Starting phenix.real_space_refine on Wed Jul 24 06:08:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brz_44846/07_2024/9brz_44846.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brz_44846/07_2024/9brz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brz_44846/07_2024/9brz_44846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brz_44846/07_2024/9brz_44846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brz_44846/07_2024/9brz_44846.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brz_44846/07_2024/9brz_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 Residue "c GLU 287": "OE1" <-> "OE2" Residue "c GLU 366": "OE1" <-> "OE2" Residue "c GLU 403": "OE1" <-> "OE2" Residue "b GLU 6": "OE1" <-> "OE2" Residue "b GLU 44": "OE1" <-> "OE2" Residue "d GLU 8": "OE1" <-> "OE2" Residue "d GLU 177": "OE1" <-> "OE2" Residue "d GLU 193": "OE1" <-> "OE2" Residue "d GLU 215": "OE1" <-> "OE2" Residue "d GLU 217": "OE1" <-> "OE2" Residue "d GLU 237": "OE1" <-> "OE2" Residue "d GLU 336": "OE1" <-> "OE2" Residue "f TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 50": "OE1" <-> "OE2" Residue "i GLU 50": "OE1" <-> "OE2" Residue "k GLU 139": "OE1" <-> "OE2" Residue "l GLU 9": "OE1" <-> "OE2" Residue "l TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 139": "OE1" <-> "OE2" Residue "n GLU 9": "OE1" <-> "OE2" Residue "n TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 50": "OE1" <-> "OE2" Residue "n GLU 139": "OE1" <-> "OE2" Residue "o GLU 9": "OE1" <-> "OE2" Residue "o GLU 50": "OE1" <-> "OE2" Residue "o GLU 139": "OE1" <-> "OE2" Residue "p TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 634": "OD1" <-> "OD2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 50": "OE1" <-> "OE2" Residue "s GLU 180": "OE1" <-> "OE2" Residue "a GLU 87": "OE1" <-> "OE2" Residue "a GLU 107": "OE1" <-> "OE2" Residue "a GLU 110": "OE1" <-> "OE2" Residue "a GLU 184": "OE1" <-> "OE2" Residue "a GLU 201": "OE1" <-> "OE2" Residue "a GLU 427": "OE1" <-> "OE2" Residue "a GLU 727": "OE1" <-> "OE2" Residue "a GLU 754": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 13.25, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 9.74 Conformation dependent library (CDL) restraints added in 4.6 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: 2.18 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: 7.91 Time building geometry restraints manager: 10.66 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: 97.51 - 104.89: 410 104.89 - 112.26: 12663 112.26 - 119.63: 9344 119.63 - 127.01: 12246 127.01 - 134.38: 240 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 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.240 Process input model: 62.610 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.130 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.670 ------------------------------------------------------------------------------- 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 25749 Z= 0.359 Angle : 0.924 11.800 34903 Z= 0.513 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 *********************** 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 fitting. rotamer outliers: 95 poor density : 728 time to evaluate : 2.528 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: 0.3283 time to fit residues: 410.1827 Evaluate side-chains 720 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 640 time to evaluate : 2.758 ------------------------------------------------------------------------------- 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: 0.0470 chunk 246 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 295 optimal weight: 0.4980 overall best weight: 3.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 392 ASN d 167 GLN d 304 ASN f 56 GLN j 92 GLN n 92 GLN s 18 GLN ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 106 ASN a 502 GLN a 524 ASN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25749 Z= 0.304 Angle : 0.714 10.510 34903 Z= 0.376 Chirality : 0.044 0.437 4096 Planarity : 0.005 0.056 4332 Dihedral : 7.515 58.940 3876 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 7.36 % Allowed : 25.91 % Favored : 66.73 % 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: 0.78 (0.15), residues: 3239 helix: 1.37 (0.11), residues: 2191 sheet: -0.41 (0.51), residues: 119 loop : -1.39 (0.22), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 422 HIS 0.006 0.001 HIS d 313 PHE 0.032 0.002 PHE a 800 TYR 0.025 0.002 TYR b 71 ARG 0.019 0.001 ARG p 639 *********************** 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 858 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 663 time to evaluate : 2.634 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: 0.8371 (mt-10) cc_final: 0.7678 (tm-30) REVERT: c 392 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7519 (m110) REVERT: c 432 ILE cc_start: 0.9405 (mm) cc_final: 0.8947 (mt) REVERT: b 7 LEU cc_start: 0.9276 (tp) cc_final: 0.8945 (tt) REVERT: d 75 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8327 (mmmt) REVERT: d 197 LYS cc_start: 0.9288 (ttmm) cc_final: 0.8919 (ttmm) REVERT: d 215 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8336 (mt-10) REVERT: d 265 GLN cc_start: 0.9068 (mt0) cc_final: 0.8649 (mt0) REVERT: d 308 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8097 (t80) REVERT: f 57 ASN cc_start: 0.8211 (m-40) cc_final: 0.7867 (t0) REVERT: f 58 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7962 (pt) REVERT: f 67 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.5059 (m-80) REVERT: g 23 MET cc_start: 0.8209 (tpp) cc_final: 0.7817 (tpt) REVERT: g 139 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7271 (tm-30) REVERT: h 10 TYR cc_start: 0.7325 (p90) cc_final: 0.7019 (p90) REVERT: h 108 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8335 (t80) REVERT: i 28 MET cc_start: 0.8848 (mmm) cc_final: 0.8623 (mmt) REVERT: i 97 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7563 (mp) REVERT: j 23 MET cc_start: 0.7415 (ptt) cc_final: 0.7063 (ptt) REVERT: k 61 MET cc_start: 0.7818 (mmt) cc_final: 0.7556 (mmt) REVERT: k 87 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7376 (t80) REVERT: l 23 MET cc_start: 0.8191 (tpt) cc_final: 0.7977 (tpt) REVERT: l 61 MET cc_start: 0.8883 (tpp) cc_final: 0.8487 (mmm) REVERT: m 53 MET cc_start: 0.7244 (ppp) cc_final: 0.7041 (ppp) REVERT: m 115 ASP cc_start: 0.8172 (t70) cc_final: 0.7740 (t0) REVERT: m 136 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8105 (tt) REVERT: n 51 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8573 (tp) REVERT: n 155 LYS cc_start: 0.7403 (tttt) cc_final: 0.6638 (ttmt) REVERT: o 70 LEU cc_start: 0.9194 (tp) cc_final: 0.8881 (tt) REVERT: o 76 ILE cc_start: 0.9066 (tp) cc_final: 0.8042 (tp) REVERT: o 126 ARG cc_start: 0.8887 (tpp80) cc_final: 0.8574 (mmm-85) REVERT: p 627 TRP cc_start: 0.7156 (t60) cc_final: 0.6253 (t60) REVERT: s 116 PHE cc_start: 0.5000 (t80) cc_final: 0.4791 (t80) REVERT: s 170 MET cc_start: 0.6016 (tpt) cc_final: 0.5716 (tpt) REVERT: e 17 TRP cc_start: 0.4753 (m-10) cc_final: 0.4301 (m100) REVERT: a 90 PHE cc_start: 0.6594 (t80) cc_final: 0.6154 (t80) REVERT: a 119 LYS cc_start: 0.9297 (tppp) cc_final: 0.9029 (tppt) REVERT: a 311 ASN cc_start: 0.6868 (t0) cc_final: 0.6583 (t0) REVERT: a 338 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8206 (ttp-110) REVERT: a 479 TRP cc_start: 0.7175 (m100) cc_final: 0.6785 (m100) REVERT: a 515 TYR cc_start: 0.5544 (t80) cc_final: 0.4796 (t80) REVERT: a 732 CYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7260 (p) REVERT: a 749 HIS cc_start: 0.5757 (OUTLIER) cc_final: 0.5401 (m170) REVERT: a 827 SER cc_start: 0.8907 (m) cc_final: 0.8591 (p) outliers start: 195 outliers final: 132 residues processed: 779 average time/residue: 0.3287 time to fit residues: 418.6988 Evaluate side-chains 746 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 603 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 288 ASN 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 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 261 ASP 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 72 VAL Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 121 THR 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 84 ILE Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 147 ILE 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 97 LEU Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 147 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 121 THR 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 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 147 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 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 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 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 118 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 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 148 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 47 TYR 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 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 206 LEU 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 435 HIS 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 495 LEU 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 164 optimal weight: 0.2980 chunk 91 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 295 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 263 optimal weight: 0.0020 chunk 293 optimal weight: 0.0770 chunk 100 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 overall best weight: 1.2750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 349 HIS ** d 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 86 GLN s 18 GLN ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25749 Z= 0.212 Angle : 0.656 10.330 34903 Z= 0.335 Chirality : 0.042 0.427 4096 Planarity : 0.004 0.055 4332 Dihedral : 6.477 58.107 3798 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.76 % Allowed : 26.81 % Favored : 66.43 % 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: 1.69 (0.11), residues: 2228 sheet: 0.09 (0.53), residues: 106 loop : -1.43 (0.22), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 490 HIS 0.006 0.001 HIS s 78 PHE 0.028 0.001 PHE a 101 TYR 0.019 0.001 TYR b 71 ARG 0.005 0.000 ARG j 126 *********************** 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 843 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 664 time to evaluate : 2.436 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: symmetry clash REVERT: c 302 MET cc_start: 0.8206 (ppp) cc_final: 0.7953 (tmm) REVERT: c 337 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7508 (tm-30) REVERT: b 7 LEU cc_start: 0.9161 (tp) cc_final: 0.8833 (tt) REVERT: d 75 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8316 (mmmt) REVERT: d 197 LYS cc_start: 0.9241 (ttmm) cc_final: 0.8829 (ttmm) REVERT: d 215 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7934 (mm-30) REVERT: d 308 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.7908 (t80) REVERT: f 57 ASN cc_start: 0.8084 (m-40) cc_final: 0.7865 (t0) REVERT: f 58 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7962 (pt) REVERT: f 67 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5173 (m-80) REVERT: f 82 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7244 (t80) REVERT: f 86 GLN cc_start: 0.8147 (mm110) cc_final: 0.7855 (mm110) REVERT: f 88 ARG cc_start: 0.8320 (tmm-80) cc_final: 0.7796 (tmm-80) REVERT: g 23 MET cc_start: 0.8094 (tpp) cc_final: 0.7253 (tpt) REVERT: g 36 LYS cc_start: 0.8684 (tptt) cc_final: 0.8377 (tptt) REVERT: g 47 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6529 (ttp) REVERT: h 108 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8421 (t80) REVERT: h 128 PHE cc_start: 0.8063 (t80) cc_final: 0.7514 (t80) REVERT: i 28 MET cc_start: 0.8867 (mmm) cc_final: 0.8546 (mmt) REVERT: i 92 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7417 (mm-40) REVERT: i 97 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7646 (mp) REVERT: j 23 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7418 (ptt) REVERT: j 41 ILE cc_start: 0.8107 (tp) cc_final: 0.7769 (tp) REVERT: j 80 LEU cc_start: 0.7724 (mt) cc_final: 0.7020 (tp) REVERT: k 23 MET cc_start: 0.8423 (tpt) cc_final: 0.7800 (tpp) REVERT: k 51 LEU cc_start: 0.8001 (mm) cc_final: 0.7579 (tp) REVERT: k 87 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7167 (t80) REVERT: k 143 LEU cc_start: 0.8611 (tp) cc_final: 0.8354 (tt) REVERT: l 28 MET cc_start: 0.8219 (mmm) cc_final: 0.8014 (mmm) REVERT: l 61 MET cc_start: 0.8839 (tpp) cc_final: 0.8596 (mmm) REVERT: m 23 MET cc_start: 0.7578 (tpt) cc_final: 0.7257 (tpp) REVERT: m 48 ARG cc_start: 0.8806 (mmt180) cc_final: 0.8326 (mmt90) REVERT: m 53 MET cc_start: 0.7136 (ppp) cc_final: 0.6720 (ppp) REVERT: m 54 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8037 (mmtp) REVERT: m 87 TYR cc_start: 0.7727 (t80) cc_final: 0.7442 (t80) REVERT: m 92 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7557 (mm-40) REVERT: m 115 ASP cc_start: 0.8236 (t70) cc_final: 0.7785 (t0) REVERT: m 131 MET cc_start: 0.8771 (ttp) cc_final: 0.8147 (ttt) REVERT: n 51 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8632 (tp) REVERT: n 131 MET cc_start: 0.8724 (tmm) cc_final: 0.8471 (ttt) REVERT: n 132 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8964 (pt) REVERT: n 155 LYS cc_start: 0.7389 (tttt) cc_final: 0.6586 (ttmt) REVERT: o 53 MET cc_start: 0.7739 (ppp) cc_final: 0.7501 (ppp) REVERT: o 55 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.8903 (t) REVERT: o 70 LEU cc_start: 0.9153 (tp) cc_final: 0.8839 (tt) REVERT: o 131 MET cc_start: 0.8540 (ttp) cc_final: 0.8253 (ttm) REVERT: p 627 TRP cc_start: 0.7213 (t60) cc_final: 0.6309 (t60) REVERT: s 116 PHE cc_start: 0.5123 (t80) cc_final: 0.4921 (t80) REVERT: s 170 MET cc_start: 0.5941 (tpt) cc_final: 0.5630 (tpt) REVERT: s 181 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7774 (tpp) REVERT: e 17 TRP cc_start: 0.4976 (m-10) cc_final: 0.4564 (m100) REVERT: a 90 PHE cc_start: 0.6726 (t80) cc_final: 0.6344 (t80) REVERT: a 338 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8125 (ttp-110) REVERT: a 502 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: a 515 TYR cc_start: 0.5391 (t80) cc_final: 0.4549 (t80) REVERT: a 718 MET cc_start: 0.6497 (ptm) cc_final: 0.6063 (ptt) REVERT: a 749 HIS cc_start: 0.5664 (OUTLIER) cc_final: 0.5218 (m170) outliers start: 179 outliers final: 111 residues processed: 767 average time/residue: 0.3432 time to fit residues: 434.3464 Evaluate side-chains 740 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 613 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 292 THR Chi-restraints excluded: chain c residue 334 PHE Chi-restraints excluded: chain c residue 437 LEU 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 112 ILE Chi-restraints excluded: chain d residue 169 CYS 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 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 82 PHE Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain g residue 136 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 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 41 ILE Chi-restraints excluded: chain i residue 47 MET Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 23 MET 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 121 THR Chi-restraints excluded: chain j residue 131 MET Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 97 LEU Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain 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 113 VAL Chi-restraints excluded: chain m residue 141 LEU 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 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 39 THR 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 613 ILE Chi-restraints excluded: chain p residue 619 VAL 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 93 THR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 181 MET Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 329 ASP Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 502 GLN Chi-restraints excluded: chain a residue 520 ASP 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 786 LEU 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 292 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 296 optimal weight: 20.0000 chunk 314 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 281 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 HIS d 304 ASN ** d 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 6 ASN m 7 ASN n 92 GLN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 311 ASN ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 524 ASN ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 25749 Z= 0.439 Angle : 0.808 11.290 34903 Z= 0.422 Chirality : 0.047 0.420 4096 Planarity : 0.005 0.068 4332 Dihedral : 6.625 59.763 3772 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 10.65 % Allowed : 25.30 % 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: 0.66 (0.15), residues: 3239 helix: 1.33 (0.11), residues: 2214 sheet: -0.01 (0.52), residues: 105 loop : -1.73 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP a 324 HIS 0.005 0.001 HIS a 548 PHE 0.031 0.002 PHE a 800 TYR 0.038 0.002 TYR k 144 ARG 0.033 0.001 ARG a 387 *********************** 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 876 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 594 time to evaluate : 2.712 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 337 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7691 (tm-30) REVERT: c 382 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8675 (p) REVERT: c 404 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8674 (pp30) REVERT: b 7 LEU cc_start: 0.9255 (tp) cc_final: 0.8927 (tt) REVERT: d 68 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8457 (p) REVERT: d 75 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8415 (mmmt) REVERT: d 87 MET cc_start: 0.9143 (tpp) cc_final: 0.8915 (tpp) REVERT: d 197 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8877 (ttmm) REVERT: d 308 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.7995 (t80) REVERT: f 57 ASN cc_start: 0.8242 (m-40) cc_final: 0.7889 (t0) REVERT: f 58 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7754 (pt) REVERT: f 67 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.5253 (m-80) REVERT: f 82 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7273 (t80) REVERT: g 23 MET cc_start: 0.8399 (tpp) cc_final: 0.7841 (tpt) REVERT: g 47 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6694 (ttp) REVERT: i 13 PHE cc_start: 0.8296 (t80) cc_final: 0.8051 (t80) REVERT: i 28 MET cc_start: 0.8867 (mmm) cc_final: 0.8661 (mmt) REVERT: i 39 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.7836 (p) REVERT: i 92 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: i 97 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7745 (mp) REVERT: i 139 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6656 (tm-30) REVERT: j 11 SER cc_start: 0.7087 (OUTLIER) cc_final: 0.6049 (t) REVERT: j 23 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7487 (ptt) REVERT: j 26 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.7832 (t) REVERT: j 41 ILE cc_start: 0.8224 (tp) cc_final: 0.7863 (tp) REVERT: j 67 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8402 (tp) REVERT: k 23 MET cc_start: 0.8217 (tpt) cc_final: 0.7770 (tpp) REVERT: k 51 LEU cc_start: 0.8069 (mm) cc_final: 0.7488 (tp) REVERT: k 87 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7711 (t80) REVERT: k 139 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7754 (tm-30) REVERT: l 23 MET cc_start: 0.8216 (tpt) cc_final: 0.7955 (tpt) REVERT: l 61 MET cc_start: 0.9061 (tpp) cc_final: 0.8715 (mmm) REVERT: m 23 MET cc_start: 0.8045 (tpt) cc_final: 0.7664 (tpp) REVERT: m 48 ARG cc_start: 0.8854 (mmt180) cc_final: 0.8469 (mmt90) REVERT: m 53 MET cc_start: 0.7116 (ppp) cc_final: 0.6791 (ppp) REVERT: m 115 ASP cc_start: 0.8275 (t70) cc_final: 0.7789 (t0) REVERT: m 131 MET cc_start: 0.8773 (ttp) cc_final: 0.8381 (ttt) REVERT: n 51 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8531 (tt) REVERT: n 80 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8646 (tt) REVERT: n 132 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.8940 (pt) REVERT: n 155 LYS cc_start: 0.8063 (tttt) cc_final: 0.7443 (ttmt) REVERT: o 53 MET cc_start: 0.7784 (ppp) cc_final: 0.7567 (ppp) REVERT: o 70 LEU cc_start: 0.9276 (tp) cc_final: 0.9029 (tt) REVERT: o 139 GLU cc_start: 0.8965 (tp30) cc_final: 0.8174 (tm-30) REVERT: s 120 MET cc_start: 0.4128 (mmm) cc_final: 0.3732 (mmm) REVERT: s 170 MET cc_start: 0.6256 (tpt) cc_final: 0.6056 (tpt) REVERT: s 181 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.6600 (tpp) REVERT: s 183 MET cc_start: 0.7291 (mmm) cc_final: 0.6503 (mmm) REVERT: e 17 TRP cc_start: 0.5849 (m-10) cc_final: 0.5176 (m100) REVERT: a 71 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7866 (tm-30) REVERT: a 90 PHE cc_start: 0.7047 (t80) cc_final: 0.6650 (t80) REVERT: a 338 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8153 (ttp-110) REVERT: a 515 TYR cc_start: 0.5690 (t80) cc_final: 0.4478 (t80) REVERT: a 590 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8293 (tp) REVERT: a 650 TRP cc_start: 0.6406 (m100) cc_final: 0.5573 (m100) REVERT: a 819 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8343 (t) REVERT: a 827 SER cc_start: 0.8965 (m) cc_final: 0.8719 (p) outliers start: 282 outliers final: 196 residues processed: 767 average time/residue: 0.3180 time to fit residues: 401.9001 Evaluate side-chains 777 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 557 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 292 THR Chi-restraints excluded: chain c residue 328 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 426 THR 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 32 LEU 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 122 THR Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 175 VAL Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain d residue 68 THR 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 174 ASP 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 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 39 VAL 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 34 THR Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 47 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 84 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 121 THR 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 g residue 154 THR 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 84 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 121 THR 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 47 MET Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 128 PHE Chi-restraints excluded: chain i residue 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 11 SER Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 23 MET 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 67 ILE Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 129 VAL 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 28 MET 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 112 ILE 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 k residue 148 VAL Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 VAL Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 85 THR 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 132 ILE 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 152 LEU 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 75 LEU Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 113 VAL 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 60 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 79 SER 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 118 VAL Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain n residue 153 SER 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 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 152 LEU Chi-restraints excluded: chain p residue 599 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 47 TYR Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 88 VAL Chi-restraints excluded: chain s residue 93 THR 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 20 ILE Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 ASN Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 215 VAL Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 450 ILE Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 494 THR Chi-restraints excluded: chain a residue 495 LEU Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 573 PHE Chi-restraints excluded: chain a residue 580 MET Chi-restraints excluded: chain a residue 589 ILE 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 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 261 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 281 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** m 7 ASN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 334 GLN ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25749 Z= 0.221 Angle : 0.672 11.899 34903 Z= 0.344 Chirality : 0.043 0.424 4096 Planarity : 0.004 0.051 4332 Dihedral : 6.193 57.690 3768 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 7.33 % Allowed : 29.12 % Favored : 63.56 % 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: 1.15 (0.15), residues: 3239 helix: 1.74 (0.11), residues: 2219 sheet: 0.17 (0.52), residues: 106 loop : -1.65 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 595 HIS 0.005 0.001 HIS a 749 PHE 0.027 0.002 PHE a 714 TYR 0.024 0.002 TYR k 144 ARG 0.007 0.000 ARG s 195 *********************** 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 800 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 606 time to evaluate : 2.649 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 302 MET cc_start: 0.7998 (ppp) cc_final: 0.7745 (tmm) REVERT: c 337 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7584 (tm-30) REVERT: b 7 LEU cc_start: 0.9153 (tp) cc_final: 0.8852 (tt) REVERT: d 75 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8367 (mmmt) REVERT: d 87 MET cc_start: 0.9034 (tpp) cc_final: 0.8813 (tpp) REVERT: d 197 LYS cc_start: 0.9258 (ttmm) cc_final: 0.8924 (ttmm) REVERT: d 215 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8015 (mm-30) REVERT: d 308 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.7878 (t80) REVERT: f 36 HIS cc_start: 0.5671 (OUTLIER) cc_final: 0.5021 (m-70) REVERT: f 57 ASN cc_start: 0.8171 (m-40) cc_final: 0.7853 (t0) REVERT: f 58 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7858 (pt) REVERT: f 82 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7371 (t80) REVERT: g 23 MET cc_start: 0.8079 (tpp) cc_final: 0.7376 (tpt) REVERT: g 47 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6597 (ttp) REVERT: i 97 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7564 (mp) REVERT: i 139 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6374 (tm-30) REVERT: j 41 ILE cc_start: 0.8252 (tp) cc_final: 0.7892 (tp) REVERT: k 23 MET cc_start: 0.8355 (tpt) cc_final: 0.7899 (tpp) REVERT: k 51 LEU cc_start: 0.7994 (mm) cc_final: 0.7432 (tt) REVERT: k 87 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7330 (t80) REVERT: k 108 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7451 (t80) REVERT: k 143 LEU cc_start: 0.8347 (tp) cc_final: 0.7988 (tt) REVERT: l 23 MET cc_start: 0.7865 (tpt) cc_final: 0.7539 (tpt) REVERT: l 61 MET cc_start: 0.9010 (tpp) cc_final: 0.8770 (mmm) REVERT: m 23 MET cc_start: 0.7677 (tpt) cc_final: 0.7355 (tpp) REVERT: m 48 ARG cc_start: 0.8864 (mmt180) cc_final: 0.8513 (mmt90) REVERT: m 53 MET cc_start: 0.6916 (ppp) cc_final: 0.6684 (ppp) REVERT: m 115 ASP cc_start: 0.8334 (t70) cc_final: 0.7845 (t0) REVERT: m 131 MET cc_start: 0.8639 (ttp) cc_final: 0.7905 (ttm) REVERT: n 51 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8617 (tt) REVERT: n 132 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8955 (pt) REVERT: n 155 LYS cc_start: 0.7660 (tttt) cc_final: 0.7045 (ttmt) REVERT: o 53 MET cc_start: 0.7838 (ppp) cc_final: 0.7632 (ppp) REVERT: o 70 LEU cc_start: 0.9206 (tp) cc_final: 0.8936 (tt) REVERT: o 139 GLU cc_start: 0.8805 (tp30) cc_final: 0.8326 (tm-30) REVERT: s 181 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.6075 (tpp) REVERT: s 183 MET cc_start: 0.7106 (mmm) cc_final: 0.6422 (mmm) REVERT: e 17 TRP cc_start: 0.5732 (m-10) cc_final: 0.5186 (m100) REVERT: a 90 PHE cc_start: 0.6765 (t80) cc_final: 0.6499 (t80) REVERT: a 338 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8393 (ptp-110) REVERT: a 502 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6179 (tm130) REVERT: a 515 TYR cc_start: 0.5544 (t80) cc_final: 0.4470 (t80) REVERT: a 570 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.7100 (m-10) REVERT: a 590 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8103 (tp) REVERT: a 650 TRP cc_start: 0.6255 (m100) cc_final: 0.5421 (m100) REVERT: a 740 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7518 (mt) REVERT: a 819 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8194 (t) REVERT: a 827 SER cc_start: 0.8979 (m) cc_final: 0.8729 (p) outliers start: 194 outliers final: 123 residues processed: 725 average time/residue: 0.3165 time to fit residues: 374.9124 Evaluate side-chains 703 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 563 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 292 THR 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 b residue 202 VAL 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 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 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 g residue 47 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 121 THR 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 57 ILE Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain h residue 150 LEU Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 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 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 59 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 131 MET Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain 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 108 PHE Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 154 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 LEU 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 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 51 LEU Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 152 LEU Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain s residue 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 s residue 199 THR 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 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 187 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 224 PHE Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 502 GLN Chi-restraints excluded: chain a residue 520 ASP 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 590 LEU Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 599 ASP 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 802 HIS Chi-restraints excluded: chain a residue 819 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 105 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 314 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** m 7 ASN ** o 7 ASN ** 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 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25749 Z= 0.303 Angle : 0.708 9.921 34903 Z= 0.365 Chirality : 0.044 0.418 4096 Planarity : 0.004 0.049 4332 Dihedral : 6.199 57.341 3765 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 8.04 % Allowed : 29.27 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 3239 helix: 1.61 (0.11), residues: 2265 sheet: 0.30 (0.52), residues: 105 loop : -1.95 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP a 595 HIS 0.008 0.001 HIS a 762 PHE 0.025 0.002 PHE h 108 TYR 0.028 0.002 TYR k 144 ARG 0.008 0.000 ARG s 195 *********************** 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 781 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 568 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 302 MET cc_start: 0.8050 (ppp) cc_final: 0.7841 (tmm) REVERT: c 337 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7634 (tm-30) REVERT: b 7 LEU cc_start: 0.9185 (tp) cc_final: 0.8870 (tt) REVERT: d 75 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8395 (mmmt) REVERT: d 87 MET cc_start: 0.9048 (tpp) cc_final: 0.8837 (tpp) REVERT: d 197 LYS cc_start: 0.9261 (ttmm) cc_final: 0.8896 (ttmm) REVERT: d 215 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8026 (mm-30) REVERT: d 308 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.7852 (t80) REVERT: f 36 HIS cc_start: 0.5758 (OUTLIER) cc_final: 0.5119 (m-70) REVERT: f 57 ASN cc_start: 0.8205 (m-40) cc_final: 0.7957 (t0) REVERT: f 67 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5169 (m-80) REVERT: f 82 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7292 (t80) REVERT: f 86 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7705 (mm-40) REVERT: g 23 MET cc_start: 0.8276 (tpp) cc_final: 0.7662 (tpt) REVERT: g 47 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6779 (ttp) REVERT: i 39 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.7661 (p) REVERT: i 97 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7723 (mp) REVERT: i 139 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: j 11 SER cc_start: 0.7053 (OUTLIER) cc_final: 0.5971 (t) REVERT: j 23 MET cc_start: 0.8014 (ptm) cc_final: 0.7677 (ptm) REVERT: j 26 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.7840 (t) REVERT: j 41 ILE cc_start: 0.8233 (tp) cc_final: 0.7870 (tp) REVERT: j 151 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7281 (tp) REVERT: k 51 LEU cc_start: 0.8099 (mm) cc_final: 0.7536 (tp) REVERT: k 87 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7514 (t80) REVERT: k 108 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7437 (t80) REVERT: k 143 LEU cc_start: 0.8451 (tp) cc_final: 0.8193 (tt) REVERT: l 23 MET cc_start: 0.7866 (tpt) cc_final: 0.7566 (tpt) REVERT: l 28 MET cc_start: 0.8217 (mmm) cc_final: 0.8015 (mmp) REVERT: l 50 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8448 (mm-30) REVERT: l 61 MET cc_start: 0.9014 (tpp) cc_final: 0.8780 (mmm) REVERT: m 23 MET cc_start: 0.7760 (tpt) cc_final: 0.7424 (tpp) REVERT: m 48 ARG cc_start: 0.8859 (mmt180) cc_final: 0.8528 (mmt90) REVERT: m 53 MET cc_start: 0.6883 (ppp) cc_final: 0.6668 (ppp) REVERT: m 115 ASP cc_start: 0.8384 (t70) cc_final: 0.7772 (t0) REVERT: m 131 MET cc_start: 0.8668 (ttp) cc_final: 0.8183 (ttt) REVERT: n 51 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8607 (tt) REVERT: n 132 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.8941 (pt) REVERT: n 155 LYS cc_start: 0.7906 (tttt) cc_final: 0.7308 (ttmt) REVERT: o 55 SER cc_start: 0.9316 (OUTLIER) cc_final: 0.8795 (t) REVERT: o 70 LEU cc_start: 0.9205 (tp) cc_final: 0.8966 (tt) REVERT: o 139 GLU cc_start: 0.8836 (tp30) cc_final: 0.8125 (tm-30) REVERT: s 181 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.6035 (tpp) REVERT: s 183 MET cc_start: 0.7123 (mmm) cc_final: 0.6462 (mmm) REVERT: a 90 PHE cc_start: 0.6873 (t80) cc_final: 0.6630 (t80) REVERT: a 338 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8420 (ptp-110) REVERT: a 387 ARG cc_start: 0.5013 (ttt-90) cc_final: 0.3582 (ptm160) REVERT: a 502 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6419 (tm130) REVERT: a 515 TYR cc_start: 0.5471 (t80) cc_final: 0.4306 (t80) REVERT: a 570 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.7118 (m-10) REVERT: a 590 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8162 (tp) REVERT: a 650 TRP cc_start: 0.6324 (m100) cc_final: 0.5480 (m100) REVERT: a 740 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7627 (mt) REVERT: a 762 HIS cc_start: 0.7922 (t70) cc_final: 0.7710 (t70) REVERT: a 827 SER cc_start: 0.8981 (m) cc_final: 0.8743 (p) outliers start: 213 outliers final: 166 residues processed: 701 average time/residue: 0.3341 time to fit residues: 384.7474 Evaluate side-chains 735 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 548 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 292 THR Chi-restraints excluded: chain c residue 328 VAL 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 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 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 b residue 202 VAL 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 174 ASP 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 306 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 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 36 HIS Chi-restraints excluded: chain f residue 61 LEU 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 37 SER Chi-restraints excluded: chain g residue 47 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 101 LEU Chi-restraints excluded: chain g residue 121 THR 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 101 LEU Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 129 VAL 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 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 11 SER Chi-restraints excluded: chain j residue 20 SER 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 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 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 132 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 85 THR Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 131 MET 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 56 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 113 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 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 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 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 88 VAL Chi-restraints excluded: chain s residue 93 THR 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 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 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 271 VAL Chi-restraints excluded: chain a residue 282 VAL Chi-restraints excluded: chain a residue 290 ILE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 495 LEU Chi-restraints excluded: chain a residue 502 GLN Chi-restraints excluded: chain a residue 520 ASP 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 599 ASP 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 730 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 303 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 177 optimal weight: 0.5980 chunk 264 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 313 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 7 ASN ** o 7 ASN ** 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 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 637 GLN ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25749 Z= 0.254 Angle : 0.681 9.087 34903 Z= 0.351 Chirality : 0.043 0.421 4096 Planarity : 0.004 0.050 4332 Dihedral : 6.177 57.006 3765 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 8.16 % Allowed : 29.42 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3239 helix: 1.70 (0.11), residues: 2264 sheet: 0.28 (0.52), residues: 105 loop : -1.97 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP e 17 HIS 0.007 0.001 HIS a 661 PHE 0.027 0.002 PHE h 108 TYR 0.028 0.002 TYR s 47 ARG 0.010 0.000 ARG s 195 *********************** 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 789 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 573 time to evaluate : 2.896 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 302 MET cc_start: 0.8042 (ppp) cc_final: 0.7811 (tmm) REVERT: c 337 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7595 (tm-30) REVERT: c 341 ILE cc_start: 0.9354 (mm) cc_final: 0.9090 (mm) REVERT: b 7 LEU cc_start: 0.9153 (tp) cc_final: 0.8849 (tt) REVERT: b 101 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7949 (p) REVERT: d 75 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8396 (mmmt) REVERT: d 87 MET cc_start: 0.9032 (tpp) cc_final: 0.8812 (tpp) REVERT: d 197 LYS cc_start: 0.9272 (ttmm) cc_final: 0.8902 (ttmm) REVERT: d 215 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8023 (mm-30) REVERT: d 308 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.7825 (t80) REVERT: f 36 HIS cc_start: 0.5717 (OUTLIER) cc_final: 0.5023 (m-70) REVERT: f 57 ASN cc_start: 0.8286 (m-40) cc_final: 0.7990 (t0) REVERT: f 58 ILE cc_start: 0.8007 (pt) cc_final: 0.7722 (pp) REVERT: f 67 TYR cc_start: 0.6416 (OUTLIER) cc_final: 0.5203 (m-80) REVERT: f 82 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7298 (t80) REVERT: f 86 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7850 (mm-40) REVERT: g 23 MET cc_start: 0.8210 (tpp) cc_final: 0.7579 (tpt) REVERT: g 47 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6775 (ttp) REVERT: h 36 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7598 (ttpp) REVERT: i 39 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7557 (p) REVERT: i 51 LEU cc_start: 0.7612 (pt) cc_final: 0.7197 (pp) REVERT: i 97 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7617 (mp) REVERT: i 139 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6514 (tm-30) REVERT: j 23 MET cc_start: 0.8050 (ptm) cc_final: 0.7647 (ptm) REVERT: j 26 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.7830 (t) REVERT: j 41 ILE cc_start: 0.8200 (tp) cc_final: 0.7852 (tp) REVERT: k 23 MET cc_start: 0.8069 (tpt) cc_final: 0.7848 (tpt) REVERT: k 51 LEU cc_start: 0.8153 (mm) cc_final: 0.7563 (tp) REVERT: k 87 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7416 (t80) REVERT: k 108 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7397 (t80) REVERT: k 143 LEU cc_start: 0.8370 (tp) cc_final: 0.8011 (tt) REVERT: l 23 MET cc_start: 0.7796 (tpt) cc_final: 0.7528 (tpt) REVERT: l 50 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8451 (mm-30) REVERT: l 61 MET cc_start: 0.8991 (tpp) cc_final: 0.8769 (mmm) REVERT: m 23 MET cc_start: 0.7715 (tpt) cc_final: 0.7375 (tpp) REVERT: m 48 ARG cc_start: 0.8842 (mmt180) cc_final: 0.8288 (mmt90) REVERT: m 115 ASP cc_start: 0.8415 (t70) cc_final: 0.7820 (t0) REVERT: m 131 MET cc_start: 0.8627 (ttp) cc_final: 0.8128 (ttm) REVERT: n 51 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8637 (tt) REVERT: n 132 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8971 (pt) REVERT: n 155 LYS cc_start: 0.7901 (tttt) cc_final: 0.7278 (ttmt) REVERT: o 70 LEU cc_start: 0.9154 (tp) cc_final: 0.8899 (tt) REVERT: o 139 GLU cc_start: 0.8823 (tp30) cc_final: 0.8012 (tm-30) REVERT: s 181 MET cc_start: 0.8380 (tpp) cc_final: 0.7674 (tmm) REVERT: e 17 TRP cc_start: 0.5942 (OUTLIER) cc_final: 0.5364 (m100) REVERT: a 338 ARG cc_start: 0.8717 (ttm-80) cc_final: 0.8406 (ptp-110) REVERT: a 502 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6392 (tm130) REVERT: a 515 TYR cc_start: 0.5291 (t80) cc_final: 0.4157 (t80) REVERT: a 570 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.7113 (m-10) REVERT: a 590 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8131 (tp) REVERT: a 650 TRP cc_start: 0.6402 (m100) cc_final: 0.5505 (m100) REVERT: a 740 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7578 (mt) REVERT: a 749 HIS cc_start: 0.5597 (OUTLIER) cc_final: 0.5184 (m170) REVERT: a 827 SER cc_start: 0.8994 (m) cc_final: 0.8747 (p) outliers start: 216 outliers final: 170 residues processed: 707 average time/residue: 0.3186 time to fit residues: 368.5977 Evaluate side-chains 743 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 552 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 292 THR Chi-restraints excluded: chain c residue 328 VAL 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 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 101 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 202 VAL Chi-restraints excluded: chain d residue 39 VAL 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 174 ASP 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 306 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 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 67 TYR Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 76 ILE Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 121 THR 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 36 LYS Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 70 LEU 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 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 147 ILE Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 11 SER Chi-restraints excluded: chain j residue 12 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 115 ASP Chi-restraints excluded: chain j residue 131 MET Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 108 PHE 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 131 MET 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 56 ILE Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 82 ASP Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 113 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 79 SER 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 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 613 ILE Chi-restraints excluded: chain p residue 619 VAL Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain s residue 18 GLN 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 88 VAL Chi-restraints excluded: chain s residue 93 THR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 199 THR Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 17 TRP Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 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 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 290 ILE Chi-restraints excluded: chain a residue 292 VAL 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 502 GLN Chi-restraints excluded: chain a residue 520 ASP 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 599 ASP 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 730 LEU Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 802 HIS Chi-restraints excluded: chain a residue 823 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 193 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 187 optimal weight: 0.0980 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 299 HIS s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25749 Z= 0.195 Angle : 0.675 9.439 34903 Z= 0.340 Chirality : 0.042 0.408 4096 Planarity : 0.004 0.049 4332 Dihedral : 5.837 56.202 3759 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.04 % Allowed : 31.65 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3239 helix: 1.86 (0.11), residues: 2274 sheet: 0.44 (0.55), residues: 95 loop : -2.07 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP e 17 HIS 0.005 0.001 HIS a 343 PHE 0.028 0.001 PHE f 51 TYR 0.025 0.001 TYR k 144 ARG 0.010 0.000 ARG s 195 *********************** 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 787 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 627 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 341 ILE cc_start: 0.9272 (mm) cc_final: 0.9030 (mm) REVERT: b 101 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7802 (p) REVERT: b 108 MET cc_start: 0.9066 (tpp) cc_final: 0.8775 (tpp) REVERT: d 75 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8371 (mmmt) REVERT: d 87 MET cc_start: 0.8969 (tpp) cc_final: 0.8748 (tpp) REVERT: d 107 MET cc_start: 0.8362 (mtm) cc_final: 0.7966 (ttp) REVERT: d 197 LYS cc_start: 0.9262 (ttmm) cc_final: 0.8904 (ttmm) REVERT: d 298 GLU cc_start: 0.8903 (tt0) cc_final: 0.8670 (mt-10) REVERT: d 308 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.7756 (t80) REVERT: d 346 ILE cc_start: 0.9116 (tt) cc_final: 0.8877 (tt) REVERT: d 350 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9008 (mp) REVERT: f 36 HIS cc_start: 0.5670 (OUTLIER) cc_final: 0.5071 (m-70) REVERT: f 57 ASN cc_start: 0.8295 (m-40) cc_final: 0.8039 (t0) REVERT: f 82 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7191 (t80) REVERT: f 86 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7732 (mm-40) REVERT: g 23 MET cc_start: 0.7983 (tpp) cc_final: 0.7237 (tpt) REVERT: g 47 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6867 (ttp) REVERT: g 139 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7208 (tm-30) REVERT: i 51 LEU cc_start: 0.7458 (pt) cc_final: 0.7032 (pp) REVERT: i 61 MET cc_start: 0.7015 (mmm) cc_final: 0.6699 (mmm) REVERT: i 64 ILE cc_start: 0.8873 (mm) cc_final: 0.8434 (mt) REVERT: i 97 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7702 (mp) REVERT: i 139 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6218 (tm-30) REVERT: j 23 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7580 (ptm) REVERT: j 41 ILE cc_start: 0.8185 (tp) cc_final: 0.7829 (tp) REVERT: j 119 ARG cc_start: 0.8793 (ttm170) cc_final: 0.8556 (ttm170) REVERT: j 151 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7211 (tp) REVERT: k 51 LEU cc_start: 0.8156 (mm) cc_final: 0.7616 (tp) REVERT: k 61 MET cc_start: 0.7952 (mmt) cc_final: 0.7457 (mtp) REVERT: k 87 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7117 (t80) REVERT: k 108 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7420 (t80) REVERT: l 23 MET cc_start: 0.7574 (tpt) cc_final: 0.7143 (tpt) REVERT: l 50 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8420 (mm-30) REVERT: l 143 LEU cc_start: 0.8848 (tt) cc_final: 0.8599 (tt) REVERT: l 148 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8752 (t) REVERT: m 48 ARG cc_start: 0.8655 (mmt180) cc_final: 0.8407 (mmt90) REVERT: m 54 LYS cc_start: 0.8570 (mmtp) cc_final: 0.7993 (mmtt) REVERT: m 115 ASP cc_start: 0.8417 (t70) cc_final: 0.7822 (t0) REVERT: m 131 MET cc_start: 0.8406 (ttp) cc_final: 0.8100 (ttp) REVERT: n 51 LEU cc_start: 0.9202 (mm) cc_final: 0.8684 (tt) REVERT: n 132 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8982 (pt) REVERT: n 155 LYS cc_start: 0.7678 (tttt) cc_final: 0.7109 (ttmt) REVERT: o 55 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.9011 (t) REVERT: s 120 MET cc_start: 0.3984 (mmm) cc_final: 0.3390 (mmm) REVERT: e 17 TRP cc_start: 0.5742 (m-10) cc_final: 0.5479 (m100) REVERT: a 338 ARG cc_start: 0.8705 (ttm-80) cc_final: 0.8420 (ptp-110) REVERT: a 387 ARG cc_start: 0.5005 (ttt-90) cc_final: 0.4390 (ttm170) REVERT: a 502 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6307 (tm130) REVERT: a 515 TYR cc_start: 0.5260 (t80) cc_final: 0.4199 (t80) REVERT: a 570 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.7044 (m-10) REVERT: a 650 TRP cc_start: 0.6312 (m100) cc_final: 0.5473 (m100) REVERT: a 740 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7454 (mt) REVERT: a 749 HIS cc_start: 0.5495 (OUTLIER) cc_final: 0.4933 (m170) REVERT: a 802 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8411 (m-70) REVERT: a 827 SER cc_start: 0.8993 (m) cc_final: 0.8752 (p) outliers start: 160 outliers final: 111 residues processed: 734 average time/residue: 0.3199 time to fit residues: 381.3838 Evaluate side-chains 727 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 596 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 292 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 390 LEU Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain d residue 39 VAL 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 279 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 320 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain d residue 352 ILE Chi-restraints excluded: chain f residue 32 PHE Chi-restraints excluded: chain f residue 36 HIS Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 83 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 76 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 85 THR 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 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 12 SER Chi-restraints excluded: chain j residue 23 MET Chi-restraints excluded: chain j residue 53 MET 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 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 129 VAL 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 99 VAL Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain l residue 136 ILE 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 64 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 n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER 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 132 ILE Chi-restraints excluded: chain n residue 140 VAL 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 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 222 PHE 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 79 ILE Chi-restraints excluded: chain a residue 92 ARG 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 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 502 GLN 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 647 CYS Chi-restraints excluded: chain a residue 653 LEU Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 749 HIS 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 284 optimal weight: 8.9990 chunk 300 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 276 optimal weight: 0.7980 chunk 290 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 173 GLN ** d 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 ASN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 25749 Z= 0.335 Angle : 0.749 10.221 34903 Z= 0.385 Chirality : 0.045 0.416 4096 Planarity : 0.004 0.053 4332 Dihedral : 6.087 58.046 3759 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.76 % Allowed : 31.38 % Favored : 61.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 3239 helix: 1.63 (0.11), residues: 2268 sheet: 0.31 (0.55), residues: 95 loop : -2.04 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP e 17 HIS 0.006 0.001 HIS s 78 PHE 0.036 0.002 PHE f 51 TYR 0.029 0.002 TYR k 144 ARG 0.011 0.001 ARG s 195 *********************** 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 738 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 559 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 302 MET cc_start: 0.8058 (ppp) cc_final: 0.7807 (tmm) REVERT: c 341 ILE cc_start: 0.9352 (mm) cc_final: 0.9116 (mm) REVERT: b 101 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.8008 (p) REVERT: d 75 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8407 (mmmt) REVERT: d 197 LYS cc_start: 0.9268 (ttmm) cc_final: 0.8831 (ttmm) REVERT: d 308 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.7893 (t80) REVERT: f 36 HIS cc_start: 0.5892 (OUTLIER) cc_final: 0.5182 (m-70) REVERT: f 67 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.5427 (m-80) REVERT: f 82 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7178 (t80) REVERT: f 86 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7732 (mm-40) REVERT: g 23 MET cc_start: 0.8319 (tpp) cc_final: 0.7745 (tpt) REVERT: g 47 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6911 (ttp) REVERT: h 36 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7583 (ttpp) REVERT: i 39 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.7616 (p) REVERT: i 64 ILE cc_start: 0.8921 (mm) cc_final: 0.8666 (mm) REVERT: i 97 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7706 (mp) REVERT: i 139 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6500 (tm-30) REVERT: j 11 SER cc_start: 0.7018 (OUTLIER) cc_final: 0.5979 (t) REVERT: j 23 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7713 (ptm) REVERT: j 26 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.7885 (t) REVERT: j 41 ILE cc_start: 0.8097 (tp) cc_final: 0.7755 (tp) REVERT: j 151 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7361 (tp) REVERT: k 23 MET cc_start: 0.8001 (tpt) cc_final: 0.7798 (tpt) REVERT: k 51 LEU cc_start: 0.8100 (mm) cc_final: 0.7516 (tp) REVERT: k 87 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7550 (t80) REVERT: k 108 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7385 (t80) REVERT: l 23 MET cc_start: 0.7803 (tpt) cc_final: 0.7550 (tpt) REVERT: l 50 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8405 (mm-30) REVERT: m 23 MET cc_start: 0.7756 (tpp) cc_final: 0.7417 (tpt) REVERT: m 48 ARG cc_start: 0.8683 (mmt180) cc_final: 0.8374 (mmt90) REVERT: m 115 ASP cc_start: 0.8451 (t70) cc_final: 0.7780 (t0) REVERT: m 131 MET cc_start: 0.8479 (ttp) cc_final: 0.8199 (ttp) REVERT: n 51 LEU cc_start: 0.9271 (mm) cc_final: 0.8678 (tt) REVERT: n 132 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9003 (pt) REVERT: n 155 LYS cc_start: 0.7981 (tttt) cc_final: 0.7383 (ttmt) REVERT: o 55 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.8884 (t) REVERT: a 338 ARG cc_start: 0.8714 (ttm-80) cc_final: 0.8155 (ttp-110) REVERT: a 387 ARG cc_start: 0.5186 (ttt-90) cc_final: 0.3844 (ttm-80) REVERT: a 502 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6470 (tm130) REVERT: a 515 TYR cc_start: 0.5513 (t80) cc_final: 0.4222 (t80) REVERT: a 570 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.7024 (m-10) REVERT: a 650 TRP cc_start: 0.6456 (m100) cc_final: 0.5564 (m100) REVERT: a 740 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7700 (mt) REVERT: a 749 HIS cc_start: 0.5705 (OUTLIER) cc_final: 0.5409 (m170) REVERT: a 827 SER cc_start: 0.9000 (m) cc_final: 0.8755 (p) outliers start: 179 outliers final: 136 residues processed: 682 average time/residue: 0.3164 time to fit residues: 353.3287 Evaluate side-chains 701 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 543 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 292 THR Chi-restraints excluded: chain c residue 328 VAL Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 202 VAL Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 105 SER Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 206 THR Chi-restraints excluded: chain d residue 279 LEU Chi-restraints excluded: chain d residue 308 PHE 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 36 HIS Chi-restraints excluded: chain f residue 39 VAL Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 67 TYR Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 28 MET Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 101 LEU 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 36 LYS 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 129 VAL 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 85 THR 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 139 GLU 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 12 SER Chi-restraints excluded: chain j residue 23 MET 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 j residue 151 ILE Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 87 TYR Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 129 VAL 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 85 THR 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 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 53 MET Chi-restraints excluded: chain m residue 64 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 n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 79 SER 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 153 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 75 LEU Chi-restraints excluded: chain o residue 80 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 18 GLN Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 222 PHE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 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 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 367 THR Chi-restraints excluded: chain a residue 435 HIS Chi-restraints excluded: chain a residue 450 ILE Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 502 GLN 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 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 653 LEU Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 802 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 191 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 323 optimal weight: 0.3980 chunk 298 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 ASN s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25749 Z= 0.236 Angle : 0.732 14.985 34903 Z= 0.367 Chirality : 0.043 0.406 4096 Planarity : 0.004 0.052 4332 Dihedral : 5.927 58.088 3758 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.36 % Allowed : 33.01 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.15), residues: 3239 helix: 1.77 (0.11), residues: 2263 sheet: 0.32 (0.55), residues: 95 loop : -2.04 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP e 17 HIS 0.004 0.001 HIS a 343 PHE 0.030 0.001 PHE f 51 TYR 0.031 0.002 TYR h 32 ARG 0.012 0.000 ARG s 195 ********************** 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 719 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 577 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 302 MET cc_start: 0.8048 (ppp) cc_final: 0.7794 (tmm) REVERT: c 341 ILE cc_start: 0.9295 (mm) cc_final: 0.9053 (mm) REVERT: d 32 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7466 (pp30) REVERT: d 75 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8389 (mmmt) REVERT: d 197 LYS cc_start: 0.9282 (ttmm) cc_final: 0.8946 (ttmm) REVERT: d 308 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.7861 (t80) REVERT: d 346 ILE cc_start: 0.9184 (tt) cc_final: 0.8889 (tt) REVERT: f 36 HIS cc_start: 0.5826 (OUTLIER) cc_final: 0.5104 (m-70) REVERT: f 57 ASN cc_start: 0.8252 (m-40) cc_final: 0.7961 (t0) REVERT: f 58 ILE cc_start: 0.7814 (pp) cc_final: 0.7592 (pp) REVERT: f 82 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7167 (t80) REVERT: f 86 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7729 (mm-40) REVERT: g 23 MET cc_start: 0.8124 (tpp) cc_final: 0.7442 (tpt) REVERT: g 47 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6819 (ttp) REVERT: h 36 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7400 (ttpp) REVERT: i 51 LEU cc_start: 0.7600 (pt) cc_final: 0.7183 (pp) REVERT: i 64 ILE cc_start: 0.8884 (mm) cc_final: 0.8622 (mm) REVERT: i 97 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7688 (mp) REVERT: i 139 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: j 23 MET cc_start: 0.8002 (ptm) cc_final: 0.7579 (ptm) REVERT: j 26 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.7828 (t) REVERT: j 41 ILE cc_start: 0.8180 (tp) cc_final: 0.7845 (tp) REVERT: j 151 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7367 (tp) REVERT: k 51 LEU cc_start: 0.8185 (mm) cc_final: 0.7608 (tp) REVERT: k 61 MET cc_start: 0.7898 (mmt) cc_final: 0.7385 (mtp) REVERT: k 87 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7429 (t80) REVERT: k 108 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7398 (t80) REVERT: l 23 MET cc_start: 0.7708 (tpt) cc_final: 0.7333 (tpt) REVERT: l 50 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8375 (mm-30) REVERT: l 139 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7874 (mm-30) REVERT: m 23 MET cc_start: 0.7717 (tpp) cc_final: 0.7421 (tpt) REVERT: m 115 ASP cc_start: 0.8443 (t70) cc_final: 0.7791 (t0) REVERT: m 131 MET cc_start: 0.8406 (ttp) cc_final: 0.8146 (ttp) REVERT: n 51 LEU cc_start: 0.9251 (mm) cc_final: 0.8686 (tp) REVERT: n 132 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9031 (pt) REVERT: n 155 LYS cc_start: 0.7899 (tttt) cc_final: 0.7248 (ttmt) REVERT: o 55 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8951 (t) REVERT: s 18 GLN cc_start: 0.5038 (OUTLIER) cc_final: 0.4553 (mm110) REVERT: s 120 MET cc_start: 0.4047 (mmm) cc_final: 0.3427 (mmm) REVERT: s 181 MET cc_start: 0.8375 (tpp) cc_final: 0.7663 (tmm) REVERT: a 34 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8436 (mptt) REVERT: a 107 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8278 (tm-30) REVERT: a 338 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8420 (ptp-110) REVERT: a 387 ARG cc_start: 0.5062 (ttt-90) cc_final: 0.3980 (ttm-80) REVERT: a 502 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6405 (tm130) REVERT: a 515 TYR cc_start: 0.5420 (t80) cc_final: 0.4180 (t80) REVERT: a 570 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6968 (m-10) REVERT: a 650 TRP cc_start: 0.6456 (m100) cc_final: 0.5545 (m100) REVERT: a 740 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7509 (mt) REVERT: a 749 HIS cc_start: 0.5663 (OUTLIER) cc_final: 0.5293 (m170) REVERT: a 827 SER cc_start: 0.8980 (m) cc_final: 0.8740 (p) outliers start: 142 outliers final: 116 residues processed: 667 average time/residue: 0.3329 time to fit residues: 367.1105 Evaluate side-chains 697 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 563 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 292 THR Chi-restraints excluded: chain c residue 334 PHE Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 174 PHE Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 202 VAL Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 105 SER Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 174 ASP 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 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 61 LEU Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 37 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 121 THR Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 36 LYS Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 129 VAL 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 i residue 41 ILE Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 85 THR 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 139 GLU 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 12 SER 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 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 108 PHE Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 64 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 n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER 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 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 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 80 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 18 GLN Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 73 TYR Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 222 PHE Chi-restraints excluded: chain e residue 10 VAL 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 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 367 THR Chi-restraints excluded: chain a residue 435 HIS Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 474 ILE Chi-restraints excluded: chain a residue 502 GLN 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 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 653 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 802 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 204 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 237 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 258 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN ** s 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.139744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.120016 restraints weight = 58404.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.122486 restraints weight = 30376.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.124024 restraints weight = 18300.989| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25749 Z= 0.240 Angle : 0.727 12.049 34903 Z= 0.367 Chirality : 0.043 0.402 4096 Planarity : 0.004 0.051 4332 Dihedral : 5.914 57.613 3758 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.78 % Allowed : 32.70 % Favored : 61.52 % 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: 1.02 (0.15), residues: 3239 helix: 1.71 (0.11), residues: 2273 sheet: 0.21 (0.55), residues: 97 loop : -2.17 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP e 17 HIS 0.004 0.001 HIS a 343 PHE 0.034 0.001 PHE f 51 TYR 0.027 0.002 TYR k 144 ARG 0.012 0.000 ARG s 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6477.33 seconds wall clock time: 115 minutes 23.49 seconds (6923.49 seconds total)