------------- 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 350 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 155 CYS Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 49 LEU 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 352 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 18 LEU 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 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 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 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 121 THR 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 41 ILE 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 134 ILE Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 141 LEU 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 34 THR 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 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 148 VAL 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 57 ILE Chi-restraints excluded: chain n residue 59 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 51 LEU Chi-restraints excluded: chain o residue 70 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 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 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 15 LEU 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 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 567 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 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: 0.1980 chunk 206 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 chunk 56 optimal weight: 0.0770 chunk 152 optimal weight: 6.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.145484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.125318 restraints weight = 59444.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.128001 restraints weight = 30309.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.129664 restraints weight = 17995.628| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25761 Z= 0.146 Angle : 0.721 14.051 34939 Z= 0.355 Chirality : 0.042 0.406 4096 Planarity : 0.004 0.053 4332 Dihedral : 5.587 59.145 3761 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.87 % Allowed : 31.31 % Favored : 63.82 % 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: 2257 sheet: 0.24 (0.54), residues: 95 loop : -1.95 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP a 293 HIS 0.005 0.001 HIS a 343 PHE 0.024 0.001 PHE h 108 TYR 0.026 0.001 TYR k 144 ARG 0.016 0.000 ARG a 387 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 7) link_NAG-ASN : angle 3.95601 ( 21) link_BETA1-4 : bond 0.00552 ( 5) link_BETA1-4 : angle 2.17656 ( 15) hydrogen bonds : bond 0.05324 ( 1860) hydrogen bonds : angle 4.09233 ( 5493) covalent geometry : bond 0.00306 (25749) covalent geometry : angle 0.71338 (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 758 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 629 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 108 MET cc_start: 0.8917 (tpp) cc_final: 0.8593 (tpp) REVERT: d 75 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8314 (mmmt) REVERT: d 107 MET cc_start: 0.8277 (mtm) cc_final: 0.7987 (ttp) REVERT: d 197 LYS cc_start: 0.9226 (ttmm) cc_final: 0.8880 (ttmm) REVERT: d 215 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7875 (mm-30) REVERT: d 278 LEU cc_start: 0.9520 (tp) cc_final: 0.9262 (pp) REVERT: d 308 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8005 (t80) REVERT: d 346 ILE cc_start: 0.9111 (tt) cc_final: 0.8863 (tt) REVERT: f 57 ASN cc_start: 0.8410 (m-40) cc_final: 0.7984 (t0) REVERT: f 58 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7699 (pt) REVERT: f 82 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7627 (t80) REVERT: f 86 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7828 (mm-40) REVERT: g 17 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7648 (mtp) REVERT: g 23 MET cc_start: 0.7953 (tpp) cc_final: 0.7270 (tpt) REVERT: g 47 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6770 (ttp) REVERT: g 61 MET cc_start: 0.7135 (mtp) cc_final: 0.6852 (mtm) REVERT: g 139 GLU cc_start: 0.7540 (tm-30) cc_final: 0.6872 (tm-30) REVERT: i 51 LEU cc_start: 0.7389 (pt) cc_final: 0.6925 (pp) REVERT: i 61 MET cc_start: 0.7200 (mmm) cc_final: 0.6737 (mmm) REVERT: i 92 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: i 97 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7822 (mp) REVERT: j 41 ILE cc_start: 0.8302 (tp) cc_final: 0.8046 (tp) REVERT: j 151 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7194 (tp) REVERT: k 23 MET cc_start: 0.7908 (tpt) cc_final: 0.7698 (tpt) REVERT: k 51 LEU cc_start: 0.8143 (mm) cc_final: 0.7584 (tp) REVERT: k 61 MET cc_start: 0.7749 (mmt) cc_final: 0.6984 (mtm) REVERT: k 87 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6591 (t80) REVERT: k 144 TYR cc_start: 0.7787 (m-80) cc_final: 0.7475 (m-80) REVERT: l 61 MET cc_start: 0.8825 (mmm) cc_final: 0.8273 (mmm) REVERT: m 53 MET cc_start: 0.8082 (pmm) cc_final: 0.7346 (ppp) REVERT: m 115 ASP cc_start: 0.8364 (t70) cc_final: 0.7765 (t0) REVERT: m 131 MET cc_start: 0.8301 (ttp) cc_final: 0.8086 (ttp) REVERT: m 151 ILE cc_start: 0.8805 (tp) cc_final: 0.8574 (tp) REVERT: n 51 LEU cc_start: 0.9121 (mm) cc_final: 0.8725 (tt) REVERT: n 132 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9050 (pt) REVERT: n 155 LYS cc_start: 0.7179 (tttt) cc_final: 0.6655 (ttmt) REVERT: o 36 LYS cc_start: 0.9091 (tppp) cc_final: 0.8841 (tppt) REVERT: o 50 GLU cc_start: 0.8588 (pm20) cc_final: 0.8346 (pm20) REVERT: o 92 GLN cc_start: 0.8045 (mt0) cc_final: 0.7824 (mt0) REVERT: s 181 MET cc_start: 0.7575 (tpp) cc_final: 0.6678 (tmm) REVERT: a 34 LYS cc_start: 0.8662 (mttp) cc_final: 0.8338 (mttp) REVERT: a 515 TYR cc_start: 0.5312 (t80) cc_final: 0.4184 (t80) REVERT: a 570 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.7036 (m-10) REVERT: a 650 TRP cc_start: 0.6256 (m100) cc_final: 0.5428 (m100) REVERT: a 727 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8304 (pt0) REVERT: a 740 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7522 (mt) REVERT: a 808 TRP cc_start: 0.7633 (m-10) cc_final: 0.7403 (m-10) REVERT: a 827 SER cc_start: 0.8963 (m) cc_final: 0.8748 (p) outliers start: 129 outliers final: 103 residues processed: 709 average time/residue: 0.3180 time to fit residues: 368.3900 Evaluate side-chains 707 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 592 time to evaluate : 2.736 ------------------------------------------------------------------------------- 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 350 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 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 49 LEU Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 200 THR 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 18 LEU 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 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 101 LEU Chi-restraints excluded: chain g residue 132 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 121 THR 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 i residue 41 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 128 PHE Chi-restraints excluded: chain i residue 134 ILE 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 118 VAL 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 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 57 ILE Chi-restraints excluded: chain n residue 59 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 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 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 e residue 41 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 15 LEU 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 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 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 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: 6.9990 chunk 88 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 180 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 394 GLN d 173 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** ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** 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 = 0.4031 r_free = 0.4031 target = 0.141626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.121646 restraints weight = 59041.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.124014 restraints weight = 30566.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.125690 restraints weight = 19143.067| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25761 Z= 0.184 Angle : 0.765 14.599 34939 Z= 0.382 Chirality : 0.044 0.408 4096 Planarity : 0.004 0.053 4332 Dihedral : 5.696 57.945 3761 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.91 % Allowed : 31.76 % Favored : 63.33 % 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: 1.06 (0.15), residues: 3239 helix: 1.70 (0.11), residues: 2271 sheet: 0.20 (0.55), residues: 95 loop : -2.00 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP e 17 HIS 0.004 0.001 HIS b 129 PHE 0.034 0.002 PHE h 108 TYR 0.061 0.002 TYR h 32 ARG 0.008 0.001 ARG s 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 7) link_NAG-ASN : angle 4.04146 ( 21) link_BETA1-4 : bond 0.00532 ( 5) link_BETA1-4 : angle 2.26665 ( 15) hydrogen bonds : bond 0.05920 ( 1860) hydrogen bonds : angle 4.28149 ( 5493) covalent geometry : bond 0.00418 (25749) covalent geometry : angle 0.75731 (34903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8942.73 seconds wall clock time: 156 minutes 38.70 seconds (9398.70 seconds total)