Starting phenix.real_space_refine (version: dev) on Thu Dec 22 08:43:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1r_9571/12_2022/5h1r_9571.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1r_9571/12_2022/5h1r_9571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1r_9571/12_2022/5h1r_9571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1r_9571/12_2022/5h1r_9571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1r_9571/12_2022/5h1r_9571.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1r_9571/12_2022/5h1r_9571.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G ARG 181": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H ARG 161": "NH1" <-> "NH2" Residue "H ARG 181": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "I ARG 161": "NH1" <-> "NH2" Residue "I ARG 181": "NH1" <-> "NH2" Residue "I ARG 184": "NH1" <-> "NH2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J ARG 161": "NH1" <-> "NH2" Residue "J ARG 181": "NH1" <-> "NH2" Residue "J ARG 184": "NH1" <-> "NH2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 123": "NH1" <-> "NH2" Residue "K ARG 161": "NH1" <-> "NH2" Residue "K ARG 181": "NH1" <-> "NH2" Residue "K ARG 184": "NH1" <-> "NH2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ARG 181": "NH1" <-> "NH2" Residue "L ARG 184": "NH1" <-> "NH2" Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 123": "NH1" <-> "NH2" Residue "M ARG 161": "NH1" <-> "NH2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M ARG 184": "NH1" <-> "NH2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N ARG 161": "NH1" <-> "NH2" Residue "N ARG 181": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 123": "NH1" <-> "NH2" Residue "O ARG 161": "NH1" <-> "NH2" Residue "O ARG 181": "NH1" <-> "NH2" Residue "O ARG 184": "NH1" <-> "NH2" Residue "P PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 123": "NH1" <-> "NH2" Residue "P ARG 161": "NH1" <-> "NH2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "P ARG 184": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 47440 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2965 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 24.88, per 1000 atoms: 0.52 Number of scatterers: 47440 At special positions: 0 Unit cell: (124.23, 124.23, 207.87, 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 192 16.00 O 8256 8.00 N 7792 7.00 C 31200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 76 " - pdb=" SG CYS H 248 " distance=2.03 Simple disulfide: pdb=" SG CYS I 58 " - pdb=" SG CYS I 265 " distance=2.03 Simple disulfide: pdb=" SG CYS I 76 " - pdb=" SG CYS I 248 " distance=2.03 Simple disulfide: pdb=" SG CYS J 58 " - pdb=" SG CYS J 265 " distance=2.03 Simple disulfide: pdb=" SG CYS J 76 " - pdb=" SG CYS J 248 " distance=2.03 Simple disulfide: pdb=" SG CYS K 58 " - pdb=" SG CYS K 265 " distance=2.03 Simple disulfide: pdb=" SG CYS K 76 " - pdb=" SG CYS K 248 " distance=2.03 Simple disulfide: pdb=" SG CYS L 58 " - pdb=" SG CYS L 265 " distance=2.03 Simple disulfide: pdb=" SG CYS L 76 " - pdb=" SG CYS L 248 " distance=2.03 Simple disulfide: pdb=" SG CYS M 58 " - pdb=" SG CYS M 265 " distance=2.03 Simple disulfide: pdb=" SG CYS M 76 " - pdb=" SG CYS M 248 " distance=2.03 Simple disulfide: pdb=" SG CYS N 58 " - pdb=" SG CYS N 265 " distance=2.03 Simple disulfide: pdb=" SG CYS N 76 " - pdb=" SG CYS N 248 " distance=2.03 Simple disulfide: pdb=" SG CYS O 58 " - pdb=" SG CYS O 265 " distance=2.03 Simple disulfide: pdb=" SG CYS O 76 " - pdb=" SG CYS O 248 " distance=2.03 Simple disulfide: pdb=" SG CYS P 58 " - pdb=" SG CYS P 265 " distance=2.03 Simple disulfide: pdb=" SG CYS P 76 " - pdb=" SG CYS P 248 " distance=2.03 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: 20.46 Conformation dependent library (CDL) restraints added in 7.2 seconds 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11136 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 16 sheets defined 66.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 4.031A pdb=" N VAL A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 107 through 133 removed outlier: 3.752A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 137 through 154 removed outlier: 3.887A pdb=" N ASP A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 183 Proline residue: A 169 - end of helix removed outlier: 3.757A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 212 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 268 through 303 removed outlier: 3.891A pdb=" N TYR A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 299 " --> pdb=" O CYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 336 through 349 removed outlier: 3.791A pdb=" N ASP A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 4.325A pdb=" N ALA A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.032A pdb=" N VAL B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.430A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 107 through 133 removed outlier: 3.752A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 137 through 154 removed outlier: 3.888A pdb=" N ASP B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 183 Proline residue: B 169 - end of helix removed outlier: 3.757A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 212 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 268 through 303 removed outlier: 3.890A pdb=" N TYR B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TRP B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 299 " --> pdb=" O CYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 327 through 335 Processing helix chain 'B' and resid 336 through 349 removed outlier: 3.791A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 365 removed outlier: 4.325A pdb=" N ALA B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 21 removed outlier: 4.031A pdb=" N VAL C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 48 removed outlier: 3.864A pdb=" N ARG C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 107 through 133 removed outlier: 3.751A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 137 through 154 removed outlier: 3.887A pdb=" N ASP C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 183 Proline residue: C 169 - end of helix removed outlier: 3.756A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 212 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 268 through 303 removed outlier: 3.890A pdb=" N TYR C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 299 " --> pdb=" O CYS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 327 through 335 Processing helix chain 'C' and resid 336 through 349 removed outlier: 3.790A pdb=" N ASP C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 365 removed outlier: 4.326A pdb=" N ALA C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN C 363 " --> pdb=" O ILE C 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 21 removed outlier: 4.031A pdb=" N VAL D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.430A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 107 through 133 removed outlier: 3.751A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 137 through 154 removed outlier: 3.888A pdb=" N ASP D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 183 Proline residue: D 169 - end of helix removed outlier: 3.757A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 212 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 268 through 303 removed outlier: 3.891A pdb=" N TYR D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TRP D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 299 " --> pdb=" O CYS D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 327 through 335 Processing helix chain 'D' and resid 336 through 349 removed outlier: 3.791A pdb=" N ASP D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 365 removed outlier: 4.325A pdb=" N ALA D 354 " --> pdb=" O GLY D 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER D 355 " --> pdb=" O ASP D 351 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR D 356 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN D 363 " --> pdb=" O ILE D 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 21 removed outlier: 4.031A pdb=" N VAL E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 107 through 133 removed outlier: 3.752A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix Processing helix chain 'E' and resid 137 through 154 removed outlier: 3.887A pdb=" N ASP E 153 " --> pdb=" O SER E 149 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS E 154 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 183 Proline residue: E 169 - end of helix removed outlier: 3.756A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 212 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 236 through 240 Processing helix chain 'E' and resid 268 through 303 removed outlier: 3.891A pdb=" N TYR E 272 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE E 299 " --> pdb=" O CYS E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 336 through 349 removed outlier: 3.791A pdb=" N ASP E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 365 removed outlier: 4.325A pdb=" N ALA E 354 " --> pdb=" O GLY E 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER E 355 " --> pdb=" O ASP E 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN E 363 " --> pdb=" O ILE E 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 21 removed outlier: 4.032A pdb=" N VAL F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 47 " --> pdb=" O SER F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 Processing helix chain 'F' and resid 107 through 133 removed outlier: 3.752A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix Processing helix chain 'F' and resid 137 through 154 removed outlier: 3.888A pdb=" N ASP F 153 " --> pdb=" O SER F 149 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 183 Proline residue: F 169 - end of helix removed outlier: 3.757A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS F 183 " --> pdb=" O LEU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 212 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 236 through 240 Processing helix chain 'F' and resid 268 through 303 removed outlier: 3.890A pdb=" N TYR F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS F 295 " --> pdb=" O SER F 291 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE F 299 " --> pdb=" O CYS F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 336 through 349 removed outlier: 3.790A pdb=" N ASP F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 365 removed outlier: 4.326A pdb=" N ALA F 354 " --> pdb=" O GLY F 350 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER F 355 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR F 356 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN F 363 " --> pdb=" O ILE F 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 21 removed outlier: 4.032A pdb=" N VAL G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 47 " --> pdb=" O SER G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 4.430A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'G' and resid 107 through 133 removed outlier: 3.752A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix Processing helix chain 'G' and resid 137 through 154 removed outlier: 3.886A pdb=" N ASP G 153 " --> pdb=" O SER G 149 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 183 Proline residue: G 169 - end of helix removed outlier: 3.756A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS G 183 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 212 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 236 through 240 Processing helix chain 'G' and resid 268 through 303 removed outlier: 3.891A pdb=" N TYR G 272 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE G 278 " --> pdb=" O GLU G 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE G 279 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE G 299 " --> pdb=" O CYS G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 327 through 335 Processing helix chain 'G' and resid 336 through 349 removed outlier: 3.791A pdb=" N ASP G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 365 removed outlier: 4.325A pdb=" N ALA G 354 " --> pdb=" O GLY G 350 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER G 355 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR G 356 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN G 363 " --> pdb=" O ILE G 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 21 removed outlier: 4.031A pdb=" N VAL H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 48 removed outlier: 3.866A pdb=" N ARG H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU H 47 " --> pdb=" O SER H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 107 through 133 removed outlier: 3.751A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix Processing helix chain 'H' and resid 137 through 154 removed outlier: 3.887A pdb=" N ASP H 153 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 183 Proline residue: H 169 - end of helix removed outlier: 3.757A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS H 183 " --> pdb=" O LEU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 212 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 236 through 240 Processing helix chain 'H' and resid 268 through 303 removed outlier: 3.891A pdb=" N TYR H 272 " --> pdb=" O THR H 268 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU H 274 " --> pdb=" O ASN H 270 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE H 278 " --> pdb=" O GLU H 274 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE H 279 " --> pdb=" O LYS H 275 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN H 294 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS H 295 " --> pdb=" O SER H 291 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE H 299 " --> pdb=" O CYS H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 327 through 335 Processing helix chain 'H' and resid 336 through 349 removed outlier: 3.790A pdb=" N ASP H 343 " --> pdb=" O LEU H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 365 removed outlier: 4.326A pdb=" N ALA H 354 " --> pdb=" O GLY H 350 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER H 355 " --> pdb=" O ASP H 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR H 356 " --> pdb=" O ILE H 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN H 363 " --> pdb=" O ILE H 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 21 removed outlier: 4.031A pdb=" N VAL I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 48 removed outlier: 3.864A pdb=" N ARG I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 47 " --> pdb=" O SER I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 99 Processing helix chain 'I' and resid 107 through 133 removed outlier: 3.753A pdb=" N ALA I 113 " --> pdb=" O PRO I 109 " (cutoff:3.500A) Proline residue: I 122 - end of helix Processing helix chain 'I' and resid 137 through 154 removed outlier: 3.888A pdb=" N ASP I 153 " --> pdb=" O SER I 149 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 183 Proline residue: I 169 - end of helix removed outlier: 3.757A pdb=" N TYR I 172 " --> pdb=" O ARG I 168 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS I 182 " --> pdb=" O ARG I 178 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS I 183 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 212 Processing helix chain 'I' and resid 222 through 231 Processing helix chain 'I' and resid 236 through 240 Processing helix chain 'I' and resid 268 through 303 removed outlier: 3.890A pdb=" N TYR I 272 " --> pdb=" O THR I 268 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU I 274 " --> pdb=" O ASN I 270 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE I 278 " --> pdb=" O GLU I 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE I 279 " --> pdb=" O LYS I 275 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN I 294 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS I 295 " --> pdb=" O SER I 291 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE I 299 " --> pdb=" O CYS I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 316 Processing helix chain 'I' and resid 327 through 335 Processing helix chain 'I' and resid 336 through 349 removed outlier: 3.791A pdb=" N ASP I 343 " --> pdb=" O LEU I 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 365 removed outlier: 4.326A pdb=" N ALA I 354 " --> pdb=" O GLY I 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER I 355 " --> pdb=" O ASP I 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR I 356 " --> pdb=" O ILE I 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN I 363 " --> pdb=" O ILE I 359 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 21 removed outlier: 4.032A pdb=" N VAL J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 47 " --> pdb=" O SER J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 99 Processing helix chain 'J' and resid 107 through 133 removed outlier: 3.752A pdb=" N ALA J 113 " --> pdb=" O PRO J 109 " (cutoff:3.500A) Proline residue: J 122 - end of helix Processing helix chain 'J' and resid 137 through 154 removed outlier: 3.887A pdb=" N ASP J 153 " --> pdb=" O SER J 149 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 183 Proline residue: J 169 - end of helix removed outlier: 3.757A pdb=" N TYR J 172 " --> pdb=" O ARG J 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS J 182 " --> pdb=" O ARG J 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS J 183 " --> pdb=" O LEU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 212 Processing helix chain 'J' and resid 222 through 231 Processing helix chain 'J' and resid 236 through 240 Processing helix chain 'J' and resid 268 through 303 removed outlier: 3.891A pdb=" N TYR J 272 " --> pdb=" O THR J 268 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU J 274 " --> pdb=" O ASN J 270 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE J 278 " --> pdb=" O GLU J 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE J 279 " --> pdb=" O LYS J 275 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL J 293 " --> pdb=" O VAL J 289 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN J 294 " --> pdb=" O VAL J 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS J 295 " --> pdb=" O SER J 291 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP J 298 " --> pdb=" O ASN J 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE J 299 " --> pdb=" O CYS J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 309 through 316 Processing helix chain 'J' and resid 327 through 335 Processing helix chain 'J' and resid 336 through 349 removed outlier: 3.789A pdb=" N ASP J 343 " --> pdb=" O LEU J 339 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 365 removed outlier: 4.325A pdb=" N ALA J 354 " --> pdb=" O GLY J 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER J 355 " --> pdb=" O ASP J 351 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR J 356 " --> pdb=" O ILE J 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN J 363 " --> pdb=" O ILE J 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 21 removed outlier: 4.032A pdb=" N VAL K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 48 removed outlier: 3.864A pdb=" N ARG K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU K 47 " --> pdb=" O SER K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 79 removed outlier: 4.430A pdb=" N GLN K 74 " --> pdb=" O ASN K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 99 Processing helix chain 'K' and resid 107 through 133 removed outlier: 3.752A pdb=" N ALA K 113 " --> pdb=" O PRO K 109 " (cutoff:3.500A) Proline residue: K 122 - end of helix Processing helix chain 'K' and resid 137 through 154 removed outlier: 3.887A pdb=" N ASP K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS K 154 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 183 Proline residue: K 169 - end of helix removed outlier: 3.757A pdb=" N TYR K 172 " --> pdb=" O ARG K 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS K 182 " --> pdb=" O ARG K 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS K 183 " --> pdb=" O LEU K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 212 Processing helix chain 'K' and resid 222 through 231 Processing helix chain 'K' and resid 236 through 240 Processing helix chain 'K' and resid 268 through 303 removed outlier: 3.890A pdb=" N TYR K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU K 274 " --> pdb=" O ASN K 270 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE K 278 " --> pdb=" O GLU K 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE K 279 " --> pdb=" O LYS K 275 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL K 293 " --> pdb=" O VAL K 289 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN K 294 " --> pdb=" O VAL K 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS K 295 " --> pdb=" O SER K 291 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP K 298 " --> pdb=" O ASN K 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE K 299 " --> pdb=" O CYS K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 316 Processing helix chain 'K' and resid 327 through 335 Processing helix chain 'K' and resid 336 through 349 removed outlier: 3.791A pdb=" N ASP K 343 " --> pdb=" O LEU K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 365 removed outlier: 4.325A pdb=" N ALA K 354 " --> pdb=" O GLY K 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER K 355 " --> pdb=" O ASP K 351 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR K 356 " --> pdb=" O ILE K 352 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN K 363 " --> pdb=" O ILE K 359 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 21 removed outlier: 4.031A pdb=" N VAL L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG L 33 " --> pdb=" O ARG L 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU L 47 " --> pdb=" O SER L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN L 74 " --> pdb=" O ASN L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 107 through 133 removed outlier: 3.752A pdb=" N ALA L 113 " --> pdb=" O PRO L 109 " (cutoff:3.500A) Proline residue: L 122 - end of helix Processing helix chain 'L' and resid 137 through 154 removed outlier: 3.888A pdb=" N ASP L 153 " --> pdb=" O SER L 149 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS L 154 " --> pdb=" O GLU L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 183 Proline residue: L 169 - end of helix removed outlier: 3.757A pdb=" N TYR L 172 " --> pdb=" O ARG L 168 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS L 182 " --> pdb=" O ARG L 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS L 183 " --> pdb=" O LEU L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 212 Processing helix chain 'L' and resid 222 through 231 Processing helix chain 'L' and resid 236 through 240 Processing helix chain 'L' and resid 268 through 303 removed outlier: 3.891A pdb=" N TYR L 272 " --> pdb=" O THR L 268 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU L 274 " --> pdb=" O ASN L 270 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE L 278 " --> pdb=" O GLU L 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE L 279 " --> pdb=" O LYS L 275 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN L 294 " --> pdb=" O VAL L 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS L 295 " --> pdb=" O SER L 291 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP L 298 " --> pdb=" O ASN L 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE L 299 " --> pdb=" O CYS L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 309 through 316 Processing helix chain 'L' and resid 327 through 335 Processing helix chain 'L' and resid 336 through 349 removed outlier: 3.791A pdb=" N ASP L 343 " --> pdb=" O LEU L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 365 removed outlier: 4.326A pdb=" N ALA L 354 " --> pdb=" O GLY L 350 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER L 355 " --> pdb=" O ASP L 351 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR L 356 " --> pdb=" O ILE L 352 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN L 363 " --> pdb=" O ILE L 359 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 21 removed outlier: 4.032A pdb=" N VAL M 18 " --> pdb=" O LEU M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG M 33 " --> pdb=" O ARG M 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU M 47 " --> pdb=" O SER M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN M 74 " --> pdb=" O ASN M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 99 Processing helix chain 'M' and resid 107 through 133 removed outlier: 3.752A pdb=" N ALA M 113 " --> pdb=" O PRO M 109 " (cutoff:3.500A) Proline residue: M 122 - end of helix Processing helix chain 'M' and resid 137 through 154 removed outlier: 3.887A pdb=" N ASP M 153 " --> pdb=" O SER M 149 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS M 154 " --> pdb=" O GLU M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 183 Proline residue: M 169 - end of helix removed outlier: 3.756A pdb=" N TYR M 172 " --> pdb=" O ARG M 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS M 182 " --> pdb=" O ARG M 178 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS M 183 " --> pdb=" O LEU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 212 Processing helix chain 'M' and resid 222 through 231 Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'M' and resid 268 through 303 removed outlier: 3.891A pdb=" N TYR M 272 " --> pdb=" O THR M 268 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU M 274 " --> pdb=" O ASN M 270 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE M 278 " --> pdb=" O GLU M 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE M 279 " --> pdb=" O LYS M 275 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL M 293 " --> pdb=" O VAL M 289 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN M 294 " --> pdb=" O VAL M 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS M 295 " --> pdb=" O SER M 291 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP M 298 " --> pdb=" O ASN M 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE M 299 " --> pdb=" O CYS M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 316 Processing helix chain 'M' and resid 327 through 335 Processing helix chain 'M' and resid 336 through 349 removed outlier: 3.790A pdb=" N ASP M 343 " --> pdb=" O LEU M 339 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 365 removed outlier: 4.325A pdb=" N ALA M 354 " --> pdb=" O GLY M 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER M 355 " --> pdb=" O ASP M 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR M 356 " --> pdb=" O ILE M 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN M 363 " --> pdb=" O ILE M 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 21 removed outlier: 4.032A pdb=" N VAL N 18 " --> pdb=" O LEU N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 48 removed outlier: 3.864A pdb=" N ARG N 33 " --> pdb=" O ARG N 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU N 47 " --> pdb=" O SER N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN N 74 " --> pdb=" O ASN N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 99 Processing helix chain 'N' and resid 107 through 133 removed outlier: 3.753A pdb=" N ALA N 113 " --> pdb=" O PRO N 109 " (cutoff:3.500A) Proline residue: N 122 - end of helix Processing helix chain 'N' and resid 137 through 154 removed outlier: 3.888A pdb=" N ASP N 153 " --> pdb=" O SER N 149 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS N 154 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 183 Proline residue: N 169 - end of helix removed outlier: 3.757A pdb=" N TYR N 172 " --> pdb=" O ARG N 168 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS N 182 " --> pdb=" O ARG N 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS N 183 " --> pdb=" O LEU N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 212 Processing helix chain 'N' and resid 222 through 231 Processing helix chain 'N' and resid 236 through 240 Processing helix chain 'N' and resid 268 through 303 removed outlier: 3.890A pdb=" N TYR N 272 " --> pdb=" O THR N 268 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU N 274 " --> pdb=" O ASN N 270 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE N 279 " --> pdb=" O LYS N 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL N 293 " --> pdb=" O VAL N 289 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN N 294 " --> pdb=" O VAL N 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS N 295 " --> pdb=" O SER N 291 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP N 298 " --> pdb=" O ASN N 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE N 299 " --> pdb=" O CYS N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 327 through 335 Processing helix chain 'N' and resid 336 through 349 removed outlier: 3.791A pdb=" N ASP N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 365 removed outlier: 4.325A pdb=" N ALA N 354 " --> pdb=" O GLY N 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER N 355 " --> pdb=" O ASP N 351 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR N 356 " --> pdb=" O ILE N 352 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN N 363 " --> pdb=" O ILE N 359 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 21 removed outlier: 4.032A pdb=" N VAL O 18 " --> pdb=" O LEU O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG O 33 " --> pdb=" O ARG O 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU O 47 " --> pdb=" O SER O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN O 74 " --> pdb=" O ASN O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 99 Processing helix chain 'O' and resid 107 through 133 removed outlier: 3.753A pdb=" N ALA O 113 " --> pdb=" O PRO O 109 " (cutoff:3.500A) Proline residue: O 122 - end of helix Processing helix chain 'O' and resid 137 through 154 removed outlier: 3.887A pdb=" N ASP O 153 " --> pdb=" O SER O 149 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS O 154 " --> pdb=" O GLU O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 183 Proline residue: O 169 - end of helix removed outlier: 3.757A pdb=" N TYR O 172 " --> pdb=" O ARG O 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS O 182 " --> pdb=" O ARG O 178 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS O 183 " --> pdb=" O LEU O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 212 Processing helix chain 'O' and resid 222 through 231 Processing helix chain 'O' and resid 236 through 240 Processing helix chain 'O' and resid 268 through 303 removed outlier: 3.890A pdb=" N TYR O 272 " --> pdb=" O THR O 268 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU O 274 " --> pdb=" O ASN O 270 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE O 278 " --> pdb=" O GLU O 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE O 279 " --> pdb=" O LYS O 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL O 293 " --> pdb=" O VAL O 289 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN O 294 " --> pdb=" O VAL O 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS O 295 " --> pdb=" O SER O 291 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP O 298 " --> pdb=" O ASN O 294 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE O 299 " --> pdb=" O CYS O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 309 through 316 Processing helix chain 'O' and resid 327 through 335 Processing helix chain 'O' and resid 336 through 349 removed outlier: 3.790A pdb=" N ASP O 343 " --> pdb=" O LEU O 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 350 through 365 removed outlier: 4.325A pdb=" N ALA O 354 " --> pdb=" O GLY O 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER O 355 " --> pdb=" O ASP O 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR O 356 " --> pdb=" O ILE O 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN O 363 " --> pdb=" O ILE O 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 12 through 21 removed outlier: 4.032A pdb=" N VAL P 18 " --> pdb=" O LEU P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 48 removed outlier: 3.865A pdb=" N ARG P 33 " --> pdb=" O ARG P 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU P 47 " --> pdb=" O SER P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 79 removed outlier: 4.431A pdb=" N GLN P 74 " --> pdb=" O ASN P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 99 Processing helix chain 'P' and resid 107 through 133 removed outlier: 3.752A pdb=" N ALA P 113 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Proline residue: P 122 - end of helix Processing helix chain 'P' and resid 137 through 154 removed outlier: 3.887A pdb=" N ASP P 153 " --> pdb=" O SER P 149 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS P 154 " --> pdb=" O GLU P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 183 Proline residue: P 169 - end of helix removed outlier: 3.757A pdb=" N TYR P 172 " --> pdb=" O ARG P 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS P 182 " --> pdb=" O ARG P 178 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS P 183 " --> pdb=" O LEU P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 212 Processing helix chain 'P' and resid 222 through 231 Processing helix chain 'P' and resid 236 through 240 Processing helix chain 'P' and resid 268 through 303 removed outlier: 3.891A pdb=" N TYR P 272 " --> pdb=" O THR P 268 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU P 274 " --> pdb=" O ASN P 270 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE P 278 " --> pdb=" O GLU P 274 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE P 279 " --> pdb=" O LYS P 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL P 293 " --> pdb=" O VAL P 289 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN P 294 " --> pdb=" O VAL P 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS P 295 " --> pdb=" O SER P 291 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP P 298 " --> pdb=" O ASN P 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE P 299 " --> pdb=" O CYS P 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 309 through 316 Processing helix chain 'P' and resid 327 through 335 Processing helix chain 'P' and resid 336 through 349 removed outlier: 3.791A pdb=" N ASP P 343 " --> pdb=" O LEU P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 365 removed outlier: 4.326A pdb=" N ALA P 354 " --> pdb=" O GLY P 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER P 355 " --> pdb=" O ASP P 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR P 356 " --> pdb=" O ILE P 352 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN P 363 " --> pdb=" O ILE P 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.539A pdb=" N THR A 57 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 58 removed outlier: 3.540A pdb=" N THR B 57 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 58 removed outlier: 3.539A pdb=" N THR C 57 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 58 removed outlier: 3.540A pdb=" N THR D 57 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.539A pdb=" N THR E 57 " --> pdb=" O VAL E 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 56 through 58 removed outlier: 3.540A pdb=" N THR F 57 " --> pdb=" O VAL F 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 56 through 58 removed outlier: 3.539A pdb=" N THR G 57 " --> pdb=" O VAL G 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 56 through 58 removed outlier: 3.539A pdb=" N THR H 57 " --> pdb=" O VAL H 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 56 through 58 removed outlier: 3.539A pdb=" N THR I 57 " --> pdb=" O VAL I 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 56 through 58 removed outlier: 3.539A pdb=" N THR J 57 " --> pdb=" O VAL J 266 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 56 through 58 removed outlier: 3.539A pdb=" N THR K 57 " --> pdb=" O VAL K 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 56 through 58 removed outlier: 3.540A pdb=" N THR L 57 " --> pdb=" O VAL L 266 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 56 through 58 removed outlier: 3.539A pdb=" N THR M 57 " --> pdb=" O VAL M 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 56 through 58 removed outlier: 3.539A pdb=" N THR N 57 " --> pdb=" O VAL N 266 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 56 through 58 removed outlier: 3.540A pdb=" N THR O 57 " --> pdb=" O VAL O 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 56 through 58 removed outlier: 3.538A pdb=" N THR P 57 " --> pdb=" O VAL P 266 " (cutoff:3.500A) 2544 hydrogen bonds defined for protein. 7536 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: 15.82 Time building geometry restraints manager: 22.15 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: 12641 1.33 - 1.45: 10654 1.45 - 1.57: 25249 1.57 - 1.68: 0 1.68 - 1.80: 272 Bond restraints: 48816 Sorted by residual: bond pdb=" CB TRP D 222 " pdb=" CG TRP D 222 " ideal model delta sigma weight residual 1.498 1.407 0.091 3.10e-02 1.04e+03 8.70e+00 bond pdb=" CB TRP B 222 " pdb=" CG TRP B 222 " ideal model delta sigma weight residual 1.498 1.407 0.091 3.10e-02 1.04e+03 8.70e+00 bond pdb=" CB TRP K 222 " pdb=" CG TRP K 222 " ideal model delta sigma weight residual 1.498 1.407 0.091 3.10e-02 1.04e+03 8.65e+00 bond pdb=" CB TRP N 222 " pdb=" CG TRP N 222 " ideal model delta sigma weight residual 1.498 1.407 0.091 3.10e-02 1.04e+03 8.59e+00 bond pdb=" CB TRP P 222 " pdb=" CG TRP P 222 " ideal model delta sigma weight residual 1.498 1.407 0.091 3.10e-02 1.04e+03 8.59e+00 ... (remaining 48811 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.80: 944 105.80 - 112.87: 26033 112.87 - 119.93: 17859 119.93 - 127.00: 20844 127.00 - 134.06: 800 Bond angle restraints: 66480 Sorted by residual: angle pdb=" N LEU L 86 " pdb=" CA LEU L 86 " pdb=" C LEU L 86 " ideal model delta sigma weight residual 107.41 122.04 -14.63 2.02e+00 2.45e-01 5.25e+01 angle pdb=" N LEU J 86 " pdb=" CA LEU J 86 " pdb=" C LEU J 86 " ideal model delta sigma weight residual 107.41 122.04 -14.63 2.02e+00 2.45e-01 5.25e+01 angle pdb=" N LEU N 86 " pdb=" CA LEU N 86 " pdb=" C LEU N 86 " ideal model delta sigma weight residual 107.41 122.04 -14.63 2.02e+00 2.45e-01 5.25e+01 angle pdb=" N LEU I 86 " pdb=" CA LEU I 86 " pdb=" C LEU I 86 " ideal model delta sigma weight residual 107.41 122.04 -14.63 2.02e+00 2.45e-01 5.25e+01 angle pdb=" N LEU M 86 " pdb=" CA LEU M 86 " pdb=" C LEU M 86 " ideal model delta sigma weight residual 107.41 122.04 -14.63 2.02e+00 2.45e-01 5.25e+01 ... (remaining 66475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 26192 17.00 - 34.00: 1664 34.00 - 50.99: 304 50.99 - 67.99: 48 67.99 - 84.99: 112 Dihedral angle restraints: 28320 sinusoidal: 11152 harmonic: 17168 Sorted by residual: dihedral pdb=" CA LEU G 86 " pdb=" C LEU G 86 " pdb=" N ASP G 87 " pdb=" CA ASP G 87 " ideal model delta harmonic sigma weight residual 180.00 107.10 72.90 0 5.00e+00 4.00e-02 2.13e+02 dihedral pdb=" CA LEU A 86 " pdb=" C LEU A 86 " pdb=" N ASP A 87 " pdb=" CA ASP A 87 " ideal model delta harmonic sigma weight residual 180.00 107.10 72.90 0 5.00e+00 4.00e-02 2.13e+02 dihedral pdb=" CA LEU P 86 " pdb=" C LEU P 86 " pdb=" N ASP P 87 " pdb=" CA ASP P 87 " ideal model delta harmonic sigma weight residual 180.00 107.13 72.87 0 5.00e+00 4.00e-02 2.12e+02 ... (remaining 28317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3974 0.044 - 0.087: 1968 0.087 - 0.131: 927 0.131 - 0.174: 395 0.174 - 0.218: 64 Chirality restraints: 7328 Sorted by residual: chirality pdb=" CA GLN F 88 " pdb=" N GLN F 88 " pdb=" C GLN F 88 " pdb=" CB GLN F 88 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLN B 88 " pdb=" N GLN B 88 " pdb=" C GLN B 88 " pdb=" CB GLN B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA GLN K 88 " pdb=" N GLN K 88 " pdb=" C GLN K 88 " pdb=" CB GLN K 88 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 7325 not shown) Planarity restraints: 8240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 242 " -0.032 2.00e-02 2.50e+03 1.99e-02 6.95e+00 pdb=" CG PHE J 242 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE J 242 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE J 242 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE J 242 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE J 242 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE J 242 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 242 " 0.032 2.00e-02 2.50e+03 1.99e-02 6.94e+00 pdb=" CG PHE B 242 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 242 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 242 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 242 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 242 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 242 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 242 " -0.032 2.00e-02 2.50e+03 1.99e-02 6.91e+00 pdb=" CG PHE O 242 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE O 242 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE O 242 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE O 242 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE O 242 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE O 242 " -0.008 2.00e-02 2.50e+03 ... (remaining 8237 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 745 2.55 - 3.14: 49346 3.14 - 3.73: 72887 3.73 - 4.31: 99436 4.31 - 4.90: 155414 Nonbonded interactions: 377828 Sorted by model distance: nonbonded pdb=" O PRO J 243 " pdb=" ND2 ASN J 270 " model vdw 1.968 2.520 nonbonded pdb=" O PRO M 243 " pdb=" ND2 ASN M 270 " model vdw 1.968 2.520 nonbonded pdb=" O PRO A 243 " pdb=" ND2 ASN A 270 " model vdw 1.968 2.520 nonbonded pdb=" O PRO L 243 " pdb=" ND2 ASN L 270 " model vdw 1.969 2.520 nonbonded pdb=" O PRO H 243 " pdb=" ND2 ASN H 270 " model vdw 1.969 2.520 ... (remaining 377823 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 31200 2.51 5 N 7792 2.21 5 O 8256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 6.500 Check model and map are aligned: 0.720 Convert atoms to be neutral: 0.420 Process input model: 112.280 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.014 0.091 48816 Z= 0.913 Angle : 1.358 16.846 66480 Z= 0.717 Chirality : 0.066 0.218 7328 Planarity : 0.007 0.049 8240 Dihedral : 13.160 84.990 17088 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 31.49 Ramachandran Plot: Outliers : 1.40 % Allowed : 12.94 % Favored : 85.66 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.31 % 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: -6.24 (0.07), residues: 5696 helix: -4.32 (0.04), residues: 3264 sheet: -4.13 (0.16), residues: 368 loop : -3.45 (0.12), residues: 2064 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2674 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 2626 time to evaluate : 5.961 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 24 residues processed: 2642 average time/residue: 0.6538 time to fit residues: 2812.5709 Evaluate side-chains 1756 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1732 time to evaluate : 5.210 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. outliers start: 24 outliers final: 16 residues processed: 24 average time/residue: 0.4513 time to fit residues: 27.4794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 3.9990 chunk 436 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 294 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 451 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 274 optimal weight: 7.9990 chunk 336 optimal weight: 2.9990 chunk 523 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN B 103 GLN B 241 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN D 103 GLN D 234 ASN ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 HIS ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN F 103 GLN F 234 ASN F 241 HIS G 234 ASN ** G 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 HIS ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN H 103 GLN H 241 HIS ** I 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 HIS ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 GLN J 103 GLN J 241 HIS ** K 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 241 HIS K 329 GLN L 103 GLN L 241 HIS M 234 ASN ** M 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 241 HIS ** M 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 GLN N 103 GLN N 234 ASN N 241 HIS O 234 ASN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 241 HIS ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 329 GLN P 103 GLN P 241 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 48816 Z= 0.292 Angle : 0.925 8.839 66480 Z= 0.481 Chirality : 0.050 0.239 7328 Planarity : 0.006 0.049 8240 Dihedral : 8.533 52.510 6320 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.88 % Favored : 89.55 % Rotamer Outliers : 6.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.87 % 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: -3.24 (0.10), residues: 5696 helix: -1.31 (0.08), residues: 3520 sheet: -4.10 (0.16), residues: 368 loop : -3.16 (0.14), residues: 1808 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2484 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 2174 time to evaluate : 5.198 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 310 outliers final: 235 residues processed: 2277 average time/residue: 0.5340 time to fit residues: 2044.4207 Evaluate side-chains 1968 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1733 time to evaluate : 5.398 Switching outliers to nearest non-outliers outliers start: 235 outliers final: 0 residues processed: 235 average time/residue: 0.3936 time to fit residues: 184.6815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 435 optimal weight: 5.9990 chunk 356 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 524 optimal weight: 1.9990 chunk 566 optimal weight: 4.9990 chunk 466 optimal weight: 8.9990 chunk 519 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 420 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN G 234 ASN ** G 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** M 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN O 234 ASN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 48816 Z= 0.387 Angle : 0.893 8.768 66480 Z= 0.457 Chirality : 0.050 0.188 7328 Planarity : 0.006 0.055 8240 Dihedral : 7.845 42.197 6320 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.83 % Favored : 88.61 % Rotamer Outliers : 4.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -2.64 (0.11), residues: 5696 helix: -0.71 (0.08), residues: 3552 sheet: -4.15 (0.17), residues: 368 loop : -3.22 (0.14), residues: 1776 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2078 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1826 time to evaluate : 5.388 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 252 outliers final: 189 residues processed: 1959 average time/residue: 0.5276 time to fit residues: 1762.4410 Evaluate side-chains 1803 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1614 time to evaluate : 5.744 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 6 residues processed: 189 average time/residue: 0.4392 time to fit residues: 160.7342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 3.9990 chunk 393 optimal weight: 3.9990 chunk 271 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 351 optimal weight: 0.7980 chunk 525 optimal weight: 3.9990 chunk 556 optimal weight: 5.9990 chunk 274 optimal weight: 10.0000 chunk 498 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 48816 Z= 0.263 Angle : 0.840 8.806 66480 Z= 0.423 Chirality : 0.047 0.167 7328 Planarity : 0.005 0.049 8240 Dihedral : 7.273 37.754 6320 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.53 % Favored : 89.91 % Rotamer Outliers : 4.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -2.34 (0.11), residues: 5696 helix: -0.42 (0.08), residues: 3568 sheet: -3.77 (0.20), residues: 368 loop : -3.31 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2107 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1856 time to evaluate : 5.291 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 251 outliers final: 166 residues processed: 1978 average time/residue: 0.5405 time to fit residues: 1820.9934 Evaluate side-chains 1885 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1719 time to evaluate : 5.248 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 6 residues processed: 166 average time/residue: 0.4081 time to fit residues: 136.6282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 20.0000 chunk 316 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 414 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 475 optimal weight: 6.9990 chunk 384 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 284 optimal weight: 20.0000 chunk 499 optimal weight: 40.0000 chunk 140 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** I 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 ASN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 237 GLN ** M 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 GLN ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 48816 Z= 0.377 Angle : 0.869 10.451 66480 Z= 0.444 Chirality : 0.049 0.265 7328 Planarity : 0.005 0.049 8240 Dihedral : 7.201 36.402 6320 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.22 % Favored : 88.22 % Rotamer Outliers : 5.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -2.25 (0.11), residues: 5696 helix: -0.35 (0.08), residues: 3584 sheet: -3.73 (0.21), residues: 368 loop : -3.30 (0.15), residues: 1744 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1949 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1685 time to evaluate : 5.749 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 264 outliers final: 193 residues processed: 1782 average time/residue: 0.5281 time to fit residues: 1602.3824 Evaluate side-chains 1818 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1625 time to evaluate : 5.460 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 193 outliers final: 6 residues processed: 193 average time/residue: 0.4020 time to fit residues: 155.5953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 8.9990 chunk 501 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 326 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 557 optimal weight: 20.0000 chunk 462 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** I 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 ASN ** K 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 48816 Z= 0.321 Angle : 0.853 10.056 66480 Z= 0.431 Chirality : 0.048 0.176 7328 Planarity : 0.005 0.048 8240 Dihedral : 6.949 36.163 6320 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.62 % Favored : 87.82 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.14 (0.11), residues: 5696 helix: -0.26 (0.08), residues: 3568 sheet: -3.85 (0.21), residues: 368 loop : -3.22 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1929 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1758 time to evaluate : 5.489 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 171 outliers final: 132 residues processed: 1807 average time/residue: 0.5580 time to fit residues: 1728.7635 Evaluate side-chains 1818 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1686 time to evaluate : 5.306 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 6 residues processed: 132 average time/residue: 0.4298 time to fit residues: 114.5974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 317 optimal weight: 7.9990 chunk 406 optimal weight: 2.9990 chunk 315 optimal weight: 6.9990 chunk 469 optimal weight: 9.9990 chunk 311 optimal weight: 0.9980 chunk 555 optimal weight: 7.9990 chunk 347 optimal weight: 3.9990 chunk 338 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 GLN ** I 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 48816 Z= 0.287 Angle : 0.863 11.328 66480 Z= 0.430 Chirality : 0.047 0.191 7328 Planarity : 0.005 0.080 8240 Dihedral : 6.823 40.494 6320 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.36 % Favored : 88.08 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.05 (0.11), residues: 5696 helix: -0.18 (0.08), residues: 3568 sheet: -3.22 (0.24), residues: 288 loop : -3.40 (0.14), residues: 1840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1886 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1748 time to evaluate : 5.322 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 138 outliers final: 97 residues processed: 1775 average time/residue: 0.5571 time to fit residues: 1681.6711 Evaluate side-chains 1748 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1651 time to evaluate : 5.361 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 6 residues processed: 97 average time/residue: 0.4243 time to fit residues: 84.9279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 0.9990 chunk 221 optimal weight: 0.2980 chunk 331 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 352 optimal weight: 1.9990 chunk 378 optimal weight: 9.9990 chunk 274 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 436 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 247 HIS ** K 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 48816 Z= 0.237 Angle : 0.864 11.907 66480 Z= 0.426 Chirality : 0.045 0.206 7328 Planarity : 0.005 0.049 8240 Dihedral : 6.488 41.316 6320 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.62 % Favored : 88.82 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -1.97 (0.11), residues: 5696 helix: -0.10 (0.08), residues: 3568 sheet: -3.56 (0.23), residues: 368 loop : -3.27 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1874 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1805 time to evaluate : 5.990 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. outliers start: 69 outliers final: 38 residues processed: 1827 average time/residue: 0.5620 time to fit residues: 1750.9818 Evaluate side-chains 1700 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1662 time to evaluate : 5.118 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 3 residues processed: 38 average time/residue: 0.4320 time to fit residues: 37.7836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 0.0980 chunk 531 optimal weight: 0.9980 chunk 485 optimal weight: 5.9990 chunk 517 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 406 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 467 optimal weight: 0.9980 chunk 489 optimal weight: 7.9990 chunk 515 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS ** I 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** K 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 HIS ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 48816 Z= 0.243 Angle : 0.887 12.376 66480 Z= 0.436 Chirality : 0.046 0.192 7328 Planarity : 0.005 0.049 8240 Dihedral : 6.420 39.764 6320 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.67 % Favored : 88.76 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.88 (0.11), residues: 5696 helix: -0.07 (0.08), residues: 3584 sheet: -2.49 (0.27), residues: 256 loop : -3.40 (0.14), residues: 1856 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1856 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1760 time to evaluate : 5.409 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 96 outliers final: 64 residues processed: 1791 average time/residue: 0.5309 time to fit residues: 1626.1639 Evaluate side-chains 1714 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1650 time to evaluate : 4.968 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 4 residues processed: 64 average time/residue: 0.4139 time to fit residues: 57.1811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 8.9990 chunk 547 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 380 optimal weight: 2.9990 chunk 573 optimal weight: 5.9990 chunk 528 optimal weight: 6.9990 chunk 456 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 352 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 48816 Z= 0.307 Angle : 0.917 12.502 66480 Z= 0.456 Chirality : 0.047 0.219 7328 Planarity : 0.005 0.051 8240 Dihedral : 6.471 40.354 6320 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.96 % Favored : 88.48 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.86 (0.11), residues: 5696 helix: -0.10 (0.08), residues: 3616 sheet: -2.20 (0.29), residues: 224 loop : -3.40 (0.14), residues: 1856 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11392 Ramachandran restraints generated. 5696 Oldfield, 0 Emsley, 5696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1685 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1628 time to evaluate : 5.276 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP I 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP J 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP O 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP P 28 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 57 outliers final: 39 residues processed: 1641 average time/residue: 0.5426 time to fit residues: 1516.5723 Evaluate side-chains 1607 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1568 time to evaluate : 4.888 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 2 residues processed: 39 average time/residue: 0.4504 time to fit residues: 39.9229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 0.5980 chunk 486 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 421 optimal weight: 0.9990 chunk 67 optimal weight: 0.0060 chunk 126 optimal weight: 5.9990 chunk 457 optimal weight: 0.0170 chunk 191 optimal weight: 0.8980 chunk 469 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS ** I 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS ** K 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 HIS ** M 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.201590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.169540 restraints weight = 68433.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.175300 restraints weight = 30415.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.179050 restraints weight = 17562.760| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 48816 Z= 0.237 Angle : 0.925 12.899 66480 Z= 0.449 Chirality : 0.046 0.198 7328 Planarity : 0.005 0.061 8240 Dihedral : 6.172 41.586 6320 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.94 % Favored : 89.50 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.75 (0.11), residues: 5696 helix: -0.02 (0.08), residues: 3584 sheet: -2.23 (0.28), residues: 288 loop : -3.28 (0.14), residues: 1824 =============================================================================== Job complete usr+sys time: 22463.75 seconds wall clock time: 394 minutes 46.12 seconds (23686.12 seconds total)