Starting phenix.real_space_refine on Mon Mar 18 02:42:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6n_32330/03_2024/7w6n_32330.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6n_32330/03_2024/7w6n_32330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6n_32330/03_2024/7w6n_32330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6n_32330/03_2024/7w6n_32330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6n_32330/03_2024/7w6n_32330.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6n_32330/03_2024/7w6n_32330.pdb" } resolution = 3.4 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= -0.000 sd= 0.002 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 132 5.16 5 C 12748 2.51 5 N 3276 2.21 5 O 3564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ASP 214": "OD1" <-> "OD2" Residue "B ASP 33": "OD1" <-> "OD2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ASP 263": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 204": "OD1" <-> "OD2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ASP 263": "OD1" <-> "OD2" Residue "D PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E ASP 214": "OD1" <-> "OD2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 77": "OE1" <-> "OE2" Residue "F PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F ASP 263": "OD1" <-> "OD2" Residue "F PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F ARG 308": "NH1" <-> "NH2" Residue "F PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 183": "NH1" <-> "NH2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G ASP 214": "OD1" <-> "OD2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 139": "NH1" <-> "NH2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "H ARG 171": "NH1" <-> "NH2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H ARG 253": "NH1" <-> "NH2" Residue "H ASP 263": "OD1" <-> "OD2" Residue "H PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 302": "NH1" <-> "NH2" Residue "H ARG 308": "NH1" <-> "NH2" Residue "H PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19720 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "G" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Time building chain proxies: 9.97, per 1000 atoms: 0.51 Number of scatterers: 19720 At special positions: 0 Unit cell: (161.226, 161.226, 126.75, 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 132 16.00 O 3564 8.00 N 3276 7.00 C 12748 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 Time building additional restraints: 7.40 Conformation dependent library (CDL) restraints added in 2.7 seconds 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 8 sheets defined 67.7% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 61 through 75 removed outlier: 3.923A pdb=" N LEU A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.407A pdb=" N GLN A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 98 through 110 removed outlier: 4.414A pdb=" N TYR A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 4.133A pdb=" N ALA A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.802A pdb=" N ARG A 139 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 170 removed outlier: 3.631A pdb=" N ILE A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.525A pdb=" N VAL A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 189 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'B' and resid 3 through 7 removed outlier: 3.502A pdb=" N ALA B 6 " --> pdb=" O ALA B 3 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 7 " --> pdb=" O GLY B 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3 through 7' Processing helix chain 'B' and resid 8 through 17 removed outlier: 3.949A pdb=" N ILE B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.839A pdb=" N PHE B 73 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 74 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 75' Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 148 Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.547A pdb=" N GLU B 174 " --> pdb=" O TRP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 203 removed outlier: 3.655A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 222 through 247 removed outlier: 3.696A pdb=" N LEU B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 276 Proline residue: B 269 - end of helix removed outlier: 3.774A pdb=" N GLY B 273 " --> pdb=" O PRO B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.921A pdb=" N PHE B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 removed outlier: 3.738A pdb=" N PHE B 298 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 302 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.893A pdb=" N ARG B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 344 removed outlier: 3.604A pdb=" N LEU B 321 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.661A pdb=" N THR B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 396 removed outlier: 3.644A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 426 removed outlier: 4.350A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.804A pdb=" N LEU B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 55 Processing helix chain 'C' and resid 61 through 75 removed outlier: 3.923A pdb=" N LEU C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.407A pdb=" N GLN C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 93 Processing helix chain 'C' and resid 98 through 110 removed outlier: 4.413A pdb=" N TYR C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 105 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN C 107 " --> pdb=" O HIS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 removed outlier: 4.133A pdb=" N ALA C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.802A pdb=" N ARG C 139 " --> pdb=" O HIS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.632A pdb=" N ILE C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY C 170 " --> pdb=" O TYR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.525A pdb=" N VAL C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE C 189 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS C 192 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 213 through 220 Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.502A pdb=" N ALA D 6 " --> pdb=" O ALA D 3 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 7 " --> pdb=" O GLY D 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3 through 7' Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.950A pdb=" N ILE D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.838A pdb=" N PHE D 73 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE D 74 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 75' Processing helix chain 'D' and resid 90 through 100 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 167 through 174 removed outlier: 3.549A pdb=" N GLU D 174 " --> pdb=" O TRP D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 203 removed outlier: 3.655A pdb=" N LEU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE D 191 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 222 through 247 removed outlier: 3.696A pdb=" N LEU D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 276 Proline residue: D 269 - end of helix removed outlier: 3.774A pdb=" N GLY D 273 " --> pdb=" O PRO D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 291 removed outlier: 3.921A pdb=" N PHE D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 302 removed outlier: 3.738A pdb=" N PHE D 298 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 302 " --> pdb=" O LYS D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.892A pdb=" N ARG D 308 " --> pdb=" O SER D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 344 removed outlier: 3.604A pdb=" N LEU D 321 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 removed outlier: 3.661A pdb=" N THR D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 366 " --> pdb=" O ILE D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 396 removed outlier: 3.646A pdb=" N LEU D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 426 removed outlier: 4.350A pdb=" N VAL D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.807A pdb=" N LEU D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 480 " --> pdb=" O HIS D 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 Processing helix chain 'E' and resid 61 through 75 removed outlier: 3.923A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 removed outlier: 4.406A pdb=" N GLN E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 93 Processing helix chain 'E' and resid 98 through 110 removed outlier: 4.414A pdb=" N TYR E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 105 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN E 107 " --> pdb=" O HIS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 132 removed outlier: 4.132A pdb=" N ALA E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 146 removed outlier: 3.803A pdb=" N ARG E 139 " --> pdb=" O HIS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 170 removed outlier: 3.631A pdb=" N ILE E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY E 170 " --> pdb=" O TYR E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.525A pdb=" N VAL E 186 " --> pdb=" O PRO E 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE E 189 " --> pdb=" O HIS E 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'F' and resid 3 through 7 removed outlier: 3.502A pdb=" N ALA F 6 " --> pdb=" O ALA F 3 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA F 7 " --> pdb=" O GLY F 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 3 through 7' Processing helix chain 'F' and resid 8 through 17 removed outlier: 3.949A pdb=" N ILE F 17 " --> pdb=" O ARG F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 70 through 75 removed outlier: 3.839A pdb=" N PHE F 73 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE F 74 " --> pdb=" O LYS F 71 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE F 75 " --> pdb=" O GLU F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 70 through 75' Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 129 through 132 Processing helix chain 'F' and resid 133 through 148 Processing helix chain 'F' and resid 167 through 174 removed outlier: 3.549A pdb=" N GLU F 174 " --> pdb=" O TRP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 203 removed outlier: 3.655A pdb=" N LEU F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE F 191 " --> pdb=" O TYR F 187 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE F 192 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE F 193 " --> pdb=" O THR F 189 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 222 Processing helix chain 'F' and resid 222 through 247 removed outlier: 3.696A pdb=" N LEU F 243 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 276 Proline residue: F 269 - end of helix removed outlier: 3.774A pdb=" N GLY F 273 " --> pdb=" O PRO F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 291 removed outlier: 3.921A pdb=" N PHE F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 302 removed outlier: 3.738A pdb=" N PHE F 298 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG F 302 " --> pdb=" O LYS F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 317 removed outlier: 3.891A pdb=" N ARG F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 344 removed outlier: 3.604A pdb=" N LEU F 321 " --> pdb=" O CYS F 317 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE F 323 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 366 removed outlier: 3.660A pdb=" N THR F 361 " --> pdb=" O SER F 357 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR F 366 " --> pdb=" O ILE F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 396 removed outlier: 3.646A pdb=" N LEU F 389 " --> pdb=" O SER F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 426 removed outlier: 4.351A pdb=" N VAL F 401 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.806A pdb=" N LEU F 479 " --> pdb=" O GLN F 475 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 480 " --> pdb=" O HIS F 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 55 Processing helix chain 'G' and resid 61 through 75 removed outlier: 3.923A pdb=" N LEU G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 89 removed outlier: 4.407A pdb=" N GLN G 87 " --> pdb=" O ASP G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 93 Processing helix chain 'G' and resid 98 through 110 removed outlier: 4.413A pdb=" N TYR G 104 " --> pdb=" O THR G 100 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU G 105 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN G 107 " --> pdb=" O HIS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 132 removed outlier: 4.132A pdb=" N ALA G 125 " --> pdb=" O ASP G 121 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 146 removed outlier: 3.802A pdb=" N ARG G 139 " --> pdb=" O HIS G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.631A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA G 164 " --> pdb=" O ASP G 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP G 167 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY G 170 " --> pdb=" O TYR G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.525A pdb=" N VAL G 186 " --> pdb=" O PRO G 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE G 189 " --> pdb=" O HIS G 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE G 190 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS G 192 " --> pdb=" O VAL G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 208 Processing helix chain 'G' and resid 213 through 220 Processing helix chain 'H' and resid 3 through 7 removed outlier: 3.501A pdb=" N ALA H 6 " --> pdb=" O ALA H 3 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA H 7 " --> pdb=" O GLY H 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 3 through 7' Processing helix chain 'H' and resid 8 through 17 removed outlier: 3.950A pdb=" N ILE H 17 " --> pdb=" O ARG H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 70 through 75 removed outlier: 3.840A pdb=" N PHE H 73 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE H 74 " --> pdb=" O LYS H 71 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE H 75 " --> pdb=" O GLU H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 70 through 75' Processing helix chain 'H' and resid 90 through 100 Processing helix chain 'H' and resid 110 through 122 Processing helix chain 'H' and resid 124 through 128 Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'H' and resid 133 through 148 Processing helix chain 'H' and resid 167 through 174 removed outlier: 3.549A pdb=" N GLU H 174 " --> pdb=" O TRP H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 203 removed outlier: 3.655A pdb=" N LEU H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE H 191 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE H 192 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE H 193 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA H 194 " --> pdb=" O GLY H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 222 Processing helix chain 'H' and resid 222 through 247 removed outlier: 3.695A pdb=" N LEU H 243 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA H 247 " --> pdb=" O LEU H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 276 Proline residue: H 269 - end of helix removed outlier: 3.774A pdb=" N GLY H 273 " --> pdb=" O PRO H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 291 removed outlier: 3.922A pdb=" N PHE H 286 " --> pdb=" O VAL H 282 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL H 287 " --> pdb=" O SER H 283 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR H 288 " --> pdb=" O GLY H 284 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU H 289 " --> pdb=" O ALA H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 302 removed outlier: 3.739A pdb=" N PHE H 298 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG H 302 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 317 removed outlier: 3.893A pdb=" N ARG H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 344 removed outlier: 3.604A pdb=" N LEU H 321 " --> pdb=" O CYS H 317 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 366 removed outlier: 3.661A pdb=" N THR H 361 " --> pdb=" O SER H 357 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR H 366 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 396 removed outlier: 3.646A pdb=" N LEU H 389 " --> pdb=" O SER H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 426 removed outlier: 4.350A pdb=" N VAL H 401 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL H 403 " --> pdb=" O VAL H 399 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG H 426 " --> pdb=" O GLN H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 removed outlier: 3.804A pdb=" N LEU H 479 " --> pdb=" O GLN H 475 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU H 480 " --> pdb=" O HIS H 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 3.663A pdb=" N VAL A 201 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.663A pdb=" N VAL C 201 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 49 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.663A pdb=" N VAL E 201 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 49 through 54 Processing sheet with id=AA7, first strand: chain 'G' and resid 153 through 154 removed outlier: 3.663A pdb=" N VAL G 201 " --> pdb=" O ILE G 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 49 through 54 965 hydrogen bonds defined for protein. 2739 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: 5.46 Time building geometry restraints manager: 7.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5579 1.33 - 1.45: 3673 1.45 - 1.57: 10740 1.57 - 1.69: 0 1.69 - 1.80: 208 Bond restraints: 20200 Sorted by residual: bond pdb=" CB VAL D 46 " pdb=" CG2 VAL D 46 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.22e+00 bond pdb=" CB VAL F 46 " pdb=" CG2 VAL F 46 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.22e+00 bond pdb=" CB VAL H 46 " pdb=" CG2 VAL H 46 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.15e+00 bond pdb=" CB VAL B 46 " pdb=" CG2 VAL B 46 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 4.98e+00 bond pdb=" CE2 PHE H 91 " pdb=" CZ PHE H 91 " ideal model delta sigma weight residual 1.382 1.323 0.059 3.00e-02 1.11e+03 3.84e+00 ... (remaining 20195 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.65: 368 105.65 - 112.77: 10484 112.77 - 119.89: 7325 119.89 - 127.02: 8963 127.02 - 134.14: 188 Bond angle restraints: 27328 Sorted by residual: angle pdb=" C PHE A 223 " pdb=" N GLN A 224 " pdb=" CA GLN A 224 " ideal model delta sigma weight residual 122.55 112.73 9.82 2.03e+00 2.43e-01 2.34e+01 angle pdb=" C PHE E 223 " pdb=" N GLN E 224 " pdb=" CA GLN E 224 " ideal model delta sigma weight residual 122.55 112.76 9.79 2.03e+00 2.43e-01 2.33e+01 angle pdb=" C PHE C 223 " pdb=" N GLN C 224 " pdb=" CA GLN C 224 " ideal model delta sigma weight residual 122.55 112.76 9.79 2.03e+00 2.43e-01 2.33e+01 angle pdb=" C PHE G 223 " pdb=" N GLN G 224 " pdb=" CA GLN G 224 " ideal model delta sigma weight residual 122.55 112.79 9.76 2.03e+00 2.43e-01 2.31e+01 angle pdb=" C GLY C 78 " pdb=" N VAL C 79 " pdb=" CA VAL C 79 " ideal model delta sigma weight residual 121.97 129.38 -7.41 1.80e+00 3.09e-01 1.69e+01 ... (remaining 27323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 10068 14.91 - 29.82: 1481 29.82 - 44.74: 327 44.74 - 59.65: 88 59.65 - 74.56: 16 Dihedral angle restraints: 11980 sinusoidal: 4816 harmonic: 7164 Sorted by residual: dihedral pdb=" CA GLY C 78 " pdb=" C GLY C 78 " pdb=" N VAL C 79 " pdb=" CA VAL C 79 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLY A 78 " pdb=" C GLY A 78 " pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLY E 78 " pdb=" C GLY E 78 " pdb=" N VAL E 79 " pdb=" CA VAL E 79 " ideal model delta harmonic sigma weight residual 180.00 151.76 28.24 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 11977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1590 0.036 - 0.072: 901 0.072 - 0.108: 411 0.108 - 0.144: 94 0.144 - 0.180: 16 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CG LEU B 44 " pdb=" CB LEU B 44 " pdb=" CD1 LEU B 44 " pdb=" CD2 LEU B 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CG LEU H 44 " pdb=" CB LEU H 44 " pdb=" CD1 LEU H 44 " pdb=" CD2 LEU H 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CG LEU F 44 " pdb=" CB LEU F 44 " pdb=" CD1 LEU F 44 " pdb=" CD2 LEU F 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 3009 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 75 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO C 76 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 75 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO E 76 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 87 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 88 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.035 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 390 2.62 - 3.19: 20213 3.19 - 3.76: 30264 3.76 - 4.33: 41728 4.33 - 4.90: 67003 Nonbonded interactions: 159598 Sorted by model distance: nonbonded pdb=" O THR B 64 " pdb=" OG SER B 68 " model vdw 2.045 2.440 nonbonded pdb=" O THR F 64 " pdb=" OG SER F 68 " model vdw 2.046 2.440 nonbonded pdb=" O THR H 64 " pdb=" OG SER H 68 " model vdw 2.046 2.440 nonbonded pdb=" O THR D 64 " pdb=" OG SER D 68 " model vdw 2.047 2.440 nonbonded pdb=" O HIS F 104 " pdb=" OH TYR F 114 " model vdw 2.096 2.440 ... (remaining 159593 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 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.280 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 48.950 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.120 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.011 0.075 20200 Z= 0.713 Angle : 0.898 10.564 27328 Z= 0.502 Chirality : 0.051 0.180 3012 Planarity : 0.006 0.064 3468 Dihedral : 14.870 74.560 7356 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 0.37 % Allowed : 11.89 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.26 (0.14), residues: 2404 helix: -2.40 (0.11), residues: 1436 sheet: -3.92 (0.66), residues: 40 loop : -3.31 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP B 359 HIS 0.009 0.002 HIS B 481 PHE 0.024 0.003 PHE A 71 TYR 0.022 0.002 TYR H 270 ARG 0.006 0.001 ARG G 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 460 time to evaluate : 2.260 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: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.8221 (mtt-85) REVERT: A 204 ASP cc_start: 0.7818 (t0) cc_final: 0.7528 (t0) REVERT: B 270 TYR cc_start: 0.7198 (t80) cc_final: 0.6994 (t80) REVERT: B 292 PHE cc_start: 0.8975 (m-80) cc_final: 0.8771 (m-80) REVERT: B 299 LYS cc_start: 0.9082 (mtpt) cc_final: 0.8471 (tttp) REVERT: B 328 LEU cc_start: 0.7685 (mt) cc_final: 0.7447 (mt) REVERT: C 183 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.8222 (mtt-85) REVERT: C 204 ASP cc_start: 0.7823 (t0) cc_final: 0.7533 (t0) REVERT: D 270 TYR cc_start: 0.7195 (t80) cc_final: 0.6995 (t80) REVERT: D 292 PHE cc_start: 0.8974 (m-80) cc_final: 0.8772 (m-80) REVERT: D 299 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8472 (tttp) REVERT: D 328 LEU cc_start: 0.7682 (mt) cc_final: 0.7443 (mt) REVERT: E 183 ARG cc_start: 0.8692 (mmm-85) cc_final: 0.8210 (mtt-85) REVERT: E 204 ASP cc_start: 0.7832 (t0) cc_final: 0.7538 (t0) REVERT: F 270 TYR cc_start: 0.7200 (t80) cc_final: 0.6995 (t80) REVERT: F 292 PHE cc_start: 0.8977 (m-80) cc_final: 0.8771 (m-80) REVERT: F 299 LYS cc_start: 0.9082 (mtpt) cc_final: 0.8471 (tttp) REVERT: F 328 LEU cc_start: 0.7687 (mt) cc_final: 0.7447 (mt) REVERT: G 183 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8212 (mtt-85) REVERT: G 204 ASP cc_start: 0.7827 (t0) cc_final: 0.7535 (t0) REVERT: H 270 TYR cc_start: 0.7199 (t80) cc_final: 0.6995 (t80) REVERT: H 292 PHE cc_start: 0.8974 (m-80) cc_final: 0.8769 (m-80) REVERT: H 299 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8471 (tttp) REVERT: H 328 LEU cc_start: 0.7639 (mt) cc_final: 0.7399 (mt) outliers start: 8 outliers final: 0 residues processed: 468 average time/residue: 0.3575 time to fit residues: 240.3092 Evaluate side-chains 378 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 188 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 185 HIS A 221 GLN A 224 GLN B 24 ASN B 177 HIS B 476 HIS C 87 GLN C 185 HIS C 221 GLN C 224 GLN D 24 ASN D 177 HIS D 405 ASN D 476 HIS E 87 GLN E 185 HIS E 221 GLN E 224 GLN F 24 ASN F 177 HIS F 405 ASN F 476 HIS G 87 GLN G 185 HIS G 221 GLN G 224 GLN H 24 ASN H 177 HIS H 405 ASN H 476 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20200 Z= 0.207 Angle : 0.638 9.232 27328 Z= 0.329 Chirality : 0.041 0.148 3012 Planarity : 0.005 0.050 3468 Dihedral : 5.291 35.934 2684 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.43 % Allowed : 17.16 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.54 (0.16), residues: 2404 helix: -1.11 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -2.59 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 359 HIS 0.002 0.001 HIS B 481 PHE 0.013 0.002 PHE B 323 TYR 0.010 0.001 TYR D 186 ARG 0.003 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 469 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8458 (t0) cc_final: 0.7994 (t0) REVERT: A 104 TYR cc_start: 0.8096 (m-80) cc_final: 0.7802 (m-80) REVERT: A 107 ASN cc_start: 0.7453 (t0) cc_final: 0.7193 (t0) REVERT: A 140 TRP cc_start: 0.8543 (t60) cc_final: 0.8274 (t60) REVERT: A 183 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8137 (mtm180) REVERT: A 204 ASP cc_start: 0.7765 (t0) cc_final: 0.7430 (t0) REVERT: B 299 LYS cc_start: 0.9029 (mtpt) cc_final: 0.8296 (tttp) REVERT: B 405 ASN cc_start: 0.8837 (m110) cc_final: 0.8632 (m110) REVERT: C 73 ASN cc_start: 0.8462 (t0) cc_final: 0.7996 (t0) REVERT: C 104 TYR cc_start: 0.8096 (m-80) cc_final: 0.7803 (m-80) REVERT: C 107 ASN cc_start: 0.7451 (t0) cc_final: 0.7188 (t0) REVERT: C 140 TRP cc_start: 0.8542 (t60) cc_final: 0.8272 (t60) REVERT: C 160 ASP cc_start: 0.7005 (t0) cc_final: 0.6800 (t0) REVERT: C 183 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8133 (mtm180) REVERT: C 204 ASP cc_start: 0.7776 (t0) cc_final: 0.7436 (t0) REVERT: D 299 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8298 (tttp) REVERT: E 73 ASN cc_start: 0.8459 (t0) cc_final: 0.7995 (t0) REVERT: E 104 TYR cc_start: 0.8098 (m-80) cc_final: 0.7769 (m-80) REVERT: E 107 ASN cc_start: 0.7451 (t0) cc_final: 0.7192 (t0) REVERT: E 140 TRP cc_start: 0.8546 (t60) cc_final: 0.8275 (t60) REVERT: E 183 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8138 (mtm180) REVERT: E 204 ASP cc_start: 0.7782 (t0) cc_final: 0.7438 (t0) REVERT: F 299 LYS cc_start: 0.9029 (mtpt) cc_final: 0.8299 (tttp) REVERT: G 73 ASN cc_start: 0.8461 (t0) cc_final: 0.7997 (t0) REVERT: G 104 TYR cc_start: 0.8097 (m-80) cc_final: 0.7803 (m-80) REVERT: G 107 ASN cc_start: 0.7454 (t0) cc_final: 0.7184 (t0) REVERT: G 140 TRP cc_start: 0.8543 (t60) cc_final: 0.8274 (t60) REVERT: G 183 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8137 (mtm180) REVERT: G 204 ASP cc_start: 0.7782 (t0) cc_final: 0.7441 (t0) REVERT: H 299 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8298 (tttp) outliers start: 52 outliers final: 24 residues processed: 501 average time/residue: 0.3436 time to fit residues: 257.9969 Evaluate side-chains 421 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 397 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 366 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 0.0060 chunk 181 optimal weight: 4.9990 chunk 148 optimal weight: 0.0040 chunk 60 optimal weight: 0.0970 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 216 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 overall best weight: 0.7408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 405 ASN F 405 ASN H 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20200 Z= 0.177 Angle : 0.610 9.360 27328 Z= 0.310 Chirality : 0.040 0.135 3012 Planarity : 0.005 0.053 3468 Dihedral : 4.828 37.106 2684 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.87 % Allowed : 20.43 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.77 (0.16), residues: 2404 helix: -0.44 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -2.38 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 359 HIS 0.002 0.000 HIS H 481 PHE 0.018 0.002 PHE B 191 TYR 0.009 0.001 TYR B 186 ARG 0.002 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 465 time to evaluate : 1.795 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: A 73 ASN cc_start: 0.8456 (t0) cc_final: 0.7996 (t0) REVERT: A 107 ASN cc_start: 0.7219 (t0) cc_final: 0.7000 (t0) REVERT: A 139 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7801 (ttp80) REVERT: A 140 TRP cc_start: 0.8491 (t60) cc_final: 0.8241 (t60) REVERT: A 183 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8146 (mtm180) REVERT: A 204 ASP cc_start: 0.7872 (t0) cc_final: 0.7476 (t0) REVERT: B 299 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8209 (tttp) REVERT: B 401 VAL cc_start: 0.9277 (m) cc_final: 0.9026 (m) REVERT: C 73 ASN cc_start: 0.8459 (t0) cc_final: 0.8000 (t0) REVERT: C 104 TYR cc_start: 0.8032 (m-80) cc_final: 0.7653 (m-80) REVERT: C 107 ASN cc_start: 0.7236 (t0) cc_final: 0.7023 (t0) REVERT: C 139 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7799 (ttp80) REVERT: C 140 TRP cc_start: 0.8493 (t60) cc_final: 0.8239 (t60) REVERT: C 183 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8134 (mtm180) REVERT: C 204 ASP cc_start: 0.7877 (t0) cc_final: 0.7481 (t0) REVERT: D 299 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8206 (tttp) REVERT: D 401 VAL cc_start: 0.9220 (m) cc_final: 0.8941 (m) REVERT: D 405 ASN cc_start: 0.8704 (m110) cc_final: 0.8480 (m110) REVERT: E 73 ASN cc_start: 0.8455 (t0) cc_final: 0.7997 (t0) REVERT: E 107 ASN cc_start: 0.7219 (t0) cc_final: 0.7001 (t0) REVERT: E 135 HIS cc_start: 0.7152 (t-90) cc_final: 0.6947 (t70) REVERT: E 139 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7784 (ttp80) REVERT: E 140 TRP cc_start: 0.8496 (t60) cc_final: 0.8243 (t60) REVERT: E 183 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8148 (mtm180) REVERT: E 204 ASP cc_start: 0.7881 (t0) cc_final: 0.7483 (t0) REVERT: F 299 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8206 (tttp) REVERT: F 401 VAL cc_start: 0.9217 (m) cc_final: 0.8935 (m) REVERT: F 405 ASN cc_start: 0.8707 (m110) cc_final: 0.8482 (m110) REVERT: G 73 ASN cc_start: 0.8458 (t0) cc_final: 0.8000 (t0) REVERT: G 107 ASN cc_start: 0.7220 (t0) cc_final: 0.7001 (t0) REVERT: G 135 HIS cc_start: 0.7154 (t-90) cc_final: 0.6952 (t70) REVERT: G 139 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7805 (ttp80) REVERT: G 140 TRP cc_start: 0.8494 (t60) cc_final: 0.8242 (t60) REVERT: G 183 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8148 (mtm180) REVERT: G 204 ASP cc_start: 0.7881 (t0) cc_final: 0.7482 (t0) REVERT: H 299 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8210 (tttp) REVERT: H 401 VAL cc_start: 0.9230 (m) cc_final: 0.8946 (m) REVERT: H 405 ASN cc_start: 0.8694 (m110) cc_final: 0.8478 (m110) outliers start: 40 outliers final: 25 residues processed: 494 average time/residue: 0.3130 time to fit residues: 232.7345 Evaluate side-chains 439 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 414 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 366 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 8.9990 chunk 164 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 219 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 224 GLN B 405 ASN C 135 HIS C 224 GLN E 224 GLN G 224 GLN H 405 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20200 Z= 0.218 Angle : 0.626 9.217 27328 Z= 0.313 Chirality : 0.041 0.142 3012 Planarity : 0.004 0.054 3468 Dihedral : 4.726 34.759 2684 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.73 % Allowed : 19.92 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.43 (0.17), residues: 2404 helix: -0.18 (0.14), residues: 1500 sheet: None (None), residues: 0 loop : -2.21 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 359 HIS 0.002 0.001 HIS H 481 PHE 0.025 0.002 PHE B 191 TYR 0.009 0.001 TYR B 186 ARG 0.006 0.000 ARG F 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 436 time to evaluate : 2.114 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: symmetry clash REVERT: A 73 ASN cc_start: 0.8495 (t0) cc_final: 0.8040 (t0) REVERT: A 140 TRP cc_start: 0.8508 (t60) cc_final: 0.8243 (t60) REVERT: A 183 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8219 (mtt-85) REVERT: A 204 ASP cc_start: 0.7807 (t0) cc_final: 0.7393 (t0) REVERT: B 27 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.5360 (ppp) REVERT: B 276 MET cc_start: 0.7353 (mmt) cc_final: 0.6955 (mmm) REVERT: B 343 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: C 73 ASN cc_start: 0.8497 (t0) cc_final: 0.8038 (t0) REVERT: C 140 TRP cc_start: 0.8507 (t60) cc_final: 0.8242 (t60) REVERT: C 159 MET cc_start: 0.6801 (ttm) cc_final: 0.5895 (ttp) REVERT: C 204 ASP cc_start: 0.7811 (t0) cc_final: 0.7396 (t0) REVERT: D 27 MET cc_start: 0.5582 (OUTLIER) cc_final: 0.5371 (ppp) REVERT: D 276 MET cc_start: 0.7429 (mmt) cc_final: 0.7050 (mmm) REVERT: D 343 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6855 (tm-30) REVERT: E 73 ASN cc_start: 0.8494 (t0) cc_final: 0.8037 (t0) REVERT: E 140 TRP cc_start: 0.8513 (t60) cc_final: 0.8243 (t60) REVERT: E 183 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8221 (mtt-85) REVERT: E 204 ASP cc_start: 0.7813 (t0) cc_final: 0.7403 (t0) REVERT: F 27 MET cc_start: 0.5576 (OUTLIER) cc_final: 0.5366 (ppp) REVERT: F 276 MET cc_start: 0.7354 (mmt) cc_final: 0.6956 (mmm) REVERT: F 343 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: G 73 ASN cc_start: 0.8494 (t0) cc_final: 0.8039 (t0) REVERT: G 140 TRP cc_start: 0.8512 (t60) cc_final: 0.8242 (t60) REVERT: G 183 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8221 (mtt-85) REVERT: G 204 ASP cc_start: 0.7815 (t0) cc_final: 0.7404 (t0) REVERT: H 27 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.5368 (ppp) REVERT: H 276 MET cc_start: 0.7432 (mmt) cc_final: 0.7052 (mmm) REVERT: H 343 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6869 (tm-30) outliers start: 80 outliers final: 46 residues processed: 499 average time/residue: 0.3211 time to fit residues: 238.3317 Evaluate side-chains 468 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 414 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.0040 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 0.0040 overall best weight: 1.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN E 135 HIS F 405 ASN G 135 HIS H 405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20200 Z= 0.215 Angle : 0.628 8.998 27328 Z= 0.314 Chirality : 0.041 0.136 3012 Planarity : 0.004 0.057 3468 Dihedral : 4.647 34.529 2684 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.57 % Allowed : 19.96 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.21 (0.17), residues: 2404 helix: -0.05 (0.14), residues: 1500 sheet: None (None), residues: 0 loop : -2.05 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.002 0.001 HIS D 481 PHE 0.023 0.002 PHE H 191 TYR 0.010 0.001 TYR D 186 ARG 0.002 0.000 ARG H 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 438 time to evaluate : 2.209 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8529 (t0) cc_final: 0.8087 (t0) REVERT: A 107 ASN cc_start: 0.7028 (t0) cc_final: 0.6794 (t0) REVERT: A 140 TRP cc_start: 0.8483 (t60) cc_final: 0.8205 (t60) REVERT: A 183 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.8209 (mtt-85) REVERT: A 204 ASP cc_start: 0.7793 (t0) cc_final: 0.7405 (t0) REVERT: A 207 LEU cc_start: 0.7312 (tt) cc_final: 0.6632 (mt) REVERT: B 27 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.5333 (ppp) REVERT: B 343 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: C 73 ASN cc_start: 0.8534 (t0) cc_final: 0.8092 (t0) REVERT: C 107 ASN cc_start: 0.7033 (t0) cc_final: 0.6794 (t0) REVERT: C 140 TRP cc_start: 0.8484 (t60) cc_final: 0.8203 (t60) REVERT: C 204 ASP cc_start: 0.7705 (t0) cc_final: 0.7302 (t0) REVERT: C 207 LEU cc_start: 0.7442 (tt) cc_final: 0.6730 (mt) REVERT: D 27 MET cc_start: 0.5544 (OUTLIER) cc_final: 0.5343 (ppp) REVERT: D 224 VAL cc_start: 0.7010 (OUTLIER) cc_final: 0.6683 (t) REVERT: D 343 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: E 73 ASN cc_start: 0.8531 (t0) cc_final: 0.8088 (t0) REVERT: E 107 ASN cc_start: 0.7024 (t0) cc_final: 0.6789 (t0) REVERT: E 140 TRP cc_start: 0.8485 (t60) cc_final: 0.8203 (t60) REVERT: E 183 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.8209 (mtt-85) REVERT: E 204 ASP cc_start: 0.7939 (t0) cc_final: 0.7548 (t0) REVERT: E 207 LEU cc_start: 0.7810 (tp) cc_final: 0.7452 (mt) REVERT: F 27 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.5343 (ppp) REVERT: F 224 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6684 (t) REVERT: F 343 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: G 73 ASN cc_start: 0.8532 (t0) cc_final: 0.8087 (t0) REVERT: G 107 ASN cc_start: 0.7023 (t0) cc_final: 0.6790 (t0) REVERT: G 140 TRP cc_start: 0.8483 (t60) cc_final: 0.8203 (t60) REVERT: G 183 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8210 (mtt-85) REVERT: G 204 ASP cc_start: 0.7698 (t0) cc_final: 0.7329 (t0) REVERT: G 207 LEU cc_start: 0.7783 (tp) cc_final: 0.7422 (mt) REVERT: H 27 MET cc_start: 0.5549 (OUTLIER) cc_final: 0.5345 (ppp) REVERT: H 224 VAL cc_start: 0.7011 (OUTLIER) cc_final: 0.6680 (t) REVERT: H 343 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: H 405 ASN cc_start: 0.8643 (m110) cc_final: 0.8416 (m110) outliers start: 98 outliers final: 54 residues processed: 520 average time/residue: 0.3249 time to fit residues: 258.9934 Evaluate side-chains 469 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 404 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.7980 chunk 208 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 136 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 chunk 232 optimal weight: 0.0870 chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS ** D 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 HIS ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 HIS H 405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20200 Z= 0.163 Angle : 0.616 8.635 27328 Z= 0.304 Chirality : 0.041 0.290 3012 Planarity : 0.004 0.056 3468 Dihedral : 4.398 21.903 2684 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.24 % Allowed : 21.27 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.17), residues: 2404 helix: 0.12 (0.14), residues: 1460 sheet: None (None), residues: 0 loop : -1.79 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 359 HIS 0.002 0.000 HIS D 481 PHE 0.025 0.001 PHE B 191 TYR 0.012 0.001 TYR H 271 ARG 0.002 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 459 time to evaluate : 2.240 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8479 (t0) cc_final: 0.8011 (t0) REVERT: A 107 ASN cc_start: 0.6860 (t0) cc_final: 0.6650 (t0) REVERT: A 140 TRP cc_start: 0.8465 (t60) cc_final: 0.8129 (t60) REVERT: A 183 ARG cc_start: 0.8540 (mmm-85) cc_final: 0.8214 (mtt-85) REVERT: A 207 LEU cc_start: 0.7315 (tt) cc_final: 0.6825 (mt) REVERT: B 300 PHE cc_start: 0.8303 (m-80) cc_final: 0.8060 (m-80) REVERT: B 343 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: C 73 ASN cc_start: 0.8480 (t0) cc_final: 0.8033 (t0) REVERT: C 107 ASN cc_start: 0.6906 (t0) cc_final: 0.6689 (t0) REVERT: C 140 TRP cc_start: 0.8454 (t60) cc_final: 0.8204 (t60) REVERT: C 207 LEU cc_start: 0.7340 (tt) cc_final: 0.6824 (mt) REVERT: D 300 PHE cc_start: 0.8308 (m-80) cc_final: 0.8067 (m-80) REVERT: D 343 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: E 73 ASN cc_start: 0.8479 (t0) cc_final: 0.8028 (t0) REVERT: E 107 ASN cc_start: 0.6857 (t0) cc_final: 0.6649 (t0) REVERT: E 140 TRP cc_start: 0.8471 (t60) cc_final: 0.8132 (t60) REVERT: E 183 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.8216 (mtt-85) REVERT: E 204 ASP cc_start: 0.7790 (t0) cc_final: 0.7437 (t0) REVERT: F 300 PHE cc_start: 0.8311 (m-80) cc_final: 0.8068 (m-80) REVERT: F 343 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: G 73 ASN cc_start: 0.8479 (t0) cc_final: 0.8010 (t0) REVERT: G 107 ASN cc_start: 0.6862 (t0) cc_final: 0.6653 (t0) REVERT: G 140 TRP cc_start: 0.8469 (t60) cc_final: 0.8132 (t60) REVERT: G 183 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8217 (mtt-85) REVERT: G 204 ASP cc_start: 0.7822 (t0) cc_final: 0.7452 (t0) REVERT: G 207 LEU cc_start: 0.7691 (tp) cc_final: 0.7468 (mt) REVERT: H 300 PHE cc_start: 0.8313 (m-80) cc_final: 0.8075 (m-80) REVERT: H 343 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6887 (tm-30) outliers start: 91 outliers final: 60 residues processed: 538 average time/residue: 0.3109 time to fit residues: 251.5253 Evaluate side-chains 474 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 410 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 141 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20200 Z= 0.168 Angle : 0.636 8.739 27328 Z= 0.313 Chirality : 0.040 0.185 3012 Planarity : 0.004 0.058 3468 Dihedral : 4.276 22.866 2684 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.66 % Allowed : 22.43 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.17), residues: 2404 helix: 0.24 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -1.71 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 8 HIS 0.002 0.000 HIS E 135 PHE 0.022 0.001 PHE B 191 TYR 0.031 0.001 TYR H 270 ARG 0.006 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 443 time to evaluate : 2.205 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8457 (t0) cc_final: 0.8017 (t0) REVERT: A 107 ASN cc_start: 0.6833 (t0) cc_final: 0.6606 (t0) REVERT: A 140 TRP cc_start: 0.8416 (t60) cc_final: 0.8042 (t60) REVERT: A 183 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8199 (mtt-85) REVERT: A 207 LEU cc_start: 0.7290 (tt) cc_final: 0.6837 (mt) REVERT: A 217 MET cc_start: 0.7316 (mmm) cc_final: 0.5993 (mmm) REVERT: B 276 MET cc_start: 0.7353 (mmt) cc_final: 0.7103 (mmm) REVERT: B 343 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: C 73 ASN cc_start: 0.8467 (t0) cc_final: 0.8029 (t0) REVERT: C 107 ASN cc_start: 0.6848 (t0) cc_final: 0.6617 (t0) REVERT: C 140 TRP cc_start: 0.8403 (t60) cc_final: 0.8120 (t60) REVERT: C 183 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8164 (mtt-85) REVERT: C 207 LEU cc_start: 0.7337 (tt) cc_final: 0.6829 (mt) REVERT: C 217 MET cc_start: 0.7326 (mmm) cc_final: 0.5968 (mmm) REVERT: D 276 MET cc_start: 0.7350 (mmt) cc_final: 0.7099 (mmm) REVERT: D 343 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: E 73 ASN cc_start: 0.8463 (t0) cc_final: 0.8022 (t0) REVERT: E 107 ASN cc_start: 0.6831 (t0) cc_final: 0.6607 (t0) REVERT: E 140 TRP cc_start: 0.8410 (t60) cc_final: 0.8127 (t60) REVERT: E 183 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8197 (mtt-85) REVERT: E 217 MET cc_start: 0.7334 (mmm) cc_final: 0.5995 (mmm) REVERT: F 276 MET cc_start: 0.7353 (mmt) cc_final: 0.7101 (mmm) REVERT: F 343 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: G 73 ASN cc_start: 0.8455 (t0) cc_final: 0.8012 (t0) REVERT: G 107 ASN cc_start: 0.6840 (t0) cc_final: 0.6614 (t0) REVERT: G 140 TRP cc_start: 0.8412 (t60) cc_final: 0.8126 (t60) REVERT: G 183 ARG cc_start: 0.8479 (mmm-85) cc_final: 0.8209 (mtt-85) REVERT: G 217 MET cc_start: 0.7329 (mmm) cc_final: 0.5959 (mmm) REVERT: H 270 TYR cc_start: 0.5789 (t80) cc_final: 0.5579 (t80) REVERT: H 276 MET cc_start: 0.7364 (mmt) cc_final: 0.7142 (mmm) REVERT: H 343 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6980 (tm-30) outliers start: 100 outliers final: 71 residues processed: 523 average time/residue: 0.3054 time to fit residues: 242.3319 Evaluate side-chains 493 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 418 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 0.4980 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 147 optimal weight: 0.0170 chunk 157 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20200 Z= 0.173 Angle : 0.650 9.385 27328 Z= 0.319 Chirality : 0.040 0.185 3012 Planarity : 0.004 0.058 3468 Dihedral : 4.164 20.941 2684 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.62 % Allowed : 22.67 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.17), residues: 2404 helix: 0.28 (0.14), residues: 1492 sheet: None (None), residues: 0 loop : -1.69 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 170 HIS 0.001 0.000 HIS H 481 PHE 0.021 0.001 PHE B 191 TYR 0.047 0.001 TYR F 270 ARG 0.005 0.000 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 448 time to evaluate : 2.216 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8414 (t0) cc_final: 0.8014 (t0) REVERT: A 140 TRP cc_start: 0.8402 (t60) cc_final: 0.7978 (t60) REVERT: A 183 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8228 (mtt-85) REVERT: A 207 LEU cc_start: 0.7185 (tt) cc_final: 0.6811 (mt) REVERT: A 217 MET cc_start: 0.6897 (mmm) cc_final: 0.6267 (mmm) REVERT: B 343 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: C 73 ASN cc_start: 0.8428 (t0) cc_final: 0.8008 (t0) REVERT: C 107 ASN cc_start: 0.6847 (t0) cc_final: 0.6607 (t0) REVERT: C 140 TRP cc_start: 0.8391 (t60) cc_final: 0.8074 (t60) REVERT: C 183 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.8347 (mtt-85) REVERT: C 207 LEU cc_start: 0.7255 (tt) cc_final: 0.6787 (mt) REVERT: C 217 MET cc_start: 0.6898 (mmm) cc_final: 0.6260 (mmm) REVERT: D 343 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: E 73 ASN cc_start: 0.8421 (t0) cc_final: 0.8003 (t0) REVERT: E 140 TRP cc_start: 0.8420 (t60) cc_final: 0.8024 (t60) REVERT: E 183 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8230 (mtt-85) REVERT: E 204 ASP cc_start: 0.7687 (t0) cc_final: 0.7472 (p0) REVERT: E 217 MET cc_start: 0.6914 (mmm) cc_final: 0.6269 (mmm) REVERT: F 343 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: G 73 ASN cc_start: 0.8413 (t0) cc_final: 0.8014 (t0) REVERT: G 140 TRP cc_start: 0.8391 (t60) cc_final: 0.8081 (t60) REVERT: G 183 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8212 (mtt-85) REVERT: G 217 MET cc_start: 0.6893 (mmm) cc_final: 0.6249 (mmm) REVERT: H 343 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6982 (tm-30) outliers start: 99 outliers final: 64 residues processed: 530 average time/residue: 0.3001 time to fit residues: 241.5635 Evaluate side-chains 488 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 420 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS ** D 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 20200 Z= 0.419 Angle : 0.745 9.658 27328 Z= 0.375 Chirality : 0.045 0.189 3012 Planarity : 0.005 0.065 3468 Dihedral : 4.685 25.119 2684 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.15 % Allowed : 23.04 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.17 (0.17), residues: 2404 helix: -0.05 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : -1.93 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 170 HIS 0.004 0.001 HIS H 481 PHE 0.024 0.002 PHE E 142 TYR 0.028 0.002 TYR F 270 ARG 0.006 0.001 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 415 time to evaluate : 1.769 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: A 73 ASN cc_start: 0.8488 (t0) cc_final: 0.8102 (t0) REVERT: A 183 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8265 (mtt-85) REVERT: A 207 LEU cc_start: 0.7187 (tt) cc_final: 0.6975 (mt) REVERT: B 343 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6899 (tm-30) REVERT: C 73 ASN cc_start: 0.8493 (t0) cc_final: 0.8103 (t0) REVERT: C 207 LEU cc_start: 0.7234 (tt) cc_final: 0.6983 (mt) REVERT: D 343 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: E 73 ASN cc_start: 0.8487 (t0) cc_final: 0.8100 (t0) REVERT: E 183 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8251 (mtt-85) REVERT: F 343 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: G 73 ASN cc_start: 0.8488 (t0) cc_final: 0.8101 (t0) REVERT: G 183 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8265 (mtt-85) REVERT: G 204 ASP cc_start: 0.7657 (t0) cc_final: 0.7445 (p0) REVERT: H 343 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6936 (tm-30) outliers start: 89 outliers final: 69 residues processed: 478 average time/residue: 0.2964 time to fit residues: 214.8969 Evaluate side-chains 475 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 404 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.8980 chunk 227 optimal weight: 0.5980 chunk 139 optimal weight: 0.0020 chunk 108 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20200 Z= 0.196 Angle : 0.709 10.183 27328 Z= 0.347 Chirality : 0.041 0.189 3012 Planarity : 0.005 0.063 3468 Dihedral : 4.303 21.115 2684 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.89 % Allowed : 25.23 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.17), residues: 2404 helix: 0.14 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -1.72 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 170 HIS 0.002 0.000 HIS E 135 PHE 0.025 0.001 PHE F 191 TYR 0.038 0.001 TYR H 270 ARG 0.007 0.000 ARG B 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 416 time to evaluate : 2.078 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8422 (t0) cc_final: 0.8056 (t0) REVERT: A 140 TRP cc_start: 0.8441 (t60) cc_final: 0.8033 (t60) REVERT: A 183 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8235 (mtt-85) REVERT: A 207 LEU cc_start: 0.7218 (tt) cc_final: 0.6982 (mt) REVERT: A 217 MET cc_start: 0.7157 (mmm) cc_final: 0.6806 (tpp) REVERT: B 268 MET cc_start: 0.6977 (tpp) cc_final: 0.6314 (ppp) REVERT: B 343 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: C 73 ASN cc_start: 0.8423 (t0) cc_final: 0.8056 (t0) REVERT: C 140 TRP cc_start: 0.8380 (t60) cc_final: 0.8089 (t60) REVERT: C 183 ARG cc_start: 0.8408 (mtt-85) cc_final: 0.8044 (mmt-90) REVERT: C 207 LEU cc_start: 0.7240 (tt) cc_final: 0.6974 (mt) REVERT: C 217 MET cc_start: 0.7143 (mmm) cc_final: 0.6789 (tpp) REVERT: D 268 MET cc_start: 0.6968 (tpp) cc_final: 0.6311 (ppp) REVERT: D 343 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: E 73 ASN cc_start: 0.8416 (t0) cc_final: 0.8053 (t0) REVERT: E 140 TRP cc_start: 0.8444 (t60) cc_final: 0.8010 (t60) REVERT: E 183 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8208 (mtt-85) REVERT: E 217 MET cc_start: 0.7171 (mmm) cc_final: 0.6819 (tpp) REVERT: F 268 MET cc_start: 0.6975 (tpp) cc_final: 0.6313 (ppp) REVERT: F 343 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: G 73 ASN cc_start: 0.8421 (t0) cc_final: 0.8057 (t0) REVERT: G 140 TRP cc_start: 0.8447 (t60) cc_final: 0.8042 (t60) REVERT: G 183 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8201 (mtt-85) REVERT: G 217 MET cc_start: 0.7155 (mmm) cc_final: 0.6817 (tpp) REVERT: H 268 MET cc_start: 0.7077 (tpp) cc_final: 0.6412 (ppp) REVERT: H 343 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6926 (tm-30) outliers start: 62 outliers final: 42 residues processed: 462 average time/residue: 0.3013 time to fit residues: 211.3723 Evaluate side-chains 452 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 406 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 175 optimal weight: 0.0670 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 79 optimal weight: 0.0570 chunk 195 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.174008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127825 restraints weight = 32555.936| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.38 r_work: 0.3509 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20200 Z= 0.189 Angle : 0.691 9.828 27328 Z= 0.341 Chirality : 0.041 0.187 3012 Planarity : 0.005 0.059 3468 Dihedral : 4.168 19.964 2684 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.71 % Allowed : 25.51 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.17), residues: 2404 helix: 0.25 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -1.52 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 170 HIS 0.001 0.000 HIS E 135 PHE 0.028 0.001 PHE B 191 TYR 0.036 0.001 TYR B 270 ARG 0.007 0.000 ARG H 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4973.04 seconds wall clock time: 90 minutes 18.82 seconds (5418.82 seconds total)