Starting phenix.real_space_refine (version: dev) on Fri Feb 24 20:53:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/02_2023/5h1q_9570.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/02_2023/5h1q_9570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/02_2023/5h1q_9570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/02_2023/5h1q_9570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/02_2023/5h1q_9570.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/02_2023/5h1q_9570.pdb" } resolution = 3.3 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= 0.011 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 Process input model Symmetric amino acids flipped 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 "A TYR 219": "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 "B TYR 219": "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 "C TYR 219": "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 "D TYR 219": "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 "E TYR 219": "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 "F TYR 219": "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 "G TYR 219": "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 "H TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23784 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2973 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2973 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2973 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2973 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2973 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2973 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2973 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2973 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 14.03, per 1000 atoms: 0.59 Number of scatterers: 23784 At special positions: 0 Unit cell: (126.69, 126.69, 113.16, 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 96 16.00 O 4136 8.00 N 3904 7.00 C 15648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, 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 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: 9.87 Conformation dependent library (CDL) restraints added in 3.0 seconds 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5584 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 16 sheets defined 62.1% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 134 removed outlier: 3.803A 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 136 through 151 removed outlier: 3.611A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 3.705A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 178 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 213 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.704A pdb=" N ILE A 226 " --> pdb=" O TRP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 305 removed outlier: 4.136A pdb=" N GLU A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.544A pdb=" N ILE A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.533A pdb=" N TYR A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 134 removed outlier: 3.803A 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 136 through 151 removed outlier: 3.612A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 151 " --> pdb=" O PHE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Proline residue: B 169 - end of helix removed outlier: 3.706A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 178 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 213 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.704A pdb=" N ILE B 226 " --> pdb=" O TRP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 305 removed outlier: 4.135A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.544A pdb=" N ILE B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.532A pdb=" N TYR B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.466A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 134 removed outlier: 3.803A 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 136 through 151 removed outlier: 3.612A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Proline residue: C 169 - end of helix removed outlier: 3.705A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 178 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 213 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.705A pdb=" N ILE C 226 " --> pdb=" O TRP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 305 removed outlier: 4.134A pdb=" N GLU C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS C 275 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.543A pdb=" N ILE C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.533A pdb=" N TYR C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN C 363 " --> pdb=" O ILE C 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS D 79 " --> pdb=" O TYR D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 134 removed outlier: 3.804A 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 136 through 151 removed outlier: 3.612A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN D 151 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Proline residue: D 169 - end of helix removed outlier: 3.705A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 178 " --> pdb=" O TRP D 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 179 " --> pdb=" O ASP D 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 213 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.705A pdb=" N ILE D 226 " --> pdb=" O TRP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 305 removed outlier: 4.134A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP D 281 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.514A pdb=" N PHE D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.544A pdb=" N ILE D 341 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.532A pdb=" N TYR D 356 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN D 363 " --> pdb=" O ILE D 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 removed outlier: 4.466A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS E 79 " --> pdb=" O TYR E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 134 removed outlier: 3.804A 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 136 through 151 removed outlier: 3.611A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Proline residue: E 169 - end of helix removed outlier: 3.706A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG E 178 " --> pdb=" O TRP E 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 179 " --> pdb=" O ASP E 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 213 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.704A pdb=" N ILE E 226 " --> pdb=" O TRP E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 305 removed outlier: 4.135A pdb=" N GLU E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP E 281 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.543A pdb=" N ILE E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.533A pdb=" N TYR E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN E 363 " --> pdb=" O ILE E 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL F 37 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS F 79 " --> pdb=" O TYR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 134 removed outlier: 3.804A 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 136 through 151 removed outlier: 3.611A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F 151 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 182 removed outlier: 3.522A pdb=" N PHE F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU F 166 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Proline residue: F 169 - end of helix removed outlier: 3.705A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG F 178 " --> pdb=" O TRP F 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 213 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.704A pdb=" N ILE F 226 " --> pdb=" O TRP F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 305 removed outlier: 4.135A pdb=" N GLU F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 275 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP F 281 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS F 295 " --> pdb=" O SER F 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 327 through 335 removed outlier: 3.514A pdb=" N PHE F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.545A pdb=" N ILE F 341 " --> pdb=" O ASP F 337 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.533A pdb=" N TYR F 356 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN F 363 " --> pdb=" O ILE F 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS G 79 " --> pdb=" O TYR G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 134 removed outlier: 3.804A 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 136 through 151 removed outlier: 3.611A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE G 165 " --> pdb=" O ARG G 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Proline residue: G 169 - end of helix removed outlier: 3.705A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG G 178 " --> pdb=" O TRP G 174 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 213 Processing helix chain 'G' and resid 222 through 231 removed outlier: 3.705A pdb=" N ILE G 226 " --> pdb=" O TRP G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 305 removed outlier: 4.135A pdb=" N GLU G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS G 275 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE G 278 " --> pdb=" O GLU G 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE G 279 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP G 281 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE G 331 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.544A pdb=" N ILE G 341 " --> pdb=" O ASP G 337 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 365 removed outlier: 3.532A pdb=" N TYR G 356 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG G 362 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN G 363 " --> pdb=" O ILE G 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS H 79 " --> pdb=" O TYR H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 134 removed outlier: 3.804A 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 136 through 151 removed outlier: 3.612A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG H 146 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN H 151 " --> pdb=" O PHE H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Proline residue: H 169 - end of helix removed outlier: 3.705A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG H 178 " --> pdb=" O TRP H 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H 179 " --> pdb=" O ASP H 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 213 Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.704A pdb=" N ILE H 226 " --> pdb=" O TRP H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 305 removed outlier: 4.135A pdb=" N GLU H 274 " --> pdb=" O ASN H 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS H 275 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE H 278 " --> pdb=" O GLU H 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE H 279 " --> pdb=" O LYS H 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP H 281 " --> pdb=" O PHE H 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN H 294 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS H 295 " --> pdb=" O SER H 291 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE H 331 " --> pdb=" O ASP H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 349 removed outlier: 3.545A pdb=" N ILE H 341 " --> pdb=" O ASP H 337 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP H 343 " --> pdb=" O LEU H 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU H 347 " --> pdb=" O ASP H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.533A pdb=" N TYR H 356 " --> pdb=" O ILE H 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG H 362 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN H 363 " --> pdb=" O ILE H 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 58 Processing sheet with id=AA4, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 58 Processing sheet with id=AA6, first strand: chain 'C' and resid 249 through 251 Processing sheet with id=AA7, first strand: chain 'D' and resid 56 through 58 Processing sheet with id=AA8, first strand: chain 'D' and resid 249 through 251 Processing sheet with id=AA9, first strand: chain 'E' and resid 56 through 58 Processing sheet with id=AB1, first strand: chain 'E' and resid 249 through 251 Processing sheet with id=AB2, first strand: chain 'F' and resid 56 through 58 Processing sheet with id=AB3, first strand: chain 'F' and resid 249 through 251 Processing sheet with id=AB4, first strand: chain 'G' and resid 56 through 58 Processing sheet with id=AB5, first strand: chain 'G' and resid 249 through 251 Processing sheet with id=AB6, first strand: chain 'H' and resid 56 through 58 Processing sheet with id=AB7, first strand: chain 'H' and resid 249 through 251 1098 hydrogen bonds defined for protein. 3270 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: 6.79 Time building geometry restraints manager: 10.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7288 1.34 - 1.46: 6743 1.46 - 1.58: 10305 1.58 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 24472 Sorted by residual: bond pdb=" CB PHE A 242 " pdb=" CG PHE A 242 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.65e+00 bond pdb=" CB PHE B 242 " pdb=" CG PHE B 242 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.62e+00 bond pdb=" CB PHE F 242 " pdb=" CG PHE F 242 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.53e+00 bond pdb=" CB PHE D 242 " pdb=" CG PHE D 242 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.53e+00 bond pdb=" CB PHE E 242 " pdb=" CG PHE E 242 " ideal model delta sigma weight residual 1.502 1.444 0.058 2.30e-02 1.89e+03 6.47e+00 ... (remaining 24467 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.24: 464 106.24 - 113.18: 13027 113.18 - 120.13: 9967 120.13 - 127.08: 9486 127.08 - 134.02: 384 Bond angle restraints: 33328 Sorted by residual: angle pdb=" N LEU C 86 " pdb=" CA LEU C 86 " pdb=" C LEU C 86 " ideal model delta sigma weight residual 107.41 121.06 -13.65 2.02e+00 2.45e-01 4.57e+01 angle pdb=" N LEU F 86 " pdb=" CA LEU F 86 " pdb=" C LEU F 86 " ideal model delta sigma weight residual 107.41 121.03 -13.62 2.02e+00 2.45e-01 4.55e+01 angle pdb=" N LEU D 86 " pdb=" CA LEU D 86 " pdb=" C LEU D 86 " ideal model delta sigma weight residual 107.41 121.03 -13.62 2.02e+00 2.45e-01 4.55e+01 angle pdb=" N LEU B 86 " pdb=" CA LEU B 86 " pdb=" C LEU B 86 " ideal model delta sigma weight residual 107.41 121.02 -13.61 2.02e+00 2.45e-01 4.54e+01 angle pdb=" N LEU H 86 " pdb=" CA LEU H 86 " pdb=" C LEU H 86 " ideal model delta sigma weight residual 107.41 121.02 -13.61 2.02e+00 2.45e-01 4.54e+01 ... (remaining 33323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 13319 16.35 - 32.70: 681 32.70 - 49.04: 152 49.04 - 65.39: 8 65.39 - 81.74: 40 Dihedral angle restraints: 14200 sinusoidal: 5592 harmonic: 8608 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 98.26 81.74 0 5.00e+00 4.00e-02 2.67e+02 dihedral pdb=" CA LEU B 86 " pdb=" C LEU B 86 " pdb=" N ASP B 87 " pdb=" CA ASP B 87 " ideal model delta harmonic sigma weight residual 180.00 98.27 81.73 0 5.00e+00 4.00e-02 2.67e+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 98.29 81.71 0 5.00e+00 4.00e-02 2.67e+02 ... (remaining 14197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2013 0.040 - 0.080: 998 0.080 - 0.121: 489 0.121 - 0.161: 138 0.161 - 0.201: 42 Chirality restraints: 3680 Sorted by residual: chirality pdb=" CB ILE D 218 " pdb=" CA ILE D 218 " pdb=" CG1 ILE D 218 " pdb=" CG2 ILE D 218 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE B 218 " pdb=" CA ILE B 218 " pdb=" CG1 ILE B 218 " pdb=" CG2 ILE B 218 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CB ILE F 218 " pdb=" CA ILE F 218 " pdb=" CG1 ILE F 218 " pdb=" CG2 ILE F 218 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 3677 not shown) Planarity restraints: 4128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 222 " -0.018 2.00e-02 2.50e+03 1.38e-02 4.77e+00 pdb=" CG TRP F 222 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP F 222 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP F 222 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 222 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 222 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 222 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 222 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 222 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 222 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 222 " 0.018 2.00e-02 2.50e+03 1.38e-02 4.76e+00 pdb=" CG TRP C 222 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 222 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 222 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 222 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 222 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 222 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 222 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 222 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 222 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 222 " -0.018 2.00e-02 2.50e+03 1.38e-02 4.75e+00 pdb=" CG TRP A 222 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 222 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 222 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 222 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 222 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 222 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 222 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 222 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 222 " -0.001 2.00e-02 2.50e+03 ... (remaining 4125 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 232 2.58 - 3.16: 22439 3.16 - 3.74: 35264 3.74 - 4.32: 48194 4.32 - 4.90: 78393 Nonbonded interactions: 184522 Sorted by model distance: nonbonded pdb=" O PRO C 243 " pdb=" ND2 ASN C 270 " model vdw 1.998 2.520 nonbonded pdb=" O PRO B 243 " pdb=" ND2 ASN B 270 " model vdw 1.999 2.520 nonbonded pdb=" O PRO A 243 " pdb=" ND2 ASN A 270 " model vdw 1.999 2.520 nonbonded pdb=" O PRO F 243 " pdb=" ND2 ASN F 270 " model vdw 1.999 2.520 nonbonded pdb=" O PRO D 243 " pdb=" ND2 ASN D 270 " model vdw 1.999 2.520 ... (remaining 184517 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' } 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 96 5.16 5 C 15648 2.51 5 N 3904 2.21 5 O 4136 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 individual isotropic 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.310 Check model and map are aligned: 0.360 Process input model: 58.340 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.240 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 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 : 0.008 0.059 24472 Z= 0.543 Angle : 1.039 13.654 33328 Z= 0.568 Chirality : 0.059 0.201 3680 Planarity : 0.005 0.041 4128 Dihedral : 11.648 81.742 8568 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.61 % Favored : 86.83 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: -5.07 (0.12), residues: 2856 helix: -3.32 (0.08), residues: 1648 sheet: -2.89 (0.37), residues: 144 loop : -3.22 (0.16), residues: 1064 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1066 time to evaluate : 2.976 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 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 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 TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 1066 average time/residue: 0.4664 time to fit residues: 700.7484 Evaluate side-chains 640 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 640 time to evaluate : 2.950 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 225 optimal weight: 0.0980 chunk 87 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 89 GLN A 199 GLN B 232 GLN C 70 ASN C 89 GLN C 199 GLN D 232 GLN E 70 ASN E 89 GLN E 199 GLN F 232 GLN G 70 ASN G 89 GLN G 199 GLN H 232 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 24472 Z= 0.231 Angle : 0.808 9.529 33328 Z= 0.411 Chirality : 0.045 0.175 3680 Planarity : 0.005 0.047 4128 Dihedral : 7.522 47.940 3168 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.84 % Favored : 91.88 % Rotamer Outliers : 4.91 % 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: -2.73 (0.15), residues: 2856 helix: -1.14 (0.12), residues: 1712 sheet: -1.28 (0.46), residues: 144 loop : -2.96 (0.18), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 740 time to evaluate : 2.839 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. 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 TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 126 outliers final: 89 residues processed: 804 average time/residue: 0.4351 time to fit residues: 505.5167 Evaluate side-chains 692 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 603 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 0.2791 time to fit residues: 45.1034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 217 optimal weight: 20.0000 chunk 178 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 329 GLN B 348 ASN C 70 ASN C 89 GLN C 329 GLN E 70 ASN E 89 GLN G 70 ASN G 89 GLN H 329 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 24472 Z= 0.279 Angle : 0.766 8.313 33328 Z= 0.387 Chirality : 0.045 0.201 3680 Planarity : 0.004 0.044 4128 Dihedral : 6.918 40.815 3168 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.66 % Favored : 89.78 % Rotamer Outliers : 5.30 % 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: -2.10 (0.15), residues: 2856 helix: -0.47 (0.12), residues: 1744 sheet: -1.50 (0.47), residues: 152 loop : -3.05 (0.18), residues: 960 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 658 time to evaluate : 2.924 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 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 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 revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 136 outliers final: 73 residues processed: 751 average time/residue: 0.4185 time to fit residues: 465.1310 Evaluate side-chains 678 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 605 time to evaluate : 2.772 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.2570 time to fit residues: 36.4521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 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 70 ASN A 348 ASN B 348 ASN C 70 ASN C 329 GLN C 348 ASN D 329 GLN D 348 ASN E 70 ASN E 348 ASN F 329 GLN F 348 ASN G 70 ASN G 329 GLN G 348 ASN H 348 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 24472 Z= 0.241 Angle : 0.740 8.419 33328 Z= 0.371 Chirality : 0.044 0.182 3680 Planarity : 0.004 0.045 4128 Dihedral : 6.616 34.259 3168 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.73 % Favored : 89.71 % Rotamer Outliers : 3.54 % 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: -1.65 (0.16), residues: 2856 helix: -0.05 (0.12), residues: 1744 sheet: -1.69 (0.38), residues: 184 loop : -2.95 (0.19), residues: 928 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 597 time to evaluate : 2.763 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. 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 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. revert: symmetry clash outliers start: 91 outliers final: 55 residues processed: 650 average time/residue: 0.3851 time to fit residues: 376.2180 Evaluate side-chains 567 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 512 time to evaluate : 2.711 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.2094 time to fit residues: 25.3475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 192 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 142 optimal weight: 8.9990 chunk 249 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN E 329 GLN G 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24472 Z= 0.186 Angle : 0.711 9.875 33328 Z= 0.352 Chirality : 0.043 0.223 3680 Planarity : 0.004 0.044 4128 Dihedral : 6.300 34.848 3168 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.35 % Favored : 90.09 % Rotamer Outliers : 2.76 % 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: -1.10 (0.16), residues: 2856 helix: 0.49 (0.13), residues: 1736 sheet: -1.70 (0.37), residues: 192 loop : -2.90 (0.19), residues: 928 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 539 time to evaluate : 2.821 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. 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. 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 outliers start: 71 outliers final: 34 residues processed: 567 average time/residue: 0.3766 time to fit residues: 331.8015 Evaluate side-chains 531 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 497 time to evaluate : 2.675 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2267 time to fit residues: 18.4980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 278 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN B 348 ASN C 70 ASN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN E 70 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN F 348 ASN G 70 ASN ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 24472 Z= 0.252 Angle : 0.721 9.061 33328 Z= 0.361 Chirality : 0.044 0.190 3680 Planarity : 0.004 0.044 4128 Dihedral : 6.277 32.251 3168 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.49 % Favored : 89.95 % Rotamer Outliers : 3.39 % 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: -0.89 (0.16), residues: 2856 helix: 0.70 (0.13), residues: 1728 sheet: -1.54 (0.39), residues: 184 loop : -2.89 (0.19), residues: 944 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 485 time to evaluate : 2.906 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. 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. 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. 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 outliers start: 87 outliers final: 58 residues processed: 539 average time/residue: 0.3588 time to fit residues: 302.9220 Evaluate side-chains 518 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 460 time to evaluate : 2.509 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.2117 time to fit residues: 27.0303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 0.4980 chunk 203 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 128 optimal weight: 0.0770 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN C 70 ASN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN G 70 ASN ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 24472 Z= 0.168 Angle : 0.701 10.460 33328 Z= 0.347 Chirality : 0.042 0.228 3680 Planarity : 0.004 0.046 4128 Dihedral : 6.047 32.866 3168 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.45 % Favored : 89.99 % Rotamer Outliers : 1.05 % 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: -0.48 (0.16), residues: 2856 helix: 1.13 (0.13), residues: 1696 sheet: -1.69 (0.38), residues: 192 loop : -2.75 (0.20), residues: 968 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 517 time to evaluate : 2.647 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. 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. revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 527 average time/residue: 0.3466 time to fit residues: 288.6197 Evaluate side-chains 494 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 480 time to evaluate : 2.804 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2409 time to fit residues: 10.1755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 0.0980 chunk 25 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 270 ASN C 70 ASN C 270 ASN D 348 ASN E 70 ASN E 270 ASN E 314 ASN F 348 ASN G 70 ASN G 270 ASN H 348 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 24472 Z= 0.220 Angle : 0.719 9.237 33328 Z= 0.352 Chirality : 0.043 0.191 3680 Planarity : 0.004 0.044 4128 Dihedral : 6.070 31.674 3168 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.38 % Favored : 90.06 % Rotamer Outliers : 1.95 % 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: -0.38 (0.16), residues: 2856 helix: 1.25 (0.13), residues: 1704 sheet: -1.50 (0.39), residues: 184 loop : -2.85 (0.19), residues: 968 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 490 time to evaluate : 2.655 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. 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. 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. 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 outliers start: 50 outliers final: 42 residues processed: 512 average time/residue: 0.3420 time to fit residues: 277.3601 Evaluate side-chains 512 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 470 time to evaluate : 2.718 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2367 time to fit residues: 22.2724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 258 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 244 optimal weight: 0.3980 chunk 257 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN C 70 ASN E 70 ASN E 314 ASN G 70 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 24472 Z= 0.198 Angle : 0.713 9.463 33328 Z= 0.349 Chirality : 0.042 0.208 3680 Planarity : 0.004 0.045 4128 Dihedral : 6.042 31.825 3168 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.98 % Favored : 89.46 % Rotamer Outliers : 0.90 % 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: -0.43 (0.16), residues: 2856 helix: 1.16 (0.13), residues: 1752 sheet: -1.62 (0.39), residues: 192 loop : -2.97 (0.19), residues: 912 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 470 time to evaluate : 2.549 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. 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. 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. outliers start: 23 outliers final: 20 residues processed: 481 average time/residue: 0.3365 time to fit residues: 260.7750 Evaluate side-chains 482 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 462 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2053 time to fit residues: 11.7445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 chunk 264 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN C 70 ASN D 348 ASN E 70 ASN F 348 ASN G 70 ASN G 270 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 24472 Z= 0.231 Angle : 0.721 10.632 33328 Z= 0.352 Chirality : 0.043 0.200 3680 Planarity : 0.004 0.045 4128 Dihedral : 6.082 31.107 3168 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.63 % Favored : 89.81 % Rotamer Outliers : 0.86 % 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: -0.39 (0.16), residues: 2856 helix: 1.23 (0.13), residues: 1752 sheet: -1.70 (0.39), residues: 192 loop : -3.01 (0.19), residues: 912 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 468 time to evaluate : 3.055 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. 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. 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 outliers start: 22 outliers final: 20 residues processed: 475 average time/residue: 0.3554 time to fit residues: 267.9997 Evaluate side-chains 479 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 459 time to evaluate : 2.803 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2776 time to fit residues: 13.7636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 69 optimal weight: 0.0570 chunk 210 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN C 70 ASN C 314 ASN E 70 ASN G 70 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121155 restraints weight = 28216.025| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.62 r_work: 0.3315 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 24472 Z= 0.188 Angle : 0.710 10.330 33328 Z= 0.346 Chirality : 0.042 0.206 3680 Planarity : 0.004 0.045 4128 Dihedral : 6.001 31.321 3168 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.63 % Favored : 89.81 % Rotamer Outliers : 0.97 % 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: -0.31 (0.16), residues: 2856 helix: 1.32 (0.13), residues: 1752 sheet: -1.66 (0.38), residues: 192 loop : -3.01 (0.19), residues: 912 =============================================================================== Job complete usr+sys time: 6427.94 seconds wall clock time: 116 minutes 34.69 seconds (6994.69 seconds total)