Starting phenix.real_space_refine on Tue Mar 19 08:57:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/03_2024/5h1q_9570.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/03_2024/5h1q_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_9570/03_2024/5h1q_9570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/03_2024/5h1q_9570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/03_2024/5h1q_9570.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1q_9570/03_2024/5h1q_9570.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.35, per 1000 atoms: 0.48 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: 10.31 Conformation dependent library (CDL) restraints added in 4.1 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: 2.09 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: 6.34 Time building geometry restraints manager: 11.08 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 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: 0.160 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: 2.400 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 59.330 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 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 % Allowed : 2.49 % Favored : 97.20 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP F 222 HIS 0.005 0.002 HIS A 247 PHE 0.025 0.003 PHE E 64 TYR 0.020 0.003 TYR F 105 ARG 0.007 0.001 ARG B 168 *********************** 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 : 2.681 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 REVERT: A 69 VAL cc_start: 0.8201 (t) cc_final: 0.7955 (p) REVERT: A 89 GLN cc_start: 0.7397 (tt0) cc_final: 0.7061 (mm110) REVERT: A 99 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7898 (tppp) REVERT: A 103 GLN cc_start: 0.7738 (pt0) cc_final: 0.6698 (pt0) REVERT: A 155 ASP cc_start: 0.8357 (t70) cc_final: 0.7739 (p0) REVERT: A 186 ARG cc_start: 0.8466 (mtt-85) cc_final: 0.7922 (mtp85) REVERT: A 232 GLN cc_start: 0.8164 (mm110) cc_final: 0.7746 (mt0) REVERT: A 237 GLN cc_start: 0.8407 (pm20) cc_final: 0.7931 (pm20) REVERT: A 242 PHE cc_start: 0.7501 (t80) cc_final: 0.7100 (t80) REVERT: A 303 CYS cc_start: 0.7198 (t) cc_final: 0.6934 (m) REVERT: A 304 ASN cc_start: 0.8032 (m-40) cc_final: 0.7453 (t0) REVERT: A 315 TYR cc_start: 0.8060 (m-10) cc_final: 0.7858 (m-10) REVERT: A 329 GLN cc_start: 0.6379 (pt0) cc_final: 0.5812 (pt0) REVERT: A 332 SER cc_start: 0.8295 (t) cc_final: 0.7831 (p) REVERT: A 334 LEU cc_start: 0.7543 (tp) cc_final: 0.7028 (tp) REVERT: A 339 LEU cc_start: 0.8512 (tp) cc_final: 0.8283 (tt) REVERT: A 342 MET cc_start: 0.8138 (mmm) cc_final: 0.7710 (tpp) REVERT: A 347 LEU cc_start: 0.7288 (tt) cc_final: 0.6915 (tt) REVERT: A 349 LEU cc_start: 0.7649 (mp) cc_final: 0.7408 (mp) REVERT: A 351 ASP cc_start: 0.5673 (t0) cc_final: 0.5297 (t0) REVERT: A 368 PHE cc_start: 0.4770 (t80) cc_final: 0.3310 (t80) REVERT: B 69 VAL cc_start: 0.8221 (t) cc_final: 0.7893 (p) REVERT: B 75 TYR cc_start: 0.8503 (t80) cc_final: 0.8269 (t80) REVERT: B 89 GLN cc_start: 0.7358 (tt0) cc_final: 0.7090 (mm110) REVERT: B 99 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7930 (tppp) REVERT: B 154 LYS cc_start: 0.6668 (ttpt) cc_final: 0.6265 (ttpp) REVERT: B 155 ASP cc_start: 0.8227 (t70) cc_final: 0.7857 (p0) REVERT: B 175 ASP cc_start: 0.8544 (t0) cc_final: 0.8200 (t0) REVERT: B 184 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7246 (ttp-110) REVERT: B 186 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.7875 (mtp85) REVERT: B 232 GLN cc_start: 0.8192 (mm110) cc_final: 0.7889 (mt0) REVERT: B 303 CYS cc_start: 0.7157 (t) cc_final: 0.6816 (m) REVERT: B 304 ASN cc_start: 0.7956 (m-40) cc_final: 0.7601 (t0) REVERT: B 313 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8322 (ttmt) REVERT: B 329 GLN cc_start: 0.6665 (pt0) cc_final: 0.6187 (pt0) REVERT: B 332 SER cc_start: 0.8191 (t) cc_final: 0.7774 (p) REVERT: B 334 LEU cc_start: 0.7434 (tp) cc_final: 0.7187 (tp) REVERT: B 342 MET cc_start: 0.8157 (mmm) cc_final: 0.7859 (mmm) REVERT: C 69 VAL cc_start: 0.8201 (t) cc_final: 0.7955 (p) REVERT: C 89 GLN cc_start: 0.7407 (tt0) cc_final: 0.7071 (mm110) REVERT: C 99 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7896 (tppp) REVERT: C 103 GLN cc_start: 0.7739 (pt0) cc_final: 0.6697 (pt0) REVERT: C 155 ASP cc_start: 0.8359 (t70) cc_final: 0.7742 (p0) REVERT: C 186 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.7924 (mtp85) REVERT: C 232 GLN cc_start: 0.8150 (mm110) cc_final: 0.7726 (mt0) REVERT: C 237 GLN cc_start: 0.8409 (pm20) cc_final: 0.7932 (pm20) REVERT: C 242 PHE cc_start: 0.7443 (t80) cc_final: 0.7060 (t80) REVERT: C 303 CYS cc_start: 0.7200 (t) cc_final: 0.6936 (m) REVERT: C 304 ASN cc_start: 0.8029 (m-40) cc_final: 0.7452 (t0) REVERT: C 315 TYR cc_start: 0.8056 (m-10) cc_final: 0.7852 (m-10) REVERT: C 329 GLN cc_start: 0.6379 (pt0) cc_final: 0.5825 (pt0) REVERT: C 332 SER cc_start: 0.8297 (t) cc_final: 0.7834 (p) REVERT: C 334 LEU cc_start: 0.7543 (tp) cc_final: 0.7026 (tp) REVERT: C 339 LEU cc_start: 0.8512 (tp) cc_final: 0.8280 (tt) REVERT: C 342 MET cc_start: 0.8139 (mmm) cc_final: 0.7710 (tpp) REVERT: C 347 LEU cc_start: 0.7317 (tt) cc_final: 0.6946 (tt) REVERT: C 349 LEU cc_start: 0.7617 (mp) cc_final: 0.7367 (mp) REVERT: C 351 ASP cc_start: 0.5679 (t0) cc_final: 0.5294 (t0) REVERT: C 368 PHE cc_start: 0.4764 (t80) cc_final: 0.3309 (t80) REVERT: D 69 VAL cc_start: 0.8266 (t) cc_final: 0.7929 (p) REVERT: D 75 TYR cc_start: 0.8566 (t80) cc_final: 0.8316 (t80) REVERT: D 89 GLN cc_start: 0.7351 (tt0) cc_final: 0.6985 (mm110) REVERT: D 99 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7898 (tppp) REVERT: D 154 LYS cc_start: 0.6714 (ttpt) cc_final: 0.6271 (ttpp) REVERT: D 155 ASP cc_start: 0.8326 (t70) cc_final: 0.7827 (p0) REVERT: D 184 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7203 (ttp-110) REVERT: D 186 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.7956 (mtp85) REVERT: D 232 GLN cc_start: 0.8212 (mm110) cc_final: 0.7895 (mt0) REVERT: D 303 CYS cc_start: 0.7228 (t) cc_final: 0.6859 (m) REVERT: D 304 ASN cc_start: 0.7956 (m-40) cc_final: 0.7637 (t0) REVERT: D 329 GLN cc_start: 0.6557 (pt0) cc_final: 0.6098 (pt0) REVERT: D 332 SER cc_start: 0.8192 (t) cc_final: 0.7821 (p) REVERT: D 334 LEU cc_start: 0.7469 (tp) cc_final: 0.7220 (tp) REVERT: D 342 MET cc_start: 0.8206 (mmm) cc_final: 0.7905 (mmm) REVERT: D 362 ARG cc_start: 0.7502 (ttp80) cc_final: 0.7101 (ttp-170) REVERT: D 368 PHE cc_start: 0.4777 (t80) cc_final: 0.4425 (t80) REVERT: E 69 VAL cc_start: 0.8203 (t) cc_final: 0.7956 (p) REVERT: E 89 GLN cc_start: 0.7415 (tt0) cc_final: 0.7079 (mm110) REVERT: E 99 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7899 (tppp) REVERT: E 103 GLN cc_start: 0.7736 (pt0) cc_final: 0.6695 (pt0) REVERT: E 155 ASP cc_start: 0.8360 (t70) cc_final: 0.7738 (p0) REVERT: E 186 ARG cc_start: 0.8402 (mtt-85) cc_final: 0.7883 (mtp85) REVERT: E 232 GLN cc_start: 0.8163 (mm110) cc_final: 0.7743 (mt0) REVERT: E 237 GLN cc_start: 0.8408 (pm20) cc_final: 0.7930 (pm20) REVERT: E 242 PHE cc_start: 0.7501 (t80) cc_final: 0.7098 (t80) REVERT: E 303 CYS cc_start: 0.7196 (t) cc_final: 0.6934 (m) REVERT: E 304 ASN cc_start: 0.8032 (m-40) cc_final: 0.7456 (t0) REVERT: E 315 TYR cc_start: 0.8062 (m-10) cc_final: 0.7856 (m-10) REVERT: E 329 GLN cc_start: 0.6377 (pt0) cc_final: 0.5815 (pt0) REVERT: E 332 SER cc_start: 0.8295 (t) cc_final: 0.7831 (p) REVERT: E 334 LEU cc_start: 0.7544 (tp) cc_final: 0.7026 (tp) REVERT: E 339 LEU cc_start: 0.8514 (tp) cc_final: 0.8299 (tt) REVERT: E 342 MET cc_start: 0.8140 (mmm) cc_final: 0.7731 (tpp) REVERT: E 347 LEU cc_start: 0.7290 (tt) cc_final: 0.6917 (tt) REVERT: E 349 LEU cc_start: 0.7656 (mp) cc_final: 0.7415 (mp) REVERT: E 351 ASP cc_start: 0.5668 (t0) cc_final: 0.5274 (t0) REVERT: E 368 PHE cc_start: 0.4756 (t80) cc_final: 0.3314 (t80) REVERT: F 75 TYR cc_start: 0.8501 (t80) cc_final: 0.8255 (t80) REVERT: F 89 GLN cc_start: 0.7230 (tt0) cc_final: 0.7021 (mm110) REVERT: F 99 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7789 (tppp) REVERT: F 154 LYS cc_start: 0.6687 (ttpt) cc_final: 0.6264 (ttpp) REVERT: F 155 ASP cc_start: 0.8216 (t70) cc_final: 0.7771 (p0) REVERT: F 175 ASP cc_start: 0.8556 (t0) cc_final: 0.8190 (t0) REVERT: F 184 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7240 (ttp-110) REVERT: F 186 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.7891 (mtp85) REVERT: F 232 GLN cc_start: 0.8186 (mm110) cc_final: 0.7889 (mt0) REVERT: F 303 CYS cc_start: 0.7244 (t) cc_final: 0.6868 (m) REVERT: F 304 ASN cc_start: 0.7978 (m-40) cc_final: 0.7626 (t0) REVERT: F 313 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8354 (ttmt) REVERT: F 329 GLN cc_start: 0.6588 (pt0) cc_final: 0.6102 (pt0) REVERT: F 332 SER cc_start: 0.8174 (t) cc_final: 0.7658 (p) REVERT: F 334 LEU cc_start: 0.7470 (tp) cc_final: 0.7230 (tp) REVERT: F 342 MET cc_start: 0.8120 (mmm) cc_final: 0.7803 (mmm) REVERT: G 69 VAL cc_start: 0.8202 (t) cc_final: 0.7955 (p) REVERT: G 89 GLN cc_start: 0.7400 (tt0) cc_final: 0.7063 (mm110) REVERT: G 99 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7898 (tppp) REVERT: G 103 GLN cc_start: 0.7735 (pt0) cc_final: 0.6693 (pt0) REVERT: G 155 ASP cc_start: 0.8356 (t70) cc_final: 0.7737 (p0) REVERT: G 186 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.7923 (mtp85) REVERT: G 232 GLN cc_start: 0.8162 (mm110) cc_final: 0.7742 (mt0) REVERT: G 237 GLN cc_start: 0.8408 (pm20) cc_final: 0.7935 (pm20) REVERT: G 242 PHE cc_start: 0.7512 (t80) cc_final: 0.7114 (t80) REVERT: G 303 CYS cc_start: 0.7199 (t) cc_final: 0.6934 (m) REVERT: G 304 ASN cc_start: 0.8029 (m-40) cc_final: 0.7451 (t0) REVERT: G 329 GLN cc_start: 0.6377 (pt0) cc_final: 0.5821 (pt0) REVERT: G 332 SER cc_start: 0.8297 (t) cc_final: 0.7833 (p) REVERT: G 334 LEU cc_start: 0.7545 (tp) cc_final: 0.7031 (tp) REVERT: G 339 LEU cc_start: 0.8512 (tp) cc_final: 0.8282 (tt) REVERT: G 342 MET cc_start: 0.8137 (mmm) cc_final: 0.7711 (tpp) REVERT: G 347 LEU cc_start: 0.7310 (tt) cc_final: 0.6939 (tt) REVERT: G 349 LEU cc_start: 0.7645 (mp) cc_final: 0.7404 (mp) REVERT: G 351 ASP cc_start: 0.5666 (t0) cc_final: 0.5363 (t0) REVERT: G 368 PHE cc_start: 0.4768 (t80) cc_final: 0.3312 (t80) REVERT: H 75 TYR cc_start: 0.8499 (t80) cc_final: 0.8267 (t80) REVERT: H 89 GLN cc_start: 0.7227 (tt0) cc_final: 0.7017 (mm110) REVERT: H 99 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7885 (tppp) REVERT: H 154 LYS cc_start: 0.6686 (ttpt) cc_final: 0.6265 (ttpp) REVERT: H 155 ASP cc_start: 0.8226 (t70) cc_final: 0.7850 (p0) REVERT: H 184 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7246 (ttp-110) REVERT: H 186 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.7878 (mtp85) REVERT: H 232 GLN cc_start: 0.8191 (mm110) cc_final: 0.7889 (mt0) REVERT: H 303 CYS cc_start: 0.7153 (t) cc_final: 0.6817 (m) REVERT: H 304 ASN cc_start: 0.7986 (m-40) cc_final: 0.7636 (t0) REVERT: H 329 GLN cc_start: 0.6596 (pt0) cc_final: 0.6110 (pt0) REVERT: H 332 SER cc_start: 0.8184 (t) cc_final: 0.7772 (p) REVERT: H 342 MET cc_start: 0.8136 (mmm) cc_final: 0.7831 (mmm) outliers start: 8 outliers final: 0 residues processed: 1066 average time/residue: 0.4547 time to fit residues: 681.5266 Evaluate side-chains 698 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 698 time to evaluate : 2.726 ------------------------------------------------------------------------------- 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: 8.9990 chunk 121 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 199 GLN C 70 ASN C 199 GLN E 70 ASN E 199 GLN G 70 ASN G 199 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24472 Z= 0.274 Angle : 0.809 9.868 33328 Z= 0.415 Chirality : 0.046 0.171 3680 Planarity : 0.005 0.044 4128 Dihedral : 7.669 50.541 3168 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.65 % Favored : 91.07 % Rotamer: Outliers : 4.48 % Allowed : 14.45 % Favored : 81.07 % 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: -2.89 (0.15), residues: 2856 helix: -1.25 (0.12), residues: 1736 sheet: -1.69 (0.45), residues: 152 loop : -3.03 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 107 HIS 0.003 0.001 HIS D 247 PHE 0.015 0.002 PHE D 158 TYR 0.027 0.002 TYR D 105 ARG 0.009 0.001 ARG G 181 *********************** 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 932 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 817 time to evaluate : 2.628 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 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 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 revert: symmetry clash revert: symmetry clash REVERT: A 70 ASN cc_start: 0.8551 (t0) cc_final: 0.8284 (t0) REVERT: A 99 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8008 (ttmm) REVERT: A 154 LYS cc_start: 0.6623 (ttpt) cc_final: 0.6094 (ttpp) REVERT: A 155 ASP cc_start: 0.8293 (t70) cc_final: 0.7642 (p0) REVERT: A 186 ARG cc_start: 0.8524 (mtt-85) cc_final: 0.7806 (mtp85) REVERT: A 232 GLN cc_start: 0.8465 (mm110) cc_final: 0.8096 (mt0) REVERT: A 242 PHE cc_start: 0.7084 (t80) cc_final: 0.6857 (t80) REVERT: A 310 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7938 (tppp) REVERT: A 315 TYR cc_start: 0.8030 (m-10) cc_final: 0.7774 (m-10) REVERT: A 329 GLN cc_start: 0.6338 (pt0) cc_final: 0.5808 (tt0) REVERT: A 332 SER cc_start: 0.8337 (t) cc_final: 0.7841 (p) REVERT: A 334 LEU cc_start: 0.7679 (tp) cc_final: 0.7399 (tp) REVERT: A 347 LEU cc_start: 0.7105 (tt) cc_final: 0.6780 (tt) REVERT: B 33 ARG cc_start: 0.3309 (ttm110) cc_final: 0.3071 (ttm110) REVERT: B 99 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7780 (tppp) REVERT: B 155 ASP cc_start: 0.8332 (t70) cc_final: 0.7963 (p0) REVERT: B 160 THR cc_start: 0.7866 (p) cc_final: 0.7623 (p) REVERT: B 232 GLN cc_start: 0.8317 (mm110) cc_final: 0.8077 (mt0) REVERT: B 268 THR cc_start: 0.8566 (m) cc_final: 0.8347 (p) REVERT: B 303 CYS cc_start: 0.7540 (t) cc_final: 0.7232 (m) REVERT: B 304 ASN cc_start: 0.7901 (m-40) cc_final: 0.7454 (t0) REVERT: B 309 GLN cc_start: 0.7339 (mt0) cc_final: 0.7093 (mt0) REVERT: B 310 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7956 (tppp) REVERT: B 314 ASN cc_start: 0.8222 (t0) cc_final: 0.7887 (t0) REVERT: B 327 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6824 (t0) REVERT: B 329 GLN cc_start: 0.6550 (pt0) cc_final: 0.6111 (pt0) REVERT: B 332 SER cc_start: 0.8186 (t) cc_final: 0.7852 (p) REVERT: B 339 LEU cc_start: 0.8578 (tp) cc_final: 0.7936 (tp) REVERT: B 348 ASN cc_start: 0.5990 (m-40) cc_final: 0.5746 (m110) REVERT: C 70 ASN cc_start: 0.8548 (t0) cc_final: 0.8283 (t0) REVERT: C 99 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7886 (tppp) REVERT: C 154 LYS cc_start: 0.6609 (ttpt) cc_final: 0.6055 (ttpp) REVERT: C 155 ASP cc_start: 0.8250 (t70) cc_final: 0.7685 (p0) REVERT: C 186 ARG cc_start: 0.8523 (mtt-85) cc_final: 0.7822 (mtp85) REVERT: C 232 GLN cc_start: 0.8465 (mm110) cc_final: 0.8095 (mt0) REVERT: C 242 PHE cc_start: 0.7083 (t80) cc_final: 0.6853 (t80) REVERT: C 310 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7938 (tppp) REVERT: C 315 TYR cc_start: 0.8029 (m-10) cc_final: 0.7774 (m-10) REVERT: C 329 GLN cc_start: 0.6347 (pt0) cc_final: 0.5814 (tt0) REVERT: C 332 SER cc_start: 0.8342 (t) cc_final: 0.7846 (p) REVERT: C 334 LEU cc_start: 0.7683 (tp) cc_final: 0.7369 (tp) REVERT: C 347 LEU cc_start: 0.7114 (tt) cc_final: 0.6751 (tt) REVERT: C 348 ASN cc_start: 0.5865 (m-40) cc_final: 0.5639 (m110) REVERT: D 82 TYR cc_start: 0.8748 (p90) cc_final: 0.8369 (p90) REVERT: D 99 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7812 (tppp) REVERT: D 155 ASP cc_start: 0.8335 (t70) cc_final: 0.7942 (p0) REVERT: D 160 THR cc_start: 0.7737 (p) cc_final: 0.7487 (p) REVERT: D 184 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7316 (ttp-110) REVERT: D 232 GLN cc_start: 0.8318 (mm110) cc_final: 0.8072 (mt0) REVERT: D 237 GLN cc_start: 0.8238 (pm20) cc_final: 0.8008 (pm20) REVERT: D 249 ASP cc_start: 0.8649 (m-30) cc_final: 0.8318 (m-30) REVERT: D 268 THR cc_start: 0.8613 (m) cc_final: 0.8396 (p) REVERT: D 307 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7889 (mtmm) REVERT: D 309 GLN cc_start: 0.7323 (mt0) cc_final: 0.7122 (mt0) REVERT: D 310 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8084 (tppp) REVERT: D 314 ASN cc_start: 0.8102 (t0) cc_final: 0.7869 (t0) REVERT: D 329 GLN cc_start: 0.6584 (pt0) cc_final: 0.6249 (pt0) REVERT: D 332 SER cc_start: 0.8170 (t) cc_final: 0.7898 (p) REVERT: D 339 LEU cc_start: 0.8540 (tp) cc_final: 0.7908 (tp) REVERT: D 368 PHE cc_start: 0.5661 (t80) cc_final: 0.5302 (t80) REVERT: E 70 ASN cc_start: 0.8550 (t0) cc_final: 0.8284 (t0) REVERT: E 99 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7987 (ttmm) REVERT: E 154 LYS cc_start: 0.6691 (ttpt) cc_final: 0.6157 (ttpp) REVERT: E 155 ASP cc_start: 0.8220 (t70) cc_final: 0.7637 (p0) REVERT: E 186 ARG cc_start: 0.8523 (mtt-85) cc_final: 0.7805 (mtp85) REVERT: E 232 GLN cc_start: 0.8463 (mm110) cc_final: 0.8092 (mt0) REVERT: E 242 PHE cc_start: 0.7082 (t80) cc_final: 0.6855 (t80) REVERT: E 310 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7897 (tppp) REVERT: E 329 GLN cc_start: 0.6348 (pt0) cc_final: 0.5841 (tt0) REVERT: E 332 SER cc_start: 0.8351 (t) cc_final: 0.7850 (p) REVERT: E 334 LEU cc_start: 0.7677 (tp) cc_final: 0.7357 (tp) REVERT: E 347 LEU cc_start: 0.7114 (tt) cc_final: 0.6750 (tt) REVERT: E 348 ASN cc_start: 0.5885 (m-40) cc_final: 0.5632 (m110) REVERT: F 33 ARG cc_start: 0.3313 (ttm110) cc_final: 0.3073 (ttm110) REVERT: F 99 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7772 (tppp) REVERT: F 155 ASP cc_start: 0.8330 (t70) cc_final: 0.7945 (p0) REVERT: F 160 THR cc_start: 0.7777 (p) cc_final: 0.7530 (p) REVERT: F 232 GLN cc_start: 0.8303 (mm110) cc_final: 0.8063 (mt0) REVERT: F 268 THR cc_start: 0.8584 (m) cc_final: 0.8375 (p) REVERT: F 303 CYS cc_start: 0.7550 (t) cc_final: 0.7235 (m) REVERT: F 304 ASN cc_start: 0.7897 (m-40) cc_final: 0.7420 (t0) REVERT: F 309 GLN cc_start: 0.7333 (mt0) cc_final: 0.7089 (mt0) REVERT: F 310 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8004 (tppp) REVERT: F 314 ASN cc_start: 0.8094 (t0) cc_final: 0.7793 (t0) REVERT: F 327 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7333 (t0) REVERT: F 329 GLN cc_start: 0.6536 (pt0) cc_final: 0.6117 (pt0) REVERT: F 332 SER cc_start: 0.8177 (t) cc_final: 0.7772 (p) REVERT: F 348 ASN cc_start: 0.5993 (m-40) cc_final: 0.5762 (m110) REVERT: F 368 PHE cc_start: 0.5751 (t80) cc_final: 0.4592 (t80) REVERT: G 70 ASN cc_start: 0.8552 (t0) cc_final: 0.8286 (t0) REVERT: G 99 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7984 (ttmm) REVERT: G 154 LYS cc_start: 0.6620 (ttpt) cc_final: 0.6082 (ttpp) REVERT: G 155 ASP cc_start: 0.8174 (t70) cc_final: 0.7571 (p0) REVERT: G 186 ARG cc_start: 0.8526 (mtt-85) cc_final: 0.7822 (mtp85) REVERT: G 232 GLN cc_start: 0.8462 (mm110) cc_final: 0.8093 (mt0) REVERT: G 242 PHE cc_start: 0.7085 (t80) cc_final: 0.6857 (t80) REVERT: G 310 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7931 (tppp) REVERT: G 329 GLN cc_start: 0.6337 (pt0) cc_final: 0.5807 (tt0) REVERT: G 332 SER cc_start: 0.8341 (t) cc_final: 0.7843 (p) REVERT: G 334 LEU cc_start: 0.7618 (tp) cc_final: 0.7297 (tp) REVERT: G 347 LEU cc_start: 0.7098 (tt) cc_final: 0.6775 (tt) REVERT: H 33 ARG cc_start: 0.3253 (ttm110) cc_final: 0.3019 (ttm110) REVERT: H 99 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7777 (tppp) REVERT: H 155 ASP cc_start: 0.8331 (t70) cc_final: 0.7951 (p0) REVERT: H 160 THR cc_start: 0.7845 (p) cc_final: 0.7603 (p) REVERT: H 232 GLN cc_start: 0.8315 (mm110) cc_final: 0.8076 (mt0) REVERT: H 268 THR cc_start: 0.8567 (m) cc_final: 0.8344 (p) REVERT: H 303 CYS cc_start: 0.7536 (t) cc_final: 0.7232 (m) REVERT: H 304 ASN cc_start: 0.7905 (m-40) cc_final: 0.7455 (t0) REVERT: H 309 GLN cc_start: 0.7333 (mt0) cc_final: 0.7131 (mt0) REVERT: H 310 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8034 (tppp) REVERT: H 314 ASN cc_start: 0.8095 (t0) cc_final: 0.7766 (t0) REVERT: H 327 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6832 (t0) REVERT: H 329 GLN cc_start: 0.6550 (pt0) cc_final: 0.6113 (pt0) REVERT: H 332 SER cc_start: 0.8195 (t) cc_final: 0.7817 (p) REVERT: H 348 ASN cc_start: 0.6016 (m-40) cc_final: 0.5783 (m110) outliers start: 115 outliers final: 81 residues processed: 865 average time/residue: 0.4152 time to fit residues: 519.9742 Evaluate side-chains 786 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 702 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 262 optimal weight: 0.9980 chunk 283 optimal weight: 0.4980 chunk 233 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN D 348 ASN G 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24472 Z= 0.187 Angle : 0.719 9.000 33328 Z= 0.365 Chirality : 0.042 0.166 3680 Planarity : 0.004 0.044 4128 Dihedral : 6.815 42.447 3168 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.21 % Favored : 90.23 % Rotamer: Outliers : 7.20 % Allowed : 15.50 % Favored : 77.30 % 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: -2.16 (0.15), residues: 2856 helix: -0.49 (0.12), residues: 1736 sheet: -1.41 (0.47), residues: 152 loop : -3.13 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 236 HIS 0.001 0.000 HIS G 247 PHE 0.012 0.001 PHE D 158 TYR 0.024 0.002 TYR F 300 ARG 0.007 0.001 ARG C 123 *********************** 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 973 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 788 time to evaluate : 2.482 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 TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 70 ASN cc_start: 0.8497 (t0) cc_final: 0.7878 (t0) REVERT: A 74 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.5855 (mp10) REVERT: A 99 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7930 (ttmm) REVERT: A 154 LYS cc_start: 0.6597 (ttpt) cc_final: 0.5792 (ttpp) REVERT: A 155 ASP cc_start: 0.8230 (t70) cc_final: 0.7682 (p0) REVERT: A 186 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.7974 (mtp85) REVERT: A 232 GLN cc_start: 0.8571 (mm110) cc_final: 0.8200 (mt0) REVERT: A 250 PHE cc_start: 0.7355 (t80) cc_final: 0.7098 (t80) REVERT: A 268 THR cc_start: 0.8498 (m) cc_final: 0.8261 (p) REVERT: A 310 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7928 (tppp) REVERT: A 329 GLN cc_start: 0.6439 (pt0) cc_final: 0.5982 (tt0) REVERT: A 332 SER cc_start: 0.8369 (t) cc_final: 0.8004 (p) REVERT: A 334 LEU cc_start: 0.7677 (tp) cc_final: 0.7348 (tt) REVERT: A 339 LEU cc_start: 0.8837 (tp) cc_final: 0.8123 (tp) REVERT: A 341 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8088 (pp) REVERT: A 347 LEU cc_start: 0.7076 (tt) cc_final: 0.6748 (tt) REVERT: B 75 TYR cc_start: 0.8209 (t80) cc_final: 0.7979 (t80) REVERT: B 99 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7771 (tppp) REVERT: B 154 LYS cc_start: 0.6855 (ttpt) cc_final: 0.6316 (ttpp) REVERT: B 155 ASP cc_start: 0.8382 (t70) cc_final: 0.7932 (p0) REVERT: B 160 THR cc_start: 0.7674 (p) cc_final: 0.7291 (t) REVERT: B 268 THR cc_start: 0.8615 (m) cc_final: 0.8380 (p) REVERT: B 309 GLN cc_start: 0.7312 (mt0) cc_final: 0.7080 (mt0) REVERT: B 310 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7835 (tppp) REVERT: B 329 GLN cc_start: 0.6566 (pt0) cc_final: 0.5657 (pt0) REVERT: B 332 SER cc_start: 0.8230 (t) cc_final: 0.7976 (p) REVERT: B 339 LEU cc_start: 0.8581 (tp) cc_final: 0.7966 (tp) REVERT: B 344 GLN cc_start: 0.6994 (tp40) cc_final: 0.6621 (tp40) REVERT: C 70 ASN cc_start: 0.8525 (t0) cc_final: 0.7823 (t0) REVERT: C 74 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.5935 (mp10) REVERT: C 99 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7931 (ttmm) REVERT: C 154 LYS cc_start: 0.6599 (ttpt) cc_final: 0.5799 (ttpp) REVERT: C 155 ASP cc_start: 0.8228 (t70) cc_final: 0.7698 (p0) REVERT: C 186 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.7984 (mtp85) REVERT: C 232 GLN cc_start: 0.8573 (mm110) cc_final: 0.8188 (mt0) REVERT: C 250 PHE cc_start: 0.7357 (t80) cc_final: 0.7054 (t80) REVERT: C 268 THR cc_start: 0.8497 (m) cc_final: 0.8258 (p) REVERT: C 310 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7944 (tppp) REVERT: C 329 GLN cc_start: 0.6437 (pt0) cc_final: 0.5994 (tt0) REVERT: C 332 SER cc_start: 0.8379 (t) cc_final: 0.8014 (p) REVERT: C 334 LEU cc_start: 0.7663 (tp) cc_final: 0.7314 (tt) REVERT: C 339 LEU cc_start: 0.8852 (tp) cc_final: 0.8071 (tp) REVERT: C 341 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8089 (pp) REVERT: C 347 LEU cc_start: 0.7030 (tt) cc_final: 0.6783 (tt) REVERT: D 75 TYR cc_start: 0.8210 (t80) cc_final: 0.7970 (t80) REVERT: D 99 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7788 (tppp) REVERT: D 155 ASP cc_start: 0.8295 (t70) cc_final: 0.7960 (p0) REVERT: D 160 THR cc_start: 0.7497 (p) cc_final: 0.7107 (t) REVERT: D 184 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7397 (ttp-110) REVERT: D 268 THR cc_start: 0.8573 (m) cc_final: 0.8336 (p) REVERT: D 304 ASN cc_start: 0.8025 (m-40) cc_final: 0.7531 (t0) REVERT: D 310 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7893 (tppt) REVERT: D 329 GLN cc_start: 0.6573 (pt0) cc_final: 0.5813 (tt0) REVERT: D 332 SER cc_start: 0.8288 (t) cc_final: 0.8014 (p) REVERT: D 339 LEU cc_start: 0.8662 (tp) cc_final: 0.8334 (mt) REVERT: D 344 GLN cc_start: 0.7103 (tp40) cc_final: 0.6687 (tp40) REVERT: E 70 ASN cc_start: 0.8531 (t0) cc_final: 0.8016 (t0) REVERT: E 74 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.5912 (mp10) REVERT: E 99 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7929 (ttmm) REVERT: E 154 LYS cc_start: 0.6597 (ttpt) cc_final: 0.5798 (ttpp) REVERT: E 155 ASP cc_start: 0.8231 (t70) cc_final: 0.7695 (p0) REVERT: E 186 ARG cc_start: 0.8596 (mtt-85) cc_final: 0.7975 (mtp85) REVERT: E 232 GLN cc_start: 0.8686 (mm110) cc_final: 0.8326 (mt0) REVERT: E 250 PHE cc_start: 0.7353 (t80) cc_final: 0.7095 (t80) REVERT: E 329 GLN cc_start: 0.6460 (pt0) cc_final: 0.6013 (tt0) REVERT: E 332 SER cc_start: 0.8378 (t) cc_final: 0.8100 (p) REVERT: E 334 LEU cc_start: 0.7661 (tp) cc_final: 0.7419 (tt) REVERT: E 341 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8086 (pp) REVERT: E 347 LEU cc_start: 0.7029 (tt) cc_final: 0.6785 (tt) REVERT: F 99 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7766 (tppp) REVERT: F 155 ASP cc_start: 0.8344 (t70) cc_final: 0.7968 (p0) REVERT: F 268 THR cc_start: 0.8609 (m) cc_final: 0.8378 (p) REVERT: F 310 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7922 (tppt) REVERT: F 329 GLN cc_start: 0.6511 (pt0) cc_final: 0.6059 (tt0) REVERT: F 332 SER cc_start: 0.8228 (t) cc_final: 0.7978 (p) REVERT: F 339 LEU cc_start: 0.8605 (tp) cc_final: 0.7972 (tp) REVERT: F 344 GLN cc_start: 0.7010 (tp40) cc_final: 0.6636 (tp40) REVERT: G 70 ASN cc_start: 0.8510 (t0) cc_final: 0.7927 (t0) REVERT: G 74 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.5909 (mp10) REVERT: G 99 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7929 (ttmm) REVERT: G 154 LYS cc_start: 0.6618 (ttpt) cc_final: 0.5822 (ttpp) REVERT: G 155 ASP cc_start: 0.8229 (t70) cc_final: 0.7686 (p0) REVERT: G 186 ARG cc_start: 0.8603 (mtt-85) cc_final: 0.7984 (mtp85) REVERT: G 232 GLN cc_start: 0.8569 (mm110) cc_final: 0.8197 (mt0) REVERT: G 250 PHE cc_start: 0.7356 (t80) cc_final: 0.7099 (t80) REVERT: G 268 THR cc_start: 0.8498 (m) cc_final: 0.8261 (p) REVERT: G 310 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7940 (tppp) REVERT: G 329 GLN cc_start: 0.6431 (pt0) cc_final: 0.5985 (tt0) REVERT: G 332 SER cc_start: 0.8383 (t) cc_final: 0.8047 (p) REVERT: G 334 LEU cc_start: 0.7668 (tp) cc_final: 0.7317 (tt) REVERT: G 339 LEU cc_start: 0.8817 (tp) cc_final: 0.8065 (tp) REVERT: G 341 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8080 (pp) REVERT: G 347 LEU cc_start: 0.7063 (tt) cc_final: 0.6762 (tt) REVERT: H 99 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7769 (tppp) REVERT: H 155 ASP cc_start: 0.8397 (t70) cc_final: 0.7983 (p0) REVERT: H 268 THR cc_start: 0.8612 (m) cc_final: 0.8376 (p) REVERT: H 307 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7805 (mtmm) REVERT: H 309 GLN cc_start: 0.7310 (mt0) cc_final: 0.7104 (mt0) REVERT: H 310 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7806 (tppp) REVERT: H 329 GLN cc_start: 0.6553 (pt0) cc_final: 0.5656 (pt0) REVERT: H 332 SER cc_start: 0.8232 (t) cc_final: 0.7974 (p) REVERT: H 339 LEU cc_start: 0.8606 (tp) cc_final: 0.8091 (tp) REVERT: H 344 GLN cc_start: 0.7007 (tp40) cc_final: 0.6636 (tp40) outliers start: 185 outliers final: 111 residues processed: 902 average time/residue: 0.4118 time to fit residues: 550.8906 Evaluate side-chains 815 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 696 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 337 ASP Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 GLN B 247 HIS B 348 ASN D 232 GLN F 232 GLN F 348 ASN H 232 GLN H 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 24472 Z= 0.365 Angle : 0.794 8.878 33328 Z= 0.402 Chirality : 0.047 0.170 3680 Planarity : 0.005 0.044 4128 Dihedral : 6.784 35.174 3168 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.12 % Favored : 89.32 % Rotamer: Outliers : 8.33 % Allowed : 18.30 % Favored : 73.36 % 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: -1.77 (0.16), residues: 2856 helix: -0.15 (0.12), residues: 1744 sheet: -1.94 (0.38), residues: 184 loop : -2.95 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 236 HIS 0.004 0.001 HIS H 241 PHE 0.014 0.002 PHE F 64 TYR 0.019 0.002 TYR F 300 ARG 0.004 0.001 ARG H 181 *********************** 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 845 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 631 time to evaluate : 2.656 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 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: A 70 ASN cc_start: 0.8596 (t0) cc_final: 0.8080 (t0) REVERT: A 74 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.5939 (mp10) REVERT: A 99 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7894 (tppp) REVERT: A 155 ASP cc_start: 0.8309 (t70) cc_final: 0.7873 (p0) REVERT: A 215 ASP cc_start: 0.6340 (t0) cc_final: 0.5943 (t0) REVERT: A 232 GLN cc_start: 0.8605 (mm110) cc_final: 0.8234 (mt0) REVERT: A 250 PHE cc_start: 0.7428 (t80) cc_final: 0.7165 (t80) REVERT: A 304 ASN cc_start: 0.7885 (t0) cc_final: 0.7338 (t0) REVERT: A 310 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7958 (tppp) REVERT: A 315 TYR cc_start: 0.8181 (m-10) cc_final: 0.7897 (m-10) REVERT: A 329 GLN cc_start: 0.6228 (pt0) cc_final: 0.5798 (tt0) REVERT: A 332 SER cc_start: 0.8340 (t) cc_final: 0.8037 (p) REVERT: A 334 LEU cc_start: 0.7636 (tp) cc_final: 0.7124 (tp) REVERT: A 339 LEU cc_start: 0.8766 (tp) cc_final: 0.8183 (tp) REVERT: A 341 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8130 (pp) REVERT: A 347 LEU cc_start: 0.7145 (tt) cc_final: 0.6855 (tt) REVERT: B 99 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7753 (tppp) REVERT: B 105 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: B 154 LYS cc_start: 0.6723 (ttpt) cc_final: 0.6354 (ttpp) REVERT: B 155 ASP cc_start: 0.8386 (t70) cc_final: 0.7998 (p0) REVERT: B 160 THR cc_start: 0.7695 (p) cc_final: 0.7371 (t) REVERT: B 182 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8705 (mtmm) REVERT: B 268 THR cc_start: 0.8516 (m) cc_final: 0.8235 (p) REVERT: B 304 ASN cc_start: 0.7592 (t0) cc_final: 0.7205 (t0) REVERT: B 310 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7867 (tppp) REVERT: B 332 SER cc_start: 0.8215 (t) cc_final: 0.7990 (p) REVERT: C 70 ASN cc_start: 0.8584 (t0) cc_final: 0.7927 (t0) REVERT: C 74 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.5994 (mp10) REVERT: C 99 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7905 (tppp) REVERT: C 155 ASP cc_start: 0.8306 (t70) cc_final: 0.7885 (p0) REVERT: C 184 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7100 (ttp-110) REVERT: C 215 ASP cc_start: 0.6269 (t0) cc_final: 0.5877 (t0) REVERT: C 232 GLN cc_start: 0.8605 (mm110) cc_final: 0.8233 (mt0) REVERT: C 250 PHE cc_start: 0.7327 (t80) cc_final: 0.7071 (t80) REVERT: C 304 ASN cc_start: 0.7898 (t0) cc_final: 0.7350 (t0) REVERT: C 310 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7968 (tppp) REVERT: C 315 TYR cc_start: 0.8083 (m-10) cc_final: 0.7818 (m-10) REVERT: C 329 GLN cc_start: 0.6237 (pt0) cc_final: 0.5830 (tt0) REVERT: C 332 SER cc_start: 0.8364 (t) cc_final: 0.8036 (p) REVERT: C 334 LEU cc_start: 0.7750 (tp) cc_final: 0.7346 (tp) REVERT: C 339 LEU cc_start: 0.8799 (tp) cc_final: 0.8186 (tp) REVERT: C 341 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8101 (pp) REVERT: D 99 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7764 (tppp) REVERT: D 155 ASP cc_start: 0.8356 (t70) cc_final: 0.8009 (p0) REVERT: D 156 ASP cc_start: 0.7921 (m-30) cc_final: 0.7601 (m-30) REVERT: D 160 THR cc_start: 0.7540 (p) cc_final: 0.7324 (p) REVERT: D 184 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7582 (ttm-80) REVERT: D 268 THR cc_start: 0.8527 (m) cc_final: 0.8221 (p) REVERT: D 310 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7855 (tppp) REVERT: D 332 SER cc_start: 0.8229 (t) cc_final: 0.7985 (p) REVERT: D 339 LEU cc_start: 0.8446 (tp) cc_final: 0.8123 (mt) REVERT: D 344 GLN cc_start: 0.7011 (tp40) cc_final: 0.6663 (tp40) REVERT: E 70 ASN cc_start: 0.8597 (t0) cc_final: 0.8081 (t0) REVERT: E 74 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.5936 (mp10) REVERT: E 99 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7898 (tppp) REVERT: E 155 ASP cc_start: 0.8258 (t70) cc_final: 0.7815 (p0) REVERT: E 215 ASP cc_start: 0.6339 (t0) cc_final: 0.5942 (t0) REVERT: E 232 GLN cc_start: 0.8603 (mm110) cc_final: 0.8231 (mt0) REVERT: E 250 PHE cc_start: 0.7423 (t80) cc_final: 0.7160 (t80) REVERT: E 304 ASN cc_start: 0.7885 (t0) cc_final: 0.7335 (t0) REVERT: E 310 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7886 (tppp) REVERT: E 329 GLN cc_start: 0.6264 (pt0) cc_final: 0.5857 (tt0) REVERT: E 332 SER cc_start: 0.8337 (t) cc_final: 0.8077 (p) REVERT: E 334 LEU cc_start: 0.7637 (tp) cc_final: 0.7147 (tp) REVERT: E 339 LEU cc_start: 0.8770 (tp) cc_final: 0.8196 (mt) REVERT: E 341 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8142 (pp) REVERT: F 99 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7746 (tppp) REVERT: F 105 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: F 155 ASP cc_start: 0.8391 (t70) cc_final: 0.8003 (p0) REVERT: F 182 LYS cc_start: 0.8901 (mtmm) cc_final: 0.8697 (mtmm) REVERT: F 268 THR cc_start: 0.8511 (m) cc_final: 0.8264 (p) REVERT: F 310 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7862 (tppp) REVERT: F 329 GLN cc_start: 0.6536 (pt0) cc_final: 0.6155 (tt0) REVERT: F 332 SER cc_start: 0.8259 (t) cc_final: 0.8003 (p) REVERT: G 70 ASN cc_start: 0.8599 (t0) cc_final: 0.8083 (t0) REVERT: G 74 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.5937 (mp10) REVERT: G 99 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7895 (tppp) REVERT: G 155 ASP cc_start: 0.8257 (t70) cc_final: 0.7804 (p0) REVERT: G 184 ARG cc_start: 0.7857 (mtm-85) cc_final: 0.7089 (ttp-110) REVERT: G 232 GLN cc_start: 0.8602 (mm110) cc_final: 0.8230 (mt0) REVERT: G 250 PHE cc_start: 0.7425 (t80) cc_final: 0.7165 (t80) REVERT: G 304 ASN cc_start: 0.7884 (t0) cc_final: 0.7336 (t0) REVERT: G 310 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7965 (tppp) REVERT: G 329 GLN cc_start: 0.6226 (pt0) cc_final: 0.5819 (tt0) REVERT: G 332 SER cc_start: 0.8362 (t) cc_final: 0.8034 (p) REVERT: G 334 LEU cc_start: 0.7755 (tp) cc_final: 0.7350 (tp) REVERT: G 339 LEU cc_start: 0.8802 (tp) cc_final: 0.8185 (tp) REVERT: G 341 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8095 (pp) REVERT: G 347 LEU cc_start: 0.7165 (tt) cc_final: 0.6848 (tt) REVERT: H 99 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7749 (tppp) REVERT: H 105 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: H 155 ASP cc_start: 0.8394 (t70) cc_final: 0.8007 (p0) REVERT: H 268 THR cc_start: 0.8519 (m) cc_final: 0.8231 (p) REVERT: H 310 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7863 (tppp) REVERT: H 332 SER cc_start: 0.8210 (t) cc_final: 0.7974 (p) outliers start: 214 outliers final: 150 residues processed: 760 average time/residue: 0.4097 time to fit residues: 454.8160 Evaluate side-chains 762 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 601 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 337 ASP Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 142 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN B 329 GLN D 329 GLN G 348 ASN H 329 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24472 Z= 0.165 Angle : 0.702 9.083 33328 Z= 0.351 Chirality : 0.041 0.174 3680 Planarity : 0.004 0.046 4128 Dihedral : 6.284 34.509 3168 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.10 % Favored : 90.34 % Rotamer: Outliers : 5.72 % Allowed : 21.30 % Favored : 72.98 % 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: -1.17 (0.16), residues: 2856 helix: 0.46 (0.13), residues: 1736 sheet: -1.92 (0.36), residues: 192 loop : -2.94 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 107 HIS 0.002 0.000 HIS H 247 PHE 0.013 0.001 PHE B 158 TYR 0.028 0.001 TYR H 300 ARG 0.002 0.000 ARG F 178 *********************** 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 798 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 651 time to evaluate : 2.653 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash 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 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 REVERT: A 70 ASN cc_start: 0.8511 (t0) cc_final: 0.7968 (t0) REVERT: A 74 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6142 (mt0) REVERT: A 99 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7783 (ttmm) REVERT: A 154 LYS cc_start: 0.7321 (pttt) cc_final: 0.7110 (pttp) REVERT: A 155 ASP cc_start: 0.8154 (t70) cc_final: 0.7909 (p0) REVERT: A 178 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.7422 (ttp80) REVERT: A 182 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8922 (mtpp) REVERT: A 215 ASP cc_start: 0.6333 (t0) cc_final: 0.5934 (t0) REVERT: A 232 GLN cc_start: 0.8723 (mm110) cc_final: 0.8433 (mt0) REVERT: A 250 PHE cc_start: 0.7368 (t80) cc_final: 0.7131 (t80) REVERT: A 310 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7853 (tppp) REVERT: A 332 SER cc_start: 0.8291 (t) cc_final: 0.8053 (p) REVERT: A 334 LEU cc_start: 0.7538 (tp) cc_final: 0.7077 (tt) REVERT: A 339 LEU cc_start: 0.8781 (tp) cc_final: 0.8217 (mt) REVERT: A 341 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8027 (pp) REVERT: B 99 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7780 (tppp) REVERT: B 105 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: B 155 ASP cc_start: 0.8483 (t70) cc_final: 0.7955 (p0) REVERT: B 160 THR cc_start: 0.7458 (p) cc_final: 0.7079 (t) REVERT: B 268 THR cc_start: 0.8458 (m) cc_final: 0.8106 (p) REVERT: B 304 ASN cc_start: 0.7617 (t0) cc_final: 0.7339 (t0) REVERT: B 307 LYS cc_start: 0.7757 (mtmm) cc_final: 0.7556 (tmmt) REVERT: B 329 GLN cc_start: 0.6667 (pt0) cc_final: 0.6077 (pt0) REVERT: B 332 SER cc_start: 0.8252 (t) cc_final: 0.8024 (p) REVERT: B 339 LEU cc_start: 0.8569 (tp) cc_final: 0.8274 (mt) REVERT: C 70 ASN cc_start: 0.8539 (t0) cc_final: 0.8033 (t0) REVERT: C 74 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6122 (mt0) REVERT: C 99 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7815 (ttmm) REVERT: C 154 LYS cc_start: 0.7319 (pttt) cc_final: 0.7108 (pttp) REVERT: C 155 ASP cc_start: 0.8221 (t70) cc_final: 0.7989 (p0) REVERT: C 215 ASP cc_start: 0.6332 (t0) cc_final: 0.5936 (t0) REVERT: C 232 GLN cc_start: 0.8730 (mm110) cc_final: 0.8427 (mt0) REVERT: C 250 PHE cc_start: 0.7347 (t80) cc_final: 0.7078 (t80) REVERT: C 310 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7508 (tppp) REVERT: C 332 SER cc_start: 0.8317 (t) cc_final: 0.8041 (p) REVERT: C 334 LEU cc_start: 0.7590 (tp) cc_final: 0.7136 (tt) REVERT: C 339 LEU cc_start: 0.8759 (tp) cc_final: 0.8263 (mt) REVERT: C 341 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7897 (pp) REVERT: D 99 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7819 (tppp) REVERT: D 155 ASP cc_start: 0.8391 (t70) cc_final: 0.8059 (p0) REVERT: D 156 ASP cc_start: 0.7930 (m-30) cc_final: 0.7413 (m-30) REVERT: D 160 THR cc_start: 0.7464 (p) cc_final: 0.7144 (t) REVERT: D 184 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7387 (ttp-110) REVERT: D 268 THR cc_start: 0.8597 (m) cc_final: 0.8283 (p) REVERT: D 332 SER cc_start: 0.8218 (t) cc_final: 0.7989 (p) REVERT: D 339 LEU cc_start: 0.8436 (tp) cc_final: 0.8234 (mt) REVERT: D 344 GLN cc_start: 0.6931 (tp40) cc_final: 0.6575 (tp40) REVERT: E 70 ASN cc_start: 0.8513 (t0) cc_final: 0.7974 (t0) REVERT: E 74 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6141 (mt0) REVERT: E 99 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7756 (ttmm) REVERT: E 155 ASP cc_start: 0.8231 (t70) cc_final: 0.7982 (p0) REVERT: E 182 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8921 (mtpp) REVERT: E 215 ASP cc_start: 0.6335 (t0) cc_final: 0.5936 (t0) REVERT: E 232 GLN cc_start: 0.8722 (mm110) cc_final: 0.8432 (mt0) REVERT: E 250 PHE cc_start: 0.7442 (t80) cc_final: 0.7200 (t80) REVERT: E 329 GLN cc_start: 0.6157 (pt0) cc_final: 0.5945 (tt0) REVERT: E 332 SER cc_start: 0.8302 (t) cc_final: 0.8057 (p) REVERT: E 334 LEU cc_start: 0.7557 (tp) cc_final: 0.7082 (tt) REVERT: E 339 LEU cc_start: 0.8696 (tp) cc_final: 0.8010 (mt) REVERT: E 341 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8046 (pp) REVERT: F 99 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7798 (ttmm) REVERT: F 105 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: F 155 ASP cc_start: 0.8437 (t70) cc_final: 0.7964 (p0) REVERT: F 268 THR cc_start: 0.8438 (m) cc_final: 0.8060 (p) REVERT: F 310 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7947 (tppt) REVERT: F 329 GLN cc_start: 0.6137 (pt0) cc_final: 0.5629 (tt0) REVERT: F 332 SER cc_start: 0.8272 (t) cc_final: 0.7998 (p) REVERT: F 339 LEU cc_start: 0.8553 (tp) cc_final: 0.8211 (mt) REVERT: G 70 ASN cc_start: 0.8514 (t0) cc_final: 0.7971 (t0) REVERT: G 74 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6142 (mt0) REVERT: G 99 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7622 (ttmm) REVERT: G 154 LYS cc_start: 0.7324 (pttt) cc_final: 0.7114 (pttp) REVERT: G 155 ASP cc_start: 0.8223 (t70) cc_final: 0.7983 (p0) REVERT: G 182 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8976 (mtpp) REVERT: G 232 GLN cc_start: 0.8723 (mm110) cc_final: 0.8432 (mt0) REVERT: G 250 PHE cc_start: 0.7444 (t80) cc_final: 0.7202 (t80) REVERT: G 310 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7620 (tppp) REVERT: G 332 SER cc_start: 0.8318 (t) cc_final: 0.8038 (p) REVERT: G 334 LEU cc_start: 0.7592 (tp) cc_final: 0.7132 (tt) REVERT: G 339 LEU cc_start: 0.8758 (tp) cc_final: 0.8255 (mt) REVERT: G 341 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7885 (pp) REVERT: H 99 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7776 (tppp) REVERT: H 105 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: H 155 ASP cc_start: 0.8459 (t70) cc_final: 0.7935 (p0) REVERT: H 268 THR cc_start: 0.8464 (m) cc_final: 0.8108 (p) REVERT: H 329 GLN cc_start: 0.6675 (pt0) cc_final: 0.6035 (pt0) REVERT: H 332 SER cc_start: 0.8235 (t) cc_final: 0.8030 (p) REVERT: H 339 LEU cc_start: 0.8547 (tp) cc_final: 0.8153 (mt) outliers start: 147 outliers final: 88 residues processed: 740 average time/residue: 0.4052 time to fit residues: 438.9486 Evaluate side-chains 704 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 602 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 337 ASP Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5006 > 50: distance: 25 - 46: 5.035 distance: 29 - 58: 6.985 distance: 34 - 66: 5.155 distance: 37 - 46: 5.658 distance: 38 - 74: 12.689 distance: 48 - 49: 7.432 distance: 49 - 81: 16.917 distance: 51 - 53: 3.133 distance: 52 - 54: 3.150 distance: 54 - 56: 3.254 distance: 55 - 56: 3.516 distance: 56 - 57: 4.055 distance: 58 - 59: 4.232 distance: 59 - 62: 3.934 distance: 60 - 66: 9.485 distance: 61 - 90: 8.372 distance: 62 - 63: 11.255 distance: 62 - 64: 9.351 distance: 63 - 65: 10.310 distance: 66 - 67: 4.561 distance: 67 - 68: 12.325 distance: 67 - 70: 14.220 distance: 68 - 69: 15.167 distance: 68 - 74: 10.418 distance: 71 - 72: 5.908 distance: 71 - 73: 14.756 distance: 74 - 75: 5.576 distance: 75 - 76: 5.819 distance: 75 - 78: 4.637 distance: 76 - 77: 8.905 distance: 76 - 81: 6.594 distance: 78 - 79: 6.337 distance: 78 - 80: 9.095 distance: 81 - 82: 9.252 distance: 82 - 83: 9.189 distance: 82 - 85: 12.716 distance: 83 - 84: 8.542 distance: 83 - 90: 19.353 distance: 85 - 86: 33.396 distance: 86 - 87: 13.963 distance: 87 - 88: 6.043 distance: 87 - 89: 3.701 distance: 90 - 91: 20.435 distance: 91 - 92: 16.139 distance: 91 - 94: 17.457 distance: 92 - 93: 31.578 distance: 92 - 98: 11.120 distance: 94 - 95: 5.711 distance: 95 - 96: 11.099 distance: 95 - 97: 14.136 distance: 98 - 99: 15.228 distance: 99 - 100: 10.900 distance: 99 - 102: 7.199 distance: 100 - 101: 8.503 distance: 100 - 106: 8.920 distance: 102 - 103: 13.356 distance: 103 - 104: 7.824 distance: 103 - 105: 12.462 distance: 106 - 107: 8.695 distance: 107 - 108: 20.009 distance: 107 - 110: 8.311 distance: 108 - 109: 15.158 distance: 108 - 114: 8.061 distance: 110 - 111: 8.575 distance: 111 - 112: 8.308 distance: 111 - 113: 6.640 distance: 114 - 115: 5.282 distance: 115 - 116: 5.693 distance: 115 - 118: 13.320 distance: 116 - 117: 16.567 distance: 116 - 120: 14.855 distance: 118 - 119: 12.980 distance: 120 - 121: 11.387 distance: 121 - 122: 10.131 distance: 121 - 124: 9.589 distance: 122 - 123: 7.756 distance: 122 - 126: 9.441 distance: 124 - 125: 13.480