Starting phenix.real_space_refine on Tue Aug 26 10:44:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rjl_19251/08_2025/8rjl_19251.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rjl_19251/08_2025/8rjl_19251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rjl_19251/08_2025/8rjl_19251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rjl_19251/08_2025/8rjl_19251.map" model { file = "/net/cci-nas-00/data/ceres_data/8rjl_19251/08_2025/8rjl_19251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rjl_19251/08_2025/8rjl_19251.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.019 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 144 5.16 5 C 23388 2.51 5 N 6207 2.21 5 O 6561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36300 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1729 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1740 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 206} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2167 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2156 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2146 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2162 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1729 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1740 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 206} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2167 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2156 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2146 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2162 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1729 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1740 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 206} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2167 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2156 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2146 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2162 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 7.59, per 1000 atoms: 0.21 Number of scatterers: 36300 At special positions: 0 Unit cell: (207.77, 214.09, 107.44, 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 144 16.00 O 6561 8.00 N 6207 7.00 C 23388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.85 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8706 Finding SS restraints... Secondary structure from input PDB file: 244 helices and 18 sheets defined 63.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 61 through 72 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 94 through 110 removed outlier: 4.321A pdb=" N ALA A 98 " --> pdb=" O HIS A 94 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 4.142A pdb=" N VAL A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 removed outlier: 3.549A pdb=" N MET A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.902A pdb=" N ILE A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 185 " --> pdb=" O CYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 206 through 219 removed outlier: 3.833A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 327 removed outlier: 4.340A pdb=" N TYR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.728A pdb=" N LEU A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 334 through 351 removed outlier: 4.109A pdb=" N ALA A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 44 removed outlier: 3.593A pdb=" N GLN B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 64 through 75 removed outlier: 4.798A pdb=" N HIS B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 94 through 110 removed outlier: 3.930A pdb=" N TYR B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 139 removed outlier: 3.615A pdb=" N LEU B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Proline residue: B 133 - end of helix removed outlier: 3.622A pdb=" N VAL B 136 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 171 through 185 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 206 through 219 removed outlier: 3.564A pdb=" N VAL B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 327 removed outlier: 4.198A pdb=" N TYR B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 352 removed outlier: 3.502A pdb=" N VAL B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 345 " --> pdb=" O ARG B 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN B 352 " --> pdb=" O HIS B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 43 Processing helix chain 'C' and resid 46 through 57 removed outlier: 3.516A pdb=" N LEU C 53 " --> pdb=" O GLU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.711A pdb=" N LEU C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 4.097A pdb=" N ARG C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.771A pdb=" N ALA C 98 " --> pdb=" O HIS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 131 removed outlier: 3.721A pdb=" N VAL C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 removed outlier: 4.529A pdb=" N LYS C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 171 through 185 removed outlier: 3.598A pdb=" N ALA C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS C 185 " --> pdb=" O CYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 202 Processing helix chain 'C' and resid 206 through 219 removed outlier: 3.915A pdb=" N VAL C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 219 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 removed outlier: 4.715A pdb=" N LEU C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 326 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 327 " --> pdb=" O TYR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 352 removed outlier: 4.062A pdb=" N VAL C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA C 340 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP C 345 " --> pdb=" O ARG C 341 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 Processing helix chain 'D' and resid 46 through 57 removed outlier: 3.852A pdb=" N THR D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 75 removed outlier: 3.984A pdb=" N LEU D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 3.885A pdb=" N ARG D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.748A pdb=" N ALA D 98 " --> pdb=" O HIS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 131 through 145 removed outlier: 4.089A pdb=" N MET D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 167 Processing helix chain 'D' and resid 171 through 184 Processing helix chain 'D' and resid 191 through 202 Processing helix chain 'D' and resid 206 through 215 removed outlier: 4.028A pdb=" N VAL D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 327 removed outlier: 3.508A pdb=" N VAL D 322 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU D 326 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY D 327 " --> pdb=" O TYR D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 352 removed outlier: 3.795A pdb=" N PHE D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 340 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 57 removed outlier: 4.065A pdb=" N THR G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 74 removed outlier: 3.557A pdb=" N LEU G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 87 Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 122 through 145 Proline residue: G 133 - end of helix removed outlier: 4.652A pdb=" N PHE G 139 " --> pdb=" O MET G 135 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY G 145 " --> pdb=" O LEU G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 167 removed outlier: 3.513A pdb=" N LEU G 165 " --> pdb=" O PHE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 184 removed outlier: 3.814A pdb=" N ALA G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 202 Processing helix chain 'G' and resid 206 through 219 removed outlier: 3.860A pdb=" N VAL G 210 " --> pdb=" O ASP G 206 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA G 219 " --> pdb=" O VAL G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 326 removed outlier: 3.729A pdb=" N SER G 319 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU G 321 " --> pdb=" O PHE G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 342 removed outlier: 3.601A pdb=" N ALA G 340 " --> pdb=" O VAL G 336 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG G 341 " --> pdb=" O PHE G 337 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 352 removed outlier: 3.551A pdb=" N ALA G 347 " --> pdb=" O ALA G 343 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP G 349 " --> pdb=" O TRP G 345 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU G 351 " --> pdb=" O ALA G 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 44 removed outlier: 3.751A pdb=" N LEU H 41 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 57 Processing helix chain 'H' and resid 61 through 75 removed outlier: 3.871A pdb=" N LEU H 65 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 removed outlier: 3.983A pdb=" N ARG H 83 " --> pdb=" O LYS H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 110 removed outlier: 3.542A pdb=" N ALA H 98 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY H 107 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 143 removed outlier: 4.230A pdb=" N ALA H 124 " --> pdb=" O TYR H 120 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL H 125 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL H 126 " --> pdb=" O ARG H 122 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Proline residue: H 133 - end of helix Processing helix chain 'H' and resid 156 through 167 Processing helix chain 'H' and resid 171 through 184 removed outlier: 3.649A pdb=" N ALA H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 201 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 206 through 219 removed outlier: 3.889A pdb=" N VAL H 210 " --> pdb=" O ASP H 206 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA H 219 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 326 removed outlier: 4.109A pdb=" N LEU H 326 " --> pdb=" O VAL H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 341 removed outlier: 3.776A pdb=" N VAL H 336 " --> pdb=" O LEU H 332 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE H 337 " --> pdb=" O PHE H 333 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA H 338 " --> pdb=" O THR H 334 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE H 339 " --> pdb=" O PRO H 335 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA H 340 " --> pdb=" O VAL H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 352 removed outlier: 3.747A pdb=" N TRP H 345 " --> pdb=" O ARG H 341 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU H 346 " --> pdb=" O VAL H 342 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU H 351 " --> pdb=" O ALA H 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 61 through 72 Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 94 through 110 removed outlier: 4.322A pdb=" N ALA E 98 " --> pdb=" O HIS E 94 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 126 removed outlier: 4.142A pdb=" N VAL E 126 " --> pdb=" O ARG E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.549A pdb=" N MET E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 139 " --> pdb=" O MET E 135 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 173 through 185 removed outlier: 3.902A pdb=" N ILE E 177 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS E 185 " --> pdb=" O CYS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 206 through 219 removed outlier: 3.834A pdb=" N VAL E 210 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA E 219 " --> pdb=" O VAL E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 327 removed outlier: 4.339A pdb=" N TYR E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 333 removed outlier: 3.728A pdb=" N LEU E 332 " --> pdb=" O PRO E 329 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE E 333 " --> pdb=" O SER E 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 333' Processing helix chain 'E' and resid 334 through 351 removed outlier: 4.110A pdb=" N ALA E 340 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA E 343 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP E 345 " --> pdb=" O ARG E 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E 350 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 44 removed outlier: 3.593A pdb=" N GLN I 44 " --> pdb=" O GLN I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 64 through 75 removed outlier: 4.798A pdb=" N HIS I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU I 71 " --> pdb=" O GLU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 86 Processing helix chain 'I' and resid 87 through 89 No H-bonds generated for 'chain 'I' and resid 87 through 89' Processing helix chain 'I' and resid 94 through 110 removed outlier: 3.930A pdb=" N TYR I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 123 Processing helix chain 'I' and resid 124 through 139 removed outlier: 3.615A pdb=" N LEU I 128 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU I 129 " --> pdb=" O VAL I 125 " (cutoff:3.500A) Proline residue: I 133 - end of helix removed outlier: 3.622A pdb=" N VAL I 136 " --> pdb=" O ILE I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 142 No H-bonds generated for 'chain 'I' and resid 140 through 142' Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 171 through 185 Processing helix chain 'I' and resid 192 through 202 Processing helix chain 'I' and resid 206 through 219 removed outlier: 3.564A pdb=" N VAL I 210 " --> pdb=" O ASP I 206 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA I 219 " --> pdb=" O VAL I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 327 removed outlier: 4.197A pdb=" N TYR I 318 " --> pdb=" O ASN I 314 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU I 321 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 352 removed outlier: 3.502A pdb=" N VAL I 336 " --> pdb=" O LEU I 332 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA I 338 " --> pdb=" O THR I 334 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA I 340 " --> pdb=" O VAL I 336 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA I 343 " --> pdb=" O ILE I 339 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLY I 344 " --> pdb=" O ALA I 340 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP I 345 " --> pdb=" O ARG I 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS I 350 " --> pdb=" O LEU I 346 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU I 351 " --> pdb=" O ALA I 347 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN I 352 " --> pdb=" O HIS I 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 43 Processing helix chain 'K' and resid 46 through 57 removed outlier: 3.516A pdb=" N LEU K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 72 removed outlier: 3.711A pdb=" N LEU K 65 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 88 removed outlier: 4.097A pdb=" N ARG K 83 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 104 removed outlier: 3.771A pdb=" N ALA K 98 " --> pdb=" O HIS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 131 removed outlier: 3.720A pdb=" N VAL K 126 " --> pdb=" O ARG K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 144 removed outlier: 4.529A pdb=" N LYS K 144 " --> pdb=" O GLN K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 167 Processing helix chain 'K' and resid 171 through 185 removed outlier: 3.598A pdb=" N ALA K 175 " --> pdb=" O ASP K 171 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS K 185 " --> pdb=" O CYS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 202 Processing helix chain 'K' and resid 206 through 219 removed outlier: 3.915A pdb=" N VAL K 210 " --> pdb=" O ASP K 206 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA K 219 " --> pdb=" O VAL K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 327 removed outlier: 4.716A pdb=" N LEU K 321 " --> pdb=" O PHE K 317 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU K 326 " --> pdb=" O VAL K 322 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY K 327 " --> pdb=" O TYR K 323 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 352 removed outlier: 4.061A pdb=" N VAL K 336 " --> pdb=" O LEU K 332 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE K 337 " --> pdb=" O PHE K 333 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA K 340 " --> pdb=" O VAL K 336 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG K 341 " --> pdb=" O PHE K 337 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA K 343 " --> pdb=" O ILE K 339 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY K 344 " --> pdb=" O ALA K 340 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP K 345 " --> pdb=" O ARG K 341 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA K 347 " --> pdb=" O ALA K 343 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 42 Processing helix chain 'M' and resid 46 through 57 removed outlier: 3.852A pdb=" N THR M 50 " --> pdb=" O SER M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 75 removed outlier: 3.984A pdb=" N LEU M 65 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 87 removed outlier: 3.885A pdb=" N ARG M 83 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS M 87 " --> pdb=" O ARG M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 106 removed outlier: 3.747A pdb=" N ALA M 98 " --> pdb=" O HIS M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 131 Processing helix chain 'M' and resid 131 through 145 removed outlier: 4.088A pdb=" N MET M 135 " --> pdb=" O LYS M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 167 Processing helix chain 'M' and resid 171 through 184 Processing helix chain 'M' and resid 191 through 202 Processing helix chain 'M' and resid 206 through 215 removed outlier: 4.028A pdb=" N VAL M 210 " --> pdb=" O ASP M 206 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA M 212 " --> pdb=" O TYR M 208 " (cutoff:3.500A) Processing helix chain 'M' and resid 318 through 327 removed outlier: 3.507A pdb=" N VAL M 322 " --> pdb=" O TYR M 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU M 326 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY M 327 " --> pdb=" O TYR M 323 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 352 removed outlier: 3.796A pdb=" N PHE M 337 " --> pdb=" O PHE M 333 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA M 340 " --> pdb=" O VAL M 336 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA M 343 " --> pdb=" O ILE M 339 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY M 344 " --> pdb=" O ALA M 340 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA M 347 " --> pdb=" O ALA M 343 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS M 348 " --> pdb=" O GLY M 344 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS M 350 " --> pdb=" O LEU M 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 57 removed outlier: 4.065A pdb=" N THR O 50 " --> pdb=" O SER O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 74 removed outlier: 3.557A pdb=" N LEU O 65 " --> pdb=" O THR O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'O' and resid 94 through 104 Processing helix chain 'O' and resid 122 through 145 Proline residue: O 133 - end of helix removed outlier: 4.653A pdb=" N PHE O 139 " --> pdb=" O MET O 135 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS O 144 " --> pdb=" O GLN O 140 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY O 145 " --> pdb=" O LEU O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 167 removed outlier: 3.513A pdb=" N LEU O 165 " --> pdb=" O PHE O 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 184 removed outlier: 3.814A pdb=" N ALA O 175 " --> pdb=" O ASP O 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 202 Processing helix chain 'O' and resid 206 through 219 removed outlier: 3.860A pdb=" N VAL O 210 " --> pdb=" O ASP O 206 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA O 219 " --> pdb=" O VAL O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 315 through 326 removed outlier: 3.729A pdb=" N SER O 319 " --> pdb=" O VAL O 315 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU O 321 " --> pdb=" O PHE O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 333 through 342 removed outlier: 3.600A pdb=" N ALA O 340 " --> pdb=" O VAL O 336 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG O 341 " --> pdb=" O PHE O 337 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL O 342 " --> pdb=" O ALA O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 343 through 352 removed outlier: 3.551A pdb=" N ALA O 347 " --> pdb=" O ALA O 343 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP O 349 " --> pdb=" O TRP O 345 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU O 351 " --> pdb=" O ALA O 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.748A pdb=" N LEU Q 11 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU Q 12 " --> pdb=" O PRO Q 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 8 through 12' Processing helix chain 'Q' and resid 37 through 44 removed outlier: 3.751A pdb=" N LEU Q 41 " --> pdb=" O SER Q 37 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 57 Processing helix chain 'Q' and resid 61 through 75 removed outlier: 3.871A pdb=" N LEU Q 65 " --> pdb=" O THR Q 61 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS Q 75 " --> pdb=" O GLU Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 87 removed outlier: 3.829A pdb=" N ARG Q 83 " --> pdb=" O LYS Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 110 removed outlier: 3.543A pdb=" N ALA Q 98 " --> pdb=" O HIS Q 94 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY Q 107 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR Q 110 " --> pdb=" O LEU Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 143 removed outlier: 4.231A pdb=" N ALA Q 124 " --> pdb=" O TYR Q 120 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL Q 125 " --> pdb=" O ILE Q 121 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL Q 126 " --> pdb=" O ARG Q 122 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE Q 132 " --> pdb=" O LEU Q 128 " (cutoff:3.500A) Proline residue: Q 133 - end of helix Processing helix chain 'Q' and resid 156 through 167 Processing helix chain 'Q' and resid 171 through 184 removed outlier: 3.649A pdb=" N ALA Q 175 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 201 Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'Q' and resid 206 through 219 removed outlier: 3.806A pdb=" N VAL Q 210 " --> pdb=" O ASP Q 206 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA Q 219 " --> pdb=" O VAL Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 315 through 326 removed outlier: 4.109A pdb=" N LEU Q 326 " --> pdb=" O VAL Q 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 332 through 341 removed outlier: 3.775A pdb=" N VAL Q 336 " --> pdb=" O LEU Q 332 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE Q 337 " --> pdb=" O PHE Q 333 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA Q 338 " --> pdb=" O THR Q 334 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE Q 339 " --> pdb=" O PRO Q 335 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA Q 340 " --> pdb=" O VAL Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 341 through 352 removed outlier: 3.748A pdb=" N TRP Q 345 " --> pdb=" O ARG Q 341 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU Q 346 " --> pdb=" O VAL Q 342 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU Q 351 " --> pdb=" O ALA Q 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 61 through 72 Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 94 through 110 removed outlier: 4.321A pdb=" N ALA F 98 " --> pdb=" O HIS F 94 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 removed outlier: 4.142A pdb=" N VAL F 126 " --> pdb=" O ARG F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 145 removed outlier: 3.549A pdb=" N MET F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE F 139 " --> pdb=" O MET F 135 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS F 144 " --> pdb=" O GLN F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 167 Processing helix chain 'F' and resid 173 through 185 removed outlier: 3.902A pdb=" N ILE F 177 " --> pdb=" O VAL F 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS F 185 " --> pdb=" O CYS F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 201 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 206 through 219 removed outlier: 3.834A pdb=" N VAL F 210 " --> pdb=" O ASP F 206 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 327 removed outlier: 4.339A pdb=" N TYR F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 333 removed outlier: 3.728A pdb=" N LEU F 332 " --> pdb=" O PRO F 329 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE F 333 " --> pdb=" O SER F 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 329 through 333' Processing helix chain 'F' and resid 334 through 351 removed outlier: 4.109A pdb=" N ALA F 340 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA F 343 " --> pdb=" O ILE F 339 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP F 345 " --> pdb=" O ARG F 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 350 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU F 351 " --> pdb=" O ALA F 347 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 44 removed outlier: 3.593A pdb=" N GLN J 44 " --> pdb=" O GLN J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 56 Processing helix chain 'J' and resid 64 through 75 removed outlier: 4.798A pdb=" N HIS J 70 " --> pdb=" O THR J 66 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU J 71 " --> pdb=" O GLU J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 86 Processing helix chain 'J' and resid 87 through 89 No H-bonds generated for 'chain 'J' and resid 87 through 89' Processing helix chain 'J' and resid 94 through 110 removed outlier: 3.929A pdb=" N TYR J 110 " --> pdb=" O LEU J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 123 Processing helix chain 'J' and resid 124 through 139 removed outlier: 3.615A pdb=" N LEU J 128 " --> pdb=" O ALA J 124 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU J 129 " --> pdb=" O VAL J 125 " (cutoff:3.500A) Proline residue: J 133 - end of helix removed outlier: 3.622A pdb=" N VAL J 136 " --> pdb=" O ILE J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'J' and resid 171 through 185 Processing helix chain 'J' and resid 192 through 202 Processing helix chain 'J' and resid 206 through 219 removed outlier: 3.565A pdb=" N VAL J 210 " --> pdb=" O ASP J 206 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA J 219 " --> pdb=" O VAL J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 327 removed outlier: 4.198A pdb=" N TYR J 318 " --> pdb=" O ASN J 314 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU J 321 " --> pdb=" O PHE J 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 332 through 352 removed outlier: 3.501A pdb=" N VAL J 336 " --> pdb=" O LEU J 332 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA J 338 " --> pdb=" O THR J 334 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA J 340 " --> pdb=" O VAL J 336 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA J 343 " --> pdb=" O ILE J 339 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY J 344 " --> pdb=" O ALA J 340 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP J 345 " --> pdb=" O ARG J 341 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS J 350 " --> pdb=" O LEU J 346 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU J 351 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN J 352 " --> pdb=" O HIS J 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 43 Processing helix chain 'L' and resid 46 through 57 removed outlier: 3.516A pdb=" N LEU L 53 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 72 removed outlier: 3.711A pdb=" N LEU L 65 " --> pdb=" O THR L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 88 removed outlier: 4.096A pdb=" N ARG L 83 " --> pdb=" O LYS L 79 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS L 88 " --> pdb=" O ASP L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 104 removed outlier: 3.770A pdb=" N ALA L 98 " --> pdb=" O HIS L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 131 removed outlier: 3.721A pdb=" N VAL L 126 " --> pdb=" O ARG L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 144 removed outlier: 4.529A pdb=" N LYS L 144 " --> pdb=" O GLN L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 167 Processing helix chain 'L' and resid 171 through 185 removed outlier: 3.598A pdb=" N ALA L 175 " --> pdb=" O ASP L 171 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS L 185 " --> pdb=" O CYS L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 202 Processing helix chain 'L' and resid 206 through 219 removed outlier: 3.915A pdb=" N VAL L 210 " --> pdb=" O ASP L 206 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA L 219 " --> pdb=" O VAL L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 327 removed outlier: 4.716A pdb=" N LEU L 321 " --> pdb=" O PHE L 317 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU L 326 " --> pdb=" O VAL L 322 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY L 327 " --> pdb=" O TYR L 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 352 removed outlier: 4.061A pdb=" N VAL L 336 " --> pdb=" O LEU L 332 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE L 337 " --> pdb=" O PHE L 333 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA L 340 " --> pdb=" O VAL L 336 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG L 341 " --> pdb=" O PHE L 337 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA L 343 " --> pdb=" O ILE L 339 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY L 344 " --> pdb=" O ALA L 340 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP L 345 " --> pdb=" O ARG L 341 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA L 347 " --> pdb=" O ALA L 343 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 42 Processing helix chain 'N' and resid 46 through 57 removed outlier: 3.851A pdb=" N THR N 50 " --> pdb=" O SER N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 75 removed outlier: 3.983A pdb=" N LEU N 65 " --> pdb=" O THR N 61 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS N 75 " --> pdb=" O GLU N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 87 removed outlier: 3.885A pdb=" N ARG N 83 " --> pdb=" O LYS N 79 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS N 87 " --> pdb=" O ARG N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 106 removed outlier: 3.747A pdb=" N ALA N 98 " --> pdb=" O HIS N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 131 Processing helix chain 'N' and resid 131 through 145 removed outlier: 4.089A pdb=" N MET N 135 " --> pdb=" O LYS N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 156 through 167 Processing helix chain 'N' and resid 171 through 184 Processing helix chain 'N' and resid 191 through 202 Processing helix chain 'N' and resid 206 through 215 removed outlier: 4.028A pdb=" N VAL N 210 " --> pdb=" O ASP N 206 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA N 212 " --> pdb=" O TYR N 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 318 through 327 removed outlier: 3.509A pdb=" N VAL N 322 " --> pdb=" O TYR N 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU N 326 " --> pdb=" O VAL N 322 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY N 327 " --> pdb=" O TYR N 323 " (cutoff:3.500A) Processing helix chain 'N' and resid 332 through 352 removed outlier: 3.794A pdb=" N PHE N 337 " --> pdb=" O PHE N 333 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA N 340 " --> pdb=" O VAL N 336 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA N 343 " --> pdb=" O ILE N 339 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY N 344 " --> pdb=" O ALA N 340 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA N 347 " --> pdb=" O ALA N 343 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS N 348 " --> pdb=" O GLY N 344 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS N 350 " --> pdb=" O LEU N 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 57 removed outlier: 4.065A pdb=" N THR P 50 " --> pdb=" O SER P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 74 removed outlier: 3.557A pdb=" N LEU P 65 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 87 Processing helix chain 'P' and resid 94 through 104 Processing helix chain 'P' and resid 122 through 145 Proline residue: P 133 - end of helix removed outlier: 4.652A pdb=" N PHE P 139 " --> pdb=" O MET P 135 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS P 144 " --> pdb=" O GLN P 140 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY P 145 " --> pdb=" O LEU P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 167 removed outlier: 3.513A pdb=" N LEU P 165 " --> pdb=" O PHE P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 184 removed outlier: 3.813A pdb=" N ALA P 175 " --> pdb=" O ASP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 202 Processing helix chain 'P' and resid 206 through 219 removed outlier: 3.860A pdb=" N VAL P 210 " --> pdb=" O ASP P 206 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 326 removed outlier: 3.729A pdb=" N SER P 319 " --> pdb=" O VAL P 315 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU P 321 " --> pdb=" O PHE P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 342 removed outlier: 3.601A pdb=" N ALA P 340 " --> pdb=" O VAL P 336 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG P 341 " --> pdb=" O PHE P 337 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL P 342 " --> pdb=" O ALA P 338 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 352 removed outlier: 3.551A pdb=" N ALA P 347 " --> pdb=" O ALA P 343 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP P 349 " --> pdb=" O TRP P 345 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU P 351 " --> pdb=" O ALA P 347 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 44 removed outlier: 3.751A pdb=" N LEU R 41 " --> pdb=" O SER R 37 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN R 44 " --> pdb=" O GLN R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 57 Processing helix chain 'R' and resid 61 through 75 removed outlier: 3.871A pdb=" N LEU R 65 " --> pdb=" O THR R 61 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS R 75 " --> pdb=" O GLU R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 87 removed outlier: 3.983A pdb=" N ARG R 83 " --> pdb=" O LYS R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 110 removed outlier: 3.543A pdb=" N ALA R 98 " --> pdb=" O HIS R 94 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY R 107 " --> pdb=" O ALA R 103 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 143 removed outlier: 4.230A pdb=" N ALA R 124 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL R 126 " --> pdb=" O ARG R 122 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Proline residue: R 133 - end of helix Processing helix chain 'R' and resid 156 through 167 Processing helix chain 'R' and resid 171 through 184 removed outlier: 3.649A pdb=" N ALA R 175 " --> pdb=" O ASP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 201 Processing helix chain 'R' and resid 202 through 204 No H-bonds generated for 'chain 'R' and resid 202 through 204' Processing helix chain 'R' and resid 206 through 219 removed outlier: 3.810A pdb=" N VAL R 210 " --> pdb=" O ASP R 206 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 326 removed outlier: 4.110A pdb=" N LEU R 326 " --> pdb=" O VAL R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 341 removed outlier: 3.776A pdb=" N VAL R 336 " --> pdb=" O LEU R 332 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE R 337 " --> pdb=" O PHE R 333 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 338 " --> pdb=" O THR R 334 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE R 339 " --> pdb=" O PRO R 335 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA R 340 " --> pdb=" O VAL R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 352 removed outlier: 3.748A pdb=" N TRP R 345 " --> pdb=" O ARG R 341 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU R 346 " --> pdb=" O VAL R 342 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU R 351 " --> pdb=" O ALA R 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'C' and resid 22 through 25 Processing sheet with id=AA3, first strand: chain 'C' and resid 360 through 364 removed outlier: 8.046A pdb=" N ARG C 360 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ALA D 16 " --> pdb=" O ARG C 360 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR C 362 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU D 18 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE C 364 " --> pdb=" O LEU D 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.501A pdb=" N PHE D 23 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 24 Processing sheet with id=AA7, first strand: chain 'K' and resid 15 through 17 Processing sheet with id=AA8, first strand: chain 'K' and resid 22 through 25 Processing sheet with id=AA9, first strand: chain 'K' and resid 360 through 365 removed outlier: 8.045A pdb=" N ARG K 360 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N ALA M 16 " --> pdb=" O ARG K 360 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR K 362 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU M 18 " --> pdb=" O THR K 362 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE K 364 " --> pdb=" O LEU M 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 22 through 23 removed outlier: 3.500A pdb=" N PHE M 23 " --> pdb=" O GLU M 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 22 through 25 Processing sheet with id=AB3, first strand: chain 'Q' and resid 22 through 24 Processing sheet with id=AB4, first strand: chain 'L' and resid 15 through 17 Processing sheet with id=AB5, first strand: chain 'L' and resid 22 through 25 Processing sheet with id=AB6, first strand: chain 'L' and resid 360 through 365 removed outlier: 8.047A pdb=" N ARG L 360 " --> pdb=" O VAL N 14 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ALA N 16 " --> pdb=" O ARG L 360 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N THR L 362 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU N 18 " --> pdb=" O THR L 362 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE L 364 " --> pdb=" O LEU N 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.501A pdb=" N PHE N 23 " --> pdb=" O GLU N 32 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 22 through 25 Processing sheet with id=AB9, first strand: chain 'R' and resid 22 through 24 1578 hydrogen bonds defined for protein. 4698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.53 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5832 1.30 - 1.43: 10215 1.43 - 1.56: 20896 1.56 - 1.69: 0 1.69 - 1.82: 254 Bond restraints: 37197 Sorted by residual: bond pdb=" N PRO D 15 " pdb=" CA PRO D 15 " ideal model delta sigma weight residual 1.469 1.708 -0.239 1.28e-02 6.10e+03 3.49e+02 bond pdb=" N PRO O 15 " pdb=" CA PRO O 15 " ideal model delta sigma weight residual 1.469 1.705 -0.236 1.28e-02 6.10e+03 3.40e+02 bond pdb=" C ASN L 146 " pdb=" N ASP L 147 " ideal model delta sigma weight residual 1.331 1.242 0.089 1.59e-02 3.96e+03 3.16e+01 bond pdb=" C ASN C 146 " pdb=" N ASP C 147 " ideal model delta sigma weight residual 1.331 1.243 0.089 1.59e-02 3.96e+03 3.10e+01 bond pdb=" C ASN K 146 " pdb=" N ASP K 147 " ideal model delta sigma weight residual 1.331 1.243 0.088 1.59e-02 3.96e+03 3.07e+01 ... (remaining 37192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 49347 3.67 - 7.35: 1090 7.35 - 11.02: 85 11.02 - 14.69: 17 14.69 - 18.37: 8 Bond angle restraints: 50547 Sorted by residual: angle pdb=" C VAL O 14 " pdb=" N PRO O 15 " pdb=" CA PRO O 15 " ideal model delta sigma weight residual 119.84 138.21 -18.37 1.25e+00 6.40e-01 2.16e+02 angle pdb=" C VAL D 14 " pdb=" N PRO D 15 " pdb=" CA PRO D 15 " ideal model delta sigma weight residual 119.84 138.10 -18.26 1.25e+00 6.40e-01 2.13e+02 angle pdb=" CA PRO O 15 " pdb=" N PRO O 15 " pdb=" CD PRO O 15 " ideal model delta sigma weight residual 112.00 99.52 12.48 1.40e+00 5.10e-01 7.95e+01 angle pdb=" CA PRO D 15 " pdb=" N PRO D 15 " pdb=" CD PRO D 15 " ideal model delta sigma weight residual 112.00 100.00 12.00 1.40e+00 5.10e-01 7.35e+01 angle pdb=" N TYR K 74 " pdb=" CA TYR K 74 " pdb=" C TYR K 74 " ideal model delta sigma weight residual 113.16 103.07 10.09 1.24e+00 6.50e-01 6.62e+01 ... (remaining 50542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 18849 16.84 - 33.68: 2499 33.68 - 50.52: 610 50.52 - 67.36: 155 67.36 - 84.20: 60 Dihedral angle restraints: 22173 sinusoidal: 8748 harmonic: 13425 Sorted by residual: dihedral pdb=" CA LYS J 79 " pdb=" C LYS J 79 " pdb=" N PHE J 80 " pdb=" CA PHE J 80 " ideal model delta harmonic sigma weight residual -180.00 -147.43 -32.57 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA LYS B 79 " pdb=" C LYS B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA LYS I 79 " pdb=" C LYS I 79 " pdb=" N PHE I 80 " pdb=" CA PHE I 80 " ideal model delta harmonic sigma weight residual -180.00 -147.49 -32.51 0 5.00e+00 4.00e-02 4.23e+01 ... (remaining 22170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4897 0.092 - 0.184: 664 0.184 - 0.275: 76 0.275 - 0.367: 25 0.367 - 0.459: 14 Chirality restraints: 5676 Sorted by residual: chirality pdb=" CA PRO O 15 " pdb=" N PRO O 15 " pdb=" C PRO O 15 " pdb=" CB PRO O 15 " both_signs ideal model delta sigma weight residual False 2.72 3.18 -0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA TYR Q 120 " pdb=" N TYR Q 120 " pdb=" C TYR Q 120 " pdb=" CB TYR Q 120 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA TYR H 120 " pdb=" N TYR H 120 " pdb=" C TYR H 120 " pdb=" CB TYR H 120 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.42 2.00e-01 2.50e+01 4.51e+00 ... (remaining 5673 not shown) Planarity restraints: 6465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY P 367 " -0.032 2.00e-02 2.50e+03 6.46e-02 4.17e+01 pdb=" C GLY P 367 " 0.112 2.00e-02 2.50e+03 pdb=" O GLY P 367 " -0.043 2.00e-02 2.50e+03 pdb=" N SER P 368 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 367 " 0.032 2.00e-02 2.50e+03 6.45e-02 4.16e+01 pdb=" C GLY G 367 " -0.112 2.00e-02 2.50e+03 pdb=" O GLY G 367 " 0.043 2.00e-02 2.50e+03 pdb=" N SER G 368 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 367 " -0.032 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C GLY O 367 " 0.111 2.00e-02 2.50e+03 pdb=" O GLY O 367 " -0.043 2.00e-02 2.50e+03 pdb=" N SER O 368 " -0.037 2.00e-02 2.50e+03 ... (remaining 6462 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 38 2.27 - 2.92: 16626 2.92 - 3.58: 44562 3.58 - 4.24: 66865 4.24 - 4.90: 111979 Nonbonded interactions: 240070 Sorted by model distance: nonbonded pdb=" O VAL B 322 " pdb=" CD1 LEU B 326 " model vdw 1.607 3.460 nonbonded pdb=" O VAL J 322 " pdb=" CD1 LEU J 326 " model vdw 1.607 3.460 nonbonded pdb=" O VAL I 322 " pdb=" CD1 LEU I 326 " model vdw 1.608 3.460 nonbonded pdb=" OH TYR C 365 " pdb=" O SER D 20 " model vdw 1.631 3.040 nonbonded pdb=" O PHE O 109 " pdb=" NH1 ARG O 112 " model vdw 2.034 3.120 ... (remaining 240065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 111 or resid 119 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 352)) selection = (chain 'B' and (resid 33 through 42 or resid 47 through 167 or (resid 168 and (n \ ame N or name CA or name C or name O or name CB )) or resid 169 through 175 or ( \ resid 176 and (name N or name CA or name C or name O or name CB )) or resid 177 \ through 352)) selection = (chain 'E' and (resid 33 through 111 or resid 119 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 352)) selection = (chain 'F' and (resid 33 through 111 or resid 119 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 352)) selection = (chain 'I' and (resid 33 through 42 or resid 47 through 167 or (resid 168 and (n \ ame N or name CA or name C or name O or name CB )) or resid 169 through 175 or ( \ resid 176 and (name N or name CA or name C or name O or name CB )) or resid 177 \ through 352)) selection = (chain 'J' and (resid 33 through 42 or resid 47 through 167 or (resid 168 and (n \ ame N or name CA or name C or name O or name CB )) or resid 169 through 175 or ( \ resid 176 and (name N or name CA or name C or name O or name CB )) or resid 177 \ through 352)) } ncs_group { reference = (chain 'C' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 371 or (resid 372 and (name N or name CA or name C or name O \ or name CB )) or resid 373 through 375)) selection = (chain 'D' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) or \ resid 169 through 219 or resid 314 through 324 or (resid 325 and (name N or nam \ e CA or name C or name O or name CB )) or resid 326 through 375)) selection = (chain 'G' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 167 or (resid 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 219 or resid 314 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) \ or resid 326 through 371 or (resid 372 and (name N or name CA or name C or name \ O or name CB )) or resid 373 through 375)) selection = (chain 'H' and (resid 9 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 112 or resid 119 through 167 or (re \ sid 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 219 or resid 314 through 371 or (resid 372 and (name N or name CA or name \ C or name O or name CB )) or resid 373 through 375)) selection = (chain 'K' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 371 or (resid 372 and (name N or name CA or name C or name O \ or name CB )) or resid 373 through 375)) selection = (chain 'L' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 371 or (resid 372 and (name N or name CA or name C or name O \ or name CB )) or resid 373 through 375)) selection = (chain 'M' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) or \ resid 169 through 219 or resid 314 through 324 or (resid 325 and (name N or nam \ e CA or name C or name O or name CB )) or resid 326 through 375)) selection = (chain 'N' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) or \ resid 169 through 219 or resid 314 through 324 or (resid 325 and (name N or nam \ e CA or name C or name O or name CB )) or resid 326 through 375)) selection = (chain 'O' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 167 or (resid 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 219 or resid 314 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) \ or resid 326 through 371 or (resid 372 and (name N or name CA or name C or name \ O or name CB )) or resid 373 through 375)) selection = (chain 'P' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 167 or (resid 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 219 or resid 314 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) \ or resid 326 through 371 or (resid 372 and (name N or name CA or name C or name \ O or name CB )) or resid 373 through 375)) selection = (chain 'Q' and (resid 9 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 112 or resid 119 through 167 or (re \ sid 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 219 or resid 314 through 371 or (resid 372 and (name N or name CA or name \ C or name O or name CB )) or resid 373 through 375)) selection = (chain 'R' and (resid 9 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 112 or resid 119 through 167 or (re \ sid 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 219 or resid 314 through 371 or (resid 372 and (name N or name CA or name \ C or name O or name CB )) or resid 373 through 375)) } 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=0.00 max=1.00 mean=0.97 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: 10.990 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: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 28.470 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.012 0.239 37197 Z= 0.561 Angle : 1.324 18.368 50547 Z= 0.791 Chirality : 0.070 0.459 5676 Planarity : 0.009 0.108 6465 Dihedral : 16.843 84.196 13467 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 1.08 % Allowed : 12.55 % Favored : 86.37 % Rotamer: Outliers : 4.59 % Allowed : 16.46 % Favored : 78.95 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.23 (0.09), residues: 4455 helix: -2.72 (0.08), residues: 2598 sheet: None (None), residues: 0 loop : -4.61 (0.10), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 112 TYR 0.045 0.004 TYR N 318 PHE 0.044 0.004 PHE D 337 TRP 0.017 0.003 TRP Q 345 HIS 0.010 0.002 HIS Q 188 Details of bonding type rmsd covalent geometry : bond 0.01192 (37197) covalent geometry : angle 1.32400 (50547) hydrogen bonds : bond 0.20253 ( 1578) hydrogen bonds : angle 7.88044 ( 4698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 430 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.5959 (mmm160) REVERT: A 143 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8323 (ttp-170) REVERT: A 171 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.6351 (m-30) REVERT: A 324 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6559 (tpt90) REVERT: B 187 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: C 176 ARG cc_start: 0.7159 (tpm170) cc_final: 0.6796 (mmp-170) REVERT: D 325 LYS cc_start: 0.7637 (tppp) cc_final: 0.6783 (ttmt) REVERT: G 167 GLU cc_start: 0.6898 (pm20) cc_final: 0.6549 (pm20) REVERT: G 359 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: H 74 TYR cc_start: 0.6356 (t80) cc_final: 0.6120 (t80) REVERT: H 120 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: H 324 ARG cc_start: 0.7347 (tpt-90) cc_final: 0.6651 (tmm160) REVERT: E 81 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.5982 (mmm160) REVERT: E 171 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6063 (m-30) REVERT: E 324 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6274 (tpt90) REVERT: I 142 ILE cc_start: 0.7540 (mm) cc_final: 0.7282 (mt) REVERT: I 187 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: K 356 ASN cc_start: 0.7779 (p0) cc_final: 0.7576 (p0) REVERT: M 112 ARG cc_start: 0.6538 (mmt-90) cc_final: 0.6133 (mtm110) REVERT: M 325 LYS cc_start: 0.7801 (tppp) cc_final: 0.6952 (ttmt) REVERT: O 121 ILE cc_start: 0.8325 (mp) cc_final: 0.8007 (mm) REVERT: Q 74 TYR cc_start: 0.6411 (t80) cc_final: 0.6132 (t80) REVERT: Q 120 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6397 (t80) REVERT: Q 324 ARG cc_start: 0.7331 (tpt-90) cc_final: 0.6744 (tmm160) REVERT: F 81 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5754 (mmm160) REVERT: F 143 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8268 (ttp-170) REVERT: F 171 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.6113 (m-30) REVERT: F 324 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6206 (tpt90) REVERT: J 142 ILE cc_start: 0.7584 (mm) cc_final: 0.7258 (mt) REVERT: J 187 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: N 325 LYS cc_start: 0.7823 (tppp) cc_final: 0.6927 (ttmt) REVERT: P 167 GLU cc_start: 0.7016 (pm20) cc_final: 0.6645 (tp30) REVERT: P 184 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5828 (mp) REVERT: P 359 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: R 74 TYR cc_start: 0.6520 (t80) cc_final: 0.6256 (t80) REVERT: R 120 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: R 324 ARG cc_start: 0.7345 (tpt-90) cc_final: 0.6717 (tmm160) outliers start: 175 outliers final: 93 residues processed: 589 average time/residue: 0.2611 time to fit residues: 230.1587 Evaluate side-chains 410 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 297 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 360 ARG Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 359 PHE Chi-restraints excluded: chain G residue 368 SER Chi-restraints excluded: chain G residue 369 ARG Chi-restraints excluded: chain H residue 8 ARG Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 112 ARG Chi-restraints excluded: chain H residue 120 TYR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 152 ARG Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 77 ARG Chi-restraints excluded: chain M residue 146 ASN Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 324 ARG Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 369 ARG Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 359 PHE Chi-restraints excluded: chain O residue 369 ARG Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain Q residue 79 LYS Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 112 ARG Chi-restraints excluded: chain Q residue 120 TYR Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 206 ASP Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain Q residue 369 ARG Chi-restraints excluded: chain Q residue 371 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 324 ARG Chi-restraints excluded: chain F residue 325 LYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain L residue 5 SER Chi-restraints excluded: chain L residue 6 GLU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 368 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 77 ARG Chi-restraints excluded: chain N residue 146 ASN Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain N residue 360 ARG Chi-restraints excluded: chain N residue 369 ARG Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain P residue 359 PHE Chi-restraints excluded: chain P residue 369 ARG Chi-restraints excluded: chain R residue 6 GLU Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 112 ARG Chi-restraints excluded: chain R residue 120 TYR Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 152 ARG Chi-restraints excluded: chain R residue 206 ASP Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.9980 chunk 424 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 188 HIS B 140 GLN B 146 ASN C 40 GLN C 356 ASN D 140 GLN D 160 ASN G 100 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 HIS H 58 HIS E 188 HIS I 146 ASN K 40 GLN M 140 GLN M 160 ASN O 100 GLN O 160 ASN O 188 HIS Q 58 HIS F 188 HIS J 146 ASN L 40 GLN L 356 ASN N 140 GLN N 160 ASN P 100 GLN ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 HIS R 58 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.190372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.149794 restraints weight = 49463.987| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.31 r_work: 0.3779 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37197 Z= 0.154 Angle : 0.678 10.771 50547 Z= 0.357 Chirality : 0.042 0.186 5676 Planarity : 0.006 0.056 6465 Dihedral : 8.336 59.645 5317 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.65 % Rotamer: Outliers : 3.20 % Allowed : 18.69 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.12), residues: 4455 helix: -0.79 (0.10), residues: 2610 sheet: None (None), residues: 0 loop : -3.61 (0.12), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 28 TYR 0.019 0.001 TYR C 365 PHE 0.016 0.001 PHE K 68 TRP 0.018 0.001 TRP C 349 HIS 0.007 0.001 HIS N 58 Details of bonding type rmsd covalent geometry : bond 0.00316 (37197) covalent geometry : angle 0.67800 (50547) hydrogen bonds : bond 0.05729 ( 1578) hydrogen bonds : angle 4.96316 ( 4698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 402 time to evaluate : 1.118 Fit side-chains REVERT: A 81 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.5861 (mmm160) REVERT: C 176 ARG cc_start: 0.6128 (tpm170) cc_final: 0.5812 (mmp-170) REVERT: C 356 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.6838 (p0) REVERT: D 360 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7039 (ppt-90) REVERT: G 167 GLU cc_start: 0.7033 (pm20) cc_final: 0.6624 (tp30) REVERT: G 182 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7864 (mp) REVERT: G 187 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: H 21 ILE cc_start: 0.6872 (pt) cc_final: 0.6667 (mt) REVERT: H 110 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6147 (p90) REVERT: H 188 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.6089 (t-170) REVERT: H 324 ARG cc_start: 0.7263 (tpt-90) cc_final: 0.6438 (tmm160) REVERT: E 81 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.5784 (mmm160) REVERT: E 171 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6118 (m-30) REVERT: K 152 ARG cc_start: 0.6423 (mtm110) cc_final: 0.6164 (mtm110) REVERT: M 112 ARG cc_start: 0.6417 (mmt-90) cc_final: 0.5967 (mtm110) REVERT: M 120 TYR cc_start: 0.7134 (t80) cc_final: 0.6904 (t80) REVERT: M 187 GLU cc_start: 0.8365 (tp30) cc_final: 0.8078 (tp30) REVERT: M 360 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7202 (ppt-90) REVERT: O 187 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: Q 110 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6308 (p90) REVERT: Q 188 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6230 (t-170) REVERT: Q 324 ARG cc_start: 0.7272 (tpt-90) cc_final: 0.6508 (tmm160) REVERT: Q 371 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7184 (mt) REVERT: F 81 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.5859 (mmm160) REVERT: F 171 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6204 (m-30) REVERT: J 142 ILE cc_start: 0.7115 (mm) cc_final: 0.6870 (mt) REVERT: N 360 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6946 (ppt-90) REVERT: P 184 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5667 (mp) REVERT: P 187 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: R 74 TYR cc_start: 0.6543 (t80) cc_final: 0.6332 (t80) REVERT: R 110 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.5685 (p90) REVERT: R 324 ARG cc_start: 0.7249 (tpt-90) cc_final: 0.6480 (tmm160) outliers start: 122 outliers final: 61 residues processed: 504 average time/residue: 0.2109 time to fit residues: 171.3719 Evaluate side-chains 402 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 321 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 360 ARG Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 324 ARG Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 188 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 371 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 217 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain L residue 368 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain N residue 360 ARG Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 4.9990 chunk 326 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 chunk 444 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 313 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 354 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 GLN K 94 HIS K 356 ASN M 354 ASN O 160 ASN ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.186924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.146450 restraints weight = 49508.831| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.29 r_work: 0.3726 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37197 Z= 0.182 Angle : 0.699 12.730 50547 Z= 0.363 Chirality : 0.043 0.159 5676 Planarity : 0.006 0.053 6465 Dihedral : 6.638 59.819 5120 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.31 % Favored : 91.56 % Rotamer: Outliers : 4.20 % Allowed : 20.18 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.12), residues: 4455 helix: -0.21 (0.10), residues: 2586 sheet: None (None), residues: 0 loop : -3.19 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 369 TYR 0.030 0.002 TYR O 74 PHE 0.022 0.002 PHE M 80 TRP 0.014 0.001 TRP K 349 HIS 0.005 0.001 HIS N 58 Details of bonding type rmsd covalent geometry : bond 0.00410 (37197) covalent geometry : angle 0.69911 (50547) hydrogen bonds : bond 0.07095 ( 1578) hydrogen bonds : angle 4.82840 ( 4698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 329 time to evaluate : 1.120 Fit side-chains REVERT: A 81 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.5903 (mmm160) REVERT: B 187 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: C 86 MET cc_start: 0.7523 (ttm) cc_final: 0.7234 (mtp) REVERT: C 176 ARG cc_start: 0.6329 (tpm170) cc_final: 0.5998 (mmp-170) REVERT: C 356 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.6761 (p0) REVERT: D 360 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6925 (ppt-90) REVERT: G 167 GLU cc_start: 0.7007 (pm20) cc_final: 0.6559 (tp30) REVERT: G 182 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7782 (mp) REVERT: G 187 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: H 17 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7461 (p) REVERT: H 110 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.5771 (p90) REVERT: H 188 HIS cc_start: 0.7129 (OUTLIER) cc_final: 0.6196 (t-170) REVERT: H 321 LEU cc_start: 0.4378 (OUTLIER) cc_final: 0.4050 (mm) REVERT: H 324 ARG cc_start: 0.7251 (tpt-90) cc_final: 0.6404 (tmm160) REVERT: E 81 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.5867 (mmm160) REVERT: E 171 ASP cc_start: 0.6501 (OUTLIER) cc_final: 0.6223 (m-30) REVERT: E 324 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6665 (tpt90) REVERT: K 106 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7274 (mp) REVERT: K 358 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7769 (pt) REVERT: M 112 ARG cc_start: 0.6494 (mmt-90) cc_final: 0.5955 (mtm110) REVERT: M 360 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7015 (ppt-90) REVERT: O 106 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7709 (tt) REVERT: O 128 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6776 (mm) REVERT: O 187 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: Q 110 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.5945 (p90) REVERT: Q 188 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6279 (t-170) REVERT: Q 324 ARG cc_start: 0.7200 (tpt-90) cc_final: 0.6491 (tmm160) REVERT: F 81 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.5930 (mmm160) REVERT: J 142 ILE cc_start: 0.7398 (mm) cc_final: 0.7141 (mt) REVERT: L 356 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.6815 (p0) REVERT: N 360 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.6835 (ppt-90) REVERT: P 128 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6584 (mm) REVERT: P 184 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5689 (mp) REVERT: P 187 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: R 74 TYR cc_start: 0.6513 (t80) cc_final: 0.6245 (t80) REVERT: R 110 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.6091 (p90) REVERT: R 188 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6880 (t-90) REVERT: R 324 ARG cc_start: 0.7193 (tpt-90) cc_final: 0.6417 (tmm160) outliers start: 160 outliers final: 91 residues processed: 454 average time/residue: 0.2207 time to fit residues: 163.7437 Evaluate side-chains 407 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 287 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 360 ARG Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 324 ARG Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain O residue 165 LEU Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 188 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain L residue 368 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain N residue 360 ARG Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 182 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 188 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 399 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 chunk 73 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 195 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 357 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 216 optimal weight: 0.5980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 ASN I 352 GLN K 356 ASN O 160 ASN L 356 ASN N 354 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.193491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154156 restraints weight = 48960.783| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.26 r_work: 0.3832 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 37197 Z= 0.116 Angle : 0.568 12.417 50547 Z= 0.291 Chirality : 0.039 0.147 5676 Planarity : 0.005 0.047 6465 Dihedral : 5.784 55.905 5115 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.39 % Favored : 94.48 % Rotamer: Outliers : 3.31 % Allowed : 21.78 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.13), residues: 4455 helix: 0.44 (0.10), residues: 2595 sheet: None (None), residues: 0 loop : -2.76 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 28 TYR 0.013 0.001 TYR N 120 PHE 0.011 0.001 PHE L 68 TRP 0.014 0.001 TRP L 349 HIS 0.005 0.001 HIS M 58 Details of bonding type rmsd covalent geometry : bond 0.00235 (37197) covalent geometry : angle 0.56771 (50547) hydrogen bonds : bond 0.04264 ( 1578) hydrogen bonds : angle 4.34887 ( 4698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 374 time to evaluate : 1.423 Fit side-chains REVERT: B 81 ARG cc_start: 0.7489 (mmm160) cc_final: 0.6898 (mtm110) REVERT: B 109 PHE cc_start: 0.6241 (OUTLIER) cc_final: 0.4651 (t80) REVERT: B 187 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.6796 (tt0) REVERT: C 86 MET cc_start: 0.7394 (ttm) cc_final: 0.7180 (mtp) REVERT: C 176 ARG cc_start: 0.5951 (tpm170) cc_final: 0.5718 (mmp-170) REVERT: C 356 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.6823 (p0) REVERT: G 167 GLU cc_start: 0.6819 (pm20) cc_final: 0.6486 (tp30) REVERT: G 187 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: G 190 ILE cc_start: 0.4777 (OUTLIER) cc_final: 0.4565 (mt) REVERT: H 17 THR cc_start: 0.7524 (OUTLIER) cc_final: 0.7273 (p) REVERT: H 110 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.5972 (p90) REVERT: H 324 ARG cc_start: 0.7152 (tpt-90) cc_final: 0.6346 (tmm160) REVERT: I 81 ARG cc_start: 0.7417 (mmm160) cc_final: 0.6950 (mtm110) REVERT: I 187 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6844 (tt0) REVERT: M 112 ARG cc_start: 0.6481 (mmt-90) cc_final: 0.6000 (mtm110) REVERT: M 120 TYR cc_start: 0.7076 (t80) cc_final: 0.6875 (t80) REVERT: M 360 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7879 (ptp90) REVERT: O 187 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7248 (tt0) REVERT: Q 110 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.6155 (p90) REVERT: Q 324 ARG cc_start: 0.7158 (tpt-90) cc_final: 0.6397 (tmm160) REVERT: F 81 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.5936 (mmm160) REVERT: J 81 ARG cc_start: 0.7512 (mmm160) cc_final: 0.6915 (mtm110) REVERT: J 187 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: N 324 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5422 (ttp-170) REVERT: N 360 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7631 (ptp90) REVERT: P 106 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7005 (tt) REVERT: P 121 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6638 (mm) REVERT: P 128 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6289 (mm) REVERT: P 184 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5642 (mp) REVERT: P 187 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: R 110 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.5735 (p90) REVERT: R 324 ARG cc_start: 0.7171 (tpt-90) cc_final: 0.6437 (tmm160) outliers start: 126 outliers final: 65 residues processed: 482 average time/residue: 0.2306 time to fit residues: 182.1027 Evaluate side-chains 403 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 317 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 324 ARG Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 371 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain N residue 360 ARG Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 45 SER Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 24 optimal weight: 8.9990 chunk 436 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 414 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 430 optimal weight: 0.0870 chunk 393 optimal weight: 0.6980 chunk 448 optimal weight: 0.2980 chunk 118 optimal weight: 4.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 352 GLN O 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.194277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.154633 restraints weight = 49951.652| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.27 r_work: 0.3840 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37197 Z= 0.123 Angle : 0.584 12.638 50547 Z= 0.297 Chirality : 0.039 0.138 5676 Planarity : 0.005 0.044 6465 Dihedral : 5.277 55.889 5079 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.29 % Favored : 93.58 % Rotamer: Outliers : 3.46 % Allowed : 23.04 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.13), residues: 4455 helix: 0.64 (0.10), residues: 2595 sheet: None (None), residues: 0 loop : -2.50 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 357 TYR 0.020 0.001 TYR R 74 PHE 0.013 0.001 PHE M 80 TRP 0.012 0.001 TRP K 349 HIS 0.004 0.001 HIS N 58 Details of bonding type rmsd covalent geometry : bond 0.00253 (37197) covalent geometry : angle 0.58406 (50547) hydrogen bonds : bond 0.04669 ( 1578) hydrogen bonds : angle 4.30502 ( 4698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 348 time to evaluate : 1.413 Fit side-chains REVERT: A 81 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.5891 (mmm160) REVERT: B 81 ARG cc_start: 0.7487 (mmm160) cc_final: 0.6889 (mtm110) REVERT: C 176 ARG cc_start: 0.5920 (tpm170) cc_final: 0.5691 (mmp-170) REVERT: C 356 ASN cc_start: 0.7683 (p0) cc_final: 0.7052 (p0) REVERT: G 166 THR cc_start: 0.6609 (OUTLIER) cc_final: 0.5911 (m) REVERT: G 167 GLU cc_start: 0.6816 (pm20) cc_final: 0.6508 (tp30) REVERT: G 182 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8032 (mp) REVERT: G 187 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: H 17 THR cc_start: 0.7537 (OUTLIER) cc_final: 0.7277 (p) REVERT: H 110 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.5997 (p90) REVERT: H 185 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.6967 (t-90) REVERT: H 324 ARG cc_start: 0.7170 (tpt-90) cc_final: 0.6400 (tmm160) REVERT: E 81 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.5950 (mmm160) REVERT: I 81 ARG cc_start: 0.7414 (mmm160) cc_final: 0.6950 (mtm110) REVERT: I 187 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: M 112 ARG cc_start: 0.6460 (mmt-90) cc_final: 0.5992 (mtm110) REVERT: M 120 TYR cc_start: 0.7019 (t80) cc_final: 0.6798 (t80) REVERT: O 187 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: Q 110 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.6134 (p90) REVERT: Q 185 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.6906 (t-90) REVERT: Q 324 ARG cc_start: 0.7210 (tpt-90) cc_final: 0.6483 (tmm160) REVERT: J 81 ARG cc_start: 0.7515 (mmm160) cc_final: 0.6922 (mtm110) REVERT: J 187 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: N 324 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5560 (ttp-170) REVERT: N 360 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7740 (ptp90) REVERT: P 106 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7112 (tt) REVERT: P 121 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.6823 (mm) REVERT: P 128 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6306 (mm) REVERT: P 184 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5696 (mp) REVERT: P 187 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: R 110 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.5885 (p90) REVERT: R 185 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7014 (t-90) REVERT: R 324 ARG cc_start: 0.7140 (tpt-90) cc_final: 0.6393 (tmm160) outliers start: 132 outliers final: 83 residues processed: 458 average time/residue: 0.2290 time to fit residues: 173.0196 Evaluate side-chains 423 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 318 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 185 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 371 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain N residue 360 ARG Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 45 SER Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 182 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain P residue 371 LEU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 251 optimal weight: 0.4980 chunk 150 optimal weight: 10.0000 chunk 350 optimal weight: 2.9990 chunk 420 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 372 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 356 ASN O 160 ASN L 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.191902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.151690 restraints weight = 49455.799| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.27 r_work: 0.3813 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 37197 Z= 0.141 Angle : 0.609 12.928 50547 Z= 0.311 Chirality : 0.041 0.176 5676 Planarity : 0.005 0.059 6465 Dihedral : 5.179 56.879 5061 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.76 % Favored : 93.13 % Rotamer: Outliers : 4.17 % Allowed : 23.44 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.13), residues: 4455 helix: 0.65 (0.10), residues: 2595 sheet: None (None), residues: 0 loop : -2.43 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 28 TYR 0.034 0.001 TYR P 74 PHE 0.018 0.001 PHE M 80 TRP 0.011 0.001 TRP C 349 HIS 0.004 0.001 HIS M 185 Details of bonding type rmsd covalent geometry : bond 0.00302 (37197) covalent geometry : angle 0.60923 (50547) hydrogen bonds : bond 0.05456 ( 1578) hydrogen bonds : angle 4.40826 ( 4698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 337 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.6002 (mmm160) REVERT: B 81 ARG cc_start: 0.7550 (mmm160) cc_final: 0.6965 (mtm110) REVERT: C 176 ARG cc_start: 0.6038 (tpm170) cc_final: 0.5816 (mmp-170) REVERT: G 106 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7403 (tt) REVERT: G 166 THR cc_start: 0.6704 (OUTLIER) cc_final: 0.6034 (m) REVERT: G 167 GLU cc_start: 0.6841 (pm20) cc_final: 0.6483 (tp30) REVERT: G 182 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7943 (mp) REVERT: G 187 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: H 185 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7013 (t-90) REVERT: H 313 PRO cc_start: 0.5217 (Cg_exo) cc_final: 0.5001 (Cg_endo) REVERT: H 324 ARG cc_start: 0.7196 (tpt-90) cc_final: 0.6450 (tmm160) REVERT: E 81 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6019 (mmm160) REVERT: I 81 ARG cc_start: 0.7374 (mmm160) cc_final: 0.6987 (mtm110) REVERT: M 360 ARG cc_start: 0.7748 (ptp90) cc_final: 0.7349 (mtm-85) REVERT: O 187 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: Q 165 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7488 (tt) REVERT: Q 185 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.6946 (t-90) REVERT: Q 324 ARG cc_start: 0.7183 (tpt-90) cc_final: 0.6462 (tmm160) REVERT: F 81 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.6046 (mmm160) REVERT: J 81 ARG cc_start: 0.7497 (mmm160) cc_final: 0.6963 (mtm110) REVERT: J 187 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: L 356 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.6846 (p0) REVERT: N 360 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7729 (ptp90) REVERT: P 106 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7220 (tt) REVERT: P 121 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7189 (mm) REVERT: P 128 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6402 (mm) REVERT: P 184 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5655 (mp) REVERT: P 187 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: R 110 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.6186 (p90) REVERT: R 185 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7021 (t-90) REVERT: R 324 ARG cc_start: 0.7137 (tpt-90) cc_final: 0.6359 (tmm160) outliers start: 159 outliers final: 98 residues processed: 466 average time/residue: 0.2303 time to fit residues: 176.2561 Evaluate side-chains 425 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 306 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 165 LEU Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 190 ILE Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 165 LEU Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 185 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 371 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 146 ASN Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 360 ARG Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 45 SER Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 98 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 86 optimal weight: 0.0470 chunk 231 optimal weight: 1.9990 chunk 359 optimal weight: 4.9990 chunk 415 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 366 optimal weight: 0.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 ASN K 356 ASN O 160 ASN L 356 ASN P 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.193421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.153070 restraints weight = 49392.819| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.25 r_work: 0.3837 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 37197 Z= 0.125 Angle : 0.588 14.046 50547 Z= 0.297 Chirality : 0.040 0.174 5676 Planarity : 0.005 0.062 6465 Dihedral : 5.009 57.059 5057 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.38 % Rotamer: Outliers : 3.86 % Allowed : 24.02 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.13), residues: 4455 helix: 0.78 (0.10), residues: 2613 sheet: None (None), residues: 0 loop : -2.29 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 28 TYR 0.017 0.001 TYR H 74 PHE 0.013 0.001 PHE D 80 TRP 0.011 0.001 TRP C 349 HIS 0.003 0.001 HIS N 58 Details of bonding type rmsd covalent geometry : bond 0.00263 (37197) covalent geometry : angle 0.58810 (50547) hydrogen bonds : bond 0.04765 ( 1578) hydrogen bonds : angle 4.32527 ( 4698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 353 time to evaluate : 1.443 Fit side-chains REVERT: A 81 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.5965 (mmm160) REVERT: B 81 ARG cc_start: 0.7506 (mmm160) cc_final: 0.6960 (mtm110) REVERT: B 187 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: B 203 THR cc_start: 0.7093 (t) cc_final: 0.6854 (t) REVERT: C 176 ARG cc_start: 0.5951 (tpm170) cc_final: 0.5732 (mmp-170) REVERT: D 31 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8172 (tt) REVERT: G 166 THR cc_start: 0.6652 (OUTLIER) cc_final: 0.5964 (m) REVERT: G 167 GLU cc_start: 0.6810 (pm20) cc_final: 0.6466 (tp30) REVERT: G 182 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7876 (mp) REVERT: G 187 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: H 185 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.6973 (t-90) REVERT: H 313 PRO cc_start: 0.5317 (Cg_exo) cc_final: 0.5116 (Cg_endo) REVERT: H 324 ARG cc_start: 0.7188 (tpt-90) cc_final: 0.6417 (tmm160) REVERT: E 81 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.5972 (mmm160) REVERT: I 81 ARG cc_start: 0.7381 (mmm160) cc_final: 0.6981 (mtm110) REVERT: I 187 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: K 356 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.6941 (p0) REVERT: M 31 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7940 (tt) REVERT: O 74 TYR cc_start: 0.7241 (t80) cc_final: 0.7033 (t80) REVERT: O 187 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: Q 185 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.6944 (t-90) REVERT: Q 324 ARG cc_start: 0.7160 (tpt-90) cc_final: 0.6431 (tmm160) REVERT: F 81 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6000 (mmm160) REVERT: J 81 ARG cc_start: 0.7521 (mmm160) cc_final: 0.6984 (mtm110) REVERT: J 187 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: L 356 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.6917 (p0) REVERT: L 358 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7730 (pt) REVERT: N 31 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8003 (tt) REVERT: P 106 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7145 (tt) REVERT: P 121 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7016 (mm) REVERT: P 128 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6390 (mm) REVERT: P 184 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5569 (mp) REVERT: P 187 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: R 110 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.6023 (p90) REVERT: R 185 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.7043 (t-90) REVERT: R 324 ARG cc_start: 0.7074 (tpt-90) cc_final: 0.6318 (tmm160) outliers start: 147 outliers final: 108 residues processed: 474 average time/residue: 0.2190 time to fit residues: 173.5792 Evaluate side-chains 451 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 318 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 146 ASN Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 317 PHE Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 182 LEU Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 185 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 371 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain L residue 358 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 317 PHE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 45 SER Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 182 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain P residue 371 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 415 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 382 optimal weight: 0.5980 chunk 293 optimal weight: 0.5980 chunk 434 optimal weight: 0.0370 chunk 317 optimal weight: 1.9990 chunk 245 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 281 optimal weight: 0.0370 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 160 ASN J 352 GLN L 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.197612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.159388 restraints weight = 49206.259| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.27 r_work: 0.3889 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 37197 Z= 0.108 Angle : 0.545 13.639 50547 Z= 0.274 Chirality : 0.038 0.174 5676 Planarity : 0.004 0.062 6465 Dihedral : 4.620 57.003 5053 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.59 % Rotamer: Outliers : 2.86 % Allowed : 25.35 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.13), residues: 4455 helix: 1.08 (0.10), residues: 2631 sheet: None (None), residues: 0 loop : -2.05 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 357 TYR 0.014 0.001 TYR R 163 PHE 0.008 0.001 PHE K 359 TRP 0.012 0.001 TRP L 349 HIS 0.003 0.000 HIS N 58 Details of bonding type rmsd covalent geometry : bond 0.00216 (37197) covalent geometry : angle 0.54509 (50547) hydrogen bonds : bond 0.03512 ( 1578) hydrogen bonds : angle 4.14819 ( 4698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 371 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.5852 (mmm160) REVERT: A 350 LYS cc_start: 0.7693 (tppp) cc_final: 0.7490 (tptt) REVERT: B 81 ARG cc_start: 0.7498 (mmm160) cc_final: 0.6875 (mtm110) REVERT: B 109 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.4700 (t80) REVERT: B 187 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: D 31 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (tt) REVERT: G 166 THR cc_start: 0.6595 (OUTLIER) cc_final: 0.5909 (m) REVERT: G 167 GLU cc_start: 0.6723 (pm20) cc_final: 0.6420 (tp30) REVERT: H 185 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.6941 (t-90) REVERT: H 324 ARG cc_start: 0.7120 (tpt-90) cc_final: 0.6327 (tmm160) REVERT: E 81 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.5911 (mmm160) REVERT: I 81 ARG cc_start: 0.7412 (mmm160) cc_final: 0.6899 (mtm110) REVERT: I 187 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: M 31 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7977 (tt) REVERT: O 74 TYR cc_start: 0.7079 (t80) cc_final: 0.6811 (t80) REVERT: Q 185 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6871 (t-90) REVERT: Q 324 ARG cc_start: 0.7139 (tpt-90) cc_final: 0.6392 (tmm160) REVERT: F 81 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.5979 (mmt90) REVERT: F 352 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7134 (tp40) REVERT: J 81 ARG cc_start: 0.7432 (mmm160) cc_final: 0.6795 (mtm110) REVERT: J 187 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: L 86 MET cc_start: 0.6846 (ttt) cc_final: 0.6581 (ttt) REVERT: N 31 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7956 (tt) REVERT: N 360 ARG cc_start: 0.7625 (ptp90) cc_final: 0.7399 (mtm-85) REVERT: P 121 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.6811 (mm) REVERT: R 86 MET cc_start: 0.8533 (mtt) cc_final: 0.8312 (mtp) REVERT: R 110 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.6021 (p90) REVERT: R 185 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.6831 (t-90) REVERT: R 324 ARG cc_start: 0.7083 (tpt-90) cc_final: 0.6299 (tmm160) outliers start: 109 outliers final: 75 residues processed: 466 average time/residue: 0.2144 time to fit residues: 168.3691 Evaluate side-chains 433 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 342 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 317 PHE Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 185 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 45 SER Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 361 optimal weight: 0.8980 chunk 338 optimal weight: 0.7980 chunk 236 optimal weight: 0.1980 chunk 231 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 ASN G 356 ASN K 356 ASN O 160 ASN J 352 GLN L 356 ASN P 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.193106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153037 restraints weight = 49479.031| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.26 r_work: 0.3827 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37197 Z= 0.134 Angle : 0.598 14.080 50547 Z= 0.303 Chirality : 0.040 0.177 5676 Planarity : 0.005 0.088 6465 Dihedral : 4.777 57.853 5051 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 3.02 % Allowed : 25.62 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.13), residues: 4455 helix: 1.01 (0.10), residues: 2601 sheet: None (None), residues: 0 loop : -2.13 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 28 TYR 0.014 0.001 TYR H 74 PHE 0.018 0.001 PHE M 80 TRP 0.010 0.001 TRP K 349 HIS 0.004 0.001 HIS N 185 Details of bonding type rmsd covalent geometry : bond 0.00289 (37197) covalent geometry : angle 0.59801 (50547) hydrogen bonds : bond 0.05095 ( 1578) hydrogen bonds : angle 4.30648 ( 4698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 340 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.5943 (mmm160) REVERT: A 350 LYS cc_start: 0.7760 (tppp) cc_final: 0.7542 (tptt) REVERT: B 81 ARG cc_start: 0.7496 (mmm160) cc_final: 0.6989 (mtm110) REVERT: D 31 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8152 (tt) REVERT: G 166 THR cc_start: 0.6631 (OUTLIER) cc_final: 0.6000 (m) REVERT: G 167 GLU cc_start: 0.6791 (pm20) cc_final: 0.6487 (tp30) REVERT: G 187 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: H 185 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.6929 (t-90) REVERT: H 324 ARG cc_start: 0.7210 (tpt-90) cc_final: 0.6457 (tmm160) REVERT: E 81 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.5987 (mmm160) REVERT: I 81 ARG cc_start: 0.7400 (mmm160) cc_final: 0.7008 (mtm110) REVERT: I 202 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.7979 (p) REVERT: M 31 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8022 (tt) REVERT: O 27 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7439 (mm110) REVERT: O 74 TYR cc_start: 0.7223 (t80) cc_final: 0.7013 (t80) REVERT: Q 185 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.6991 (t-90) REVERT: Q 324 ARG cc_start: 0.7189 (tpt-90) cc_final: 0.6416 (tmm160) REVERT: F 81 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.6056 (mmm160) REVERT: F 352 GLN cc_start: 0.7438 (mm-40) cc_final: 0.7132 (tp40) REVERT: J 81 ARG cc_start: 0.7476 (mmm160) cc_final: 0.6948 (mtm110) REVERT: L 356 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.6930 (p0) REVERT: N 31 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7998 (tt) REVERT: P 128 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6333 (mm) REVERT: P 187 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: R 110 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6002 (p90) REVERT: R 185 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.6933 (t-90) REVERT: R 324 ARG cc_start: 0.7088 (tpt-90) cc_final: 0.6325 (tmm160) outliers start: 115 outliers final: 90 residues processed: 437 average time/residue: 0.2159 time to fit residues: 159.1820 Evaluate side-chains 432 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 326 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 317 PHE Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 353 LEU Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 185 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 45 SER Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 182 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 73 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 357 optimal weight: 0.8980 chunk 445 optimal weight: 0.0050 chunk 21 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 379 optimal weight: 3.9990 chunk 432 optimal weight: 3.9990 chunk 375 optimal weight: 0.9990 chunk 407 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 ASN G 356 ASN O 160 ASN J 352 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.193434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.153162 restraints weight = 49361.131| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.26 r_work: 0.3836 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 37197 Z= 0.172 Angle : 0.781 59.115 50547 Z= 0.445 Chirality : 0.040 0.396 5676 Planarity : 0.006 0.184 6465 Dihedral : 4.809 57.826 5051 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 2.99 % Allowed : 25.62 % Favored : 71.39 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.13), residues: 4455 helix: 1.01 (0.10), residues: 2601 sheet: None (None), residues: 0 loop : -2.13 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 28 TYR 0.011 0.001 TYR H 74 PHE 0.017 0.001 PHE M 80 TRP 0.010 0.001 TRP K 349 HIS 0.003 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00326 (37197) covalent geometry : angle 0.78104 (50547) hydrogen bonds : bond 0.05013 ( 1578) hydrogen bonds : angle 4.30369 ( 4698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 325 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5933 (mmm160) REVERT: A 350 LYS cc_start: 0.7774 (tppp) cc_final: 0.7555 (tptt) REVERT: B 81 ARG cc_start: 0.7477 (mmm160) cc_final: 0.6961 (mtm110) REVERT: D 31 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8143 (tt) REVERT: G 166 THR cc_start: 0.6624 (OUTLIER) cc_final: 0.5995 (m) REVERT: G 167 GLU cc_start: 0.6787 (pm20) cc_final: 0.6481 (tp30) REVERT: G 187 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: H 185 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.6907 (t-90) REVERT: H 324 ARG cc_start: 0.7212 (tpt-90) cc_final: 0.6461 (tmm160) REVERT: E 81 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.5979 (mmm160) REVERT: I 81 ARG cc_start: 0.7380 (mmm160) cc_final: 0.6994 (mtm110) REVERT: I 202 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7983 (p) REVERT: M 31 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8014 (tt) REVERT: O 27 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7446 (mm110) REVERT: O 74 TYR cc_start: 0.7199 (t80) cc_final: 0.6934 (t80) REVERT: O 187 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: Q 185 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.6975 (t-90) REVERT: Q 324 ARG cc_start: 0.7193 (tpt-90) cc_final: 0.6424 (tmm160) REVERT: F 81 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.6049 (mmm160) REVERT: F 352 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7137 (tp40) REVERT: J 81 ARG cc_start: 0.7455 (mmm160) cc_final: 0.6930 (mtm110) REVERT: N 31 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7990 (tt) REVERT: P 128 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6311 (mm) REVERT: P 187 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: R 110 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.5999 (p90) REVERT: R 185 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.6924 (t-90) REVERT: R 324 ARG cc_start: 0.7091 (tpt-90) cc_final: 0.6328 (tmm160) outliers start: 114 outliers final: 94 residues processed: 424 average time/residue: 0.2177 time to fit residues: 155.3302 Evaluate side-chains 434 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 324 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 317 PHE Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 165 LEU Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 353 LEU Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 185 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 45 SER Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 182 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 1.9990 chunk 399 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 367 optimal weight: 0.7980 chunk 318 optimal weight: 6.9990 chunk 301 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 278 optimal weight: 0.0470 chunk 225 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 ASN O 160 ASN J 352 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.194234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.153827 restraints weight = 48847.081| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.21 r_work: 0.3842 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.475 37197 Z= 0.263 Angle : 0.756 56.357 50547 Z= 0.455 Chirality : 0.040 0.393 5676 Planarity : 0.006 0.232 6465 Dihedral : 4.809 57.826 5051 Min Nonbonded Distance : 0.876 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 2.91 % Allowed : 25.70 % Favored : 71.39 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.13), residues: 4455 helix: 1.01 (0.10), residues: 2601 sheet: None (None), residues: 0 loop : -2.13 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 28 TYR 0.011 0.001 TYR H 74 PHE 0.017 0.001 PHE M 80 TRP 0.010 0.001 TRP K 349 HIS 0.003 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00512 (37197) covalent geometry : angle 0.75613 (50547) hydrogen bonds : bond 0.05015 ( 1578) hydrogen bonds : angle 4.30363 ( 4698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11507.26 seconds wall clock time: 196 minutes 44.59 seconds (11804.59 seconds total)