Starting phenix.real_space_refine on Thu Mar 5 18:04:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ubr_64015/03_2026/9ubr_64015.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ubr_64015/03_2026/9ubr_64015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ubr_64015/03_2026/9ubr_64015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ubr_64015/03_2026/9ubr_64015.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ubr_64015/03_2026/9ubr_64015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ubr_64015/03_2026/9ubr_64015.map" } resolution = 2.62 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= 0.033 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 126 5.16 5 C 15173 2.51 5 N 4039 2.21 5 O 4533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23871 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1964 Classifications: {'peptide': 259} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 246} Chain: "B" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1964 Classifications: {'peptide': 259} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 246} Chain: "C" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1964 Classifications: {'peptide': 259} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 246} Chain: "D" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1964 Classifications: {'peptide': 259} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 246} Chain: "E" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1973 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 247} Chain: "F" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1964 Classifications: {'peptide': 259} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 246} Chain: "G" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 876 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "H" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 876 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "I" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 876 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "J" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 876 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 876 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 876 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "M" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 132} Chain: "N" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 132} Chain: "O" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 132} Chain: "P" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 132} Chain: "Q" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 132} Chain: "R" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 132} Time building chain proxies: 6.19, per 1000 atoms: 0.26 Number of scatterers: 23871 At special positions: 0 Unit cell: (127.88, 126.04, 185.84, 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 126 16.00 O 4533 8.00 N 4039 7.00 C 15173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 265 " distance=2.04 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 227 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 227 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 24 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 94 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 94 " distance=2.03 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: 1.91 Conformation dependent library (CDL) restraints added in 1.3 seconds 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5726 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 49 sheets defined 35.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 removed outlier: 3.610A pdb=" N ILE A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 16 " --> pdb=" O PHE A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 39 through 73 Processing helix chain 'A' and resid 82 through 96 removed outlier: 3.611A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 117 removed outlier: 3.824A pdb=" N VAL A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.994A pdb=" N LYS A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 155 through 166 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 194 through 206 removed outlier: 4.012A pdb=" N VAL A 198 " --> pdb=" O PRO A 194 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 4.126A pdb=" N VAL A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 4.531A pdb=" N GLU A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 263 Processing helix chain 'B' and resid 9 through 17 removed outlier: 3.518A pdb=" N ILE B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 39 through 73 Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.782A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 117 through 122 removed outlier: 3.567A pdb=" N GLU B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 144 removed outlier: 3.725A pdb=" N SER B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 194 through 199 removed outlier: 4.206A pdb=" N VAL B 198 " --> pdb=" O PRO B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 removed outlier: 4.046A pdb=" N VAL B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 4.375A pdb=" N CYS B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 265 removed outlier: 3.814A pdb=" N GLY B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 removed outlier: 3.543A pdb=" N ILE C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 16 " --> pdb=" O PHE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 39 through 73 Processing helix chain 'C' and resid 82 through 96 removed outlier: 3.937A pdb=" N ALA C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 117 removed outlier: 3.650A pdb=" N VAL C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 134 through 144 Processing helix chain 'C' and resid 155 through 166 Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 194 through 199 removed outlier: 4.057A pdb=" N VAL C 198 " --> pdb=" O PRO C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 207 removed outlier: 4.082A pdb=" N VAL C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 4.605A pdb=" N CYS C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 265 removed outlier: 4.157A pdb=" N GLY C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 18 removed outlier: 3.737A pdb=" N ILE D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 16 " --> pdb=" O PHE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 39 through 73 Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 109 through 117 removed outlier: 3.533A pdb=" N VAL D 113 " --> pdb=" O ASP D 109 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 123 removed outlier: 4.198A pdb=" N LYS D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 155 through 166 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 194 through 208 removed outlier: 4.104A pdb=" N VAL D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) Proline residue: D 200 - end of helix removed outlier: 4.098A pdb=" N VAL D 203 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 247 through 264 removed outlier: 3.507A pdb=" N GLU D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 17 removed outlier: 3.708A pdb=" N ILE E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU E 16 " --> pdb=" O PHE E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 36 Processing helix chain 'E' and resid 39 through 73 Processing helix chain 'E' and resid 82 through 96 removed outlier: 3.521A pdb=" N GLY E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 116 Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.553A pdb=" N GLU E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 155 through 166 Processing helix chain 'E' and resid 175 through 184 Processing helix chain 'E' and resid 194 through 206 removed outlier: 4.445A pdb=" N VAL E 198 " --> pdb=" O PRO E 194 " (cutoff:3.500A) Proline residue: E 200 - end of helix removed outlier: 4.167A pdb=" N VAL E 203 " --> pdb=" O GLY E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 232 removed outlier: 4.016A pdb=" N CYS E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 263 Processing helix chain 'F' and resid 9 through 17 removed outlier: 3.694A pdb=" N ILE F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 39 through 73 Processing helix chain 'F' and resid 82 through 96 removed outlier: 3.719A pdb=" N ALA F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE F 87 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 117 removed outlier: 3.689A pdb=" N VAL F 113 " --> pdb=" O ASP F 109 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 122 removed outlier: 3.693A pdb=" N GLU F 122 " --> pdb=" O SER F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 144 removed outlier: 3.544A pdb=" N SER F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 166 Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 194 through 207 removed outlier: 4.095A pdb=" N VAL F 198 " --> pdb=" O PRO F 194 " (cutoff:3.500A) Proline residue: F 200 - end of helix removed outlier: 4.022A pdb=" N VAL F 203 " --> pdb=" O GLY F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 removed outlier: 4.611A pdb=" N CYS F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY F 233 " --> pdb=" O TRP F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 265 removed outlier: 3.631A pdb=" N GLY F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS F 265 " --> pdb=" O LYS F 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 89 removed outlier: 4.001A pdb=" N THR G 89 " --> pdb=" O SER G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.866A pdb=" N ARG G 106 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE G 107 " --> pdb=" O PRO G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 103 through 107' Processing helix chain 'H' and resid 85 through 89 removed outlier: 4.020A pdb=" N THR H 89 " --> pdb=" O SER H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.960A pdb=" N ARG H 106 " --> pdb=" O SER H 103 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE H 107 " --> pdb=" O PRO H 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 103 through 107' Processing helix chain 'I' and resid 85 through 89 removed outlier: 4.020A pdb=" N THR I 89 " --> pdb=" O SER I 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 89 removed outlier: 3.746A pdb=" N THR J 89 " --> pdb=" O SER J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 107 removed outlier: 3.509A pdb=" N PHE J 107 " --> pdb=" O PRO J 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.572A pdb=" N THR K 89 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 107 removed outlier: 3.683A pdb=" N ARG K 106 " --> pdb=" O SER K 103 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE K 107 " --> pdb=" O PRO K 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 103 through 107' Processing helix chain 'L' and resid 85 through 89 Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.539A pdb=" N ARG L 106 " --> pdb=" O SER L 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE L 107 " --> pdb=" O PRO L 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 103 through 107' Processing helix chain 'M' and resid 29 through 33 Processing helix chain 'N' and resid 29 through 33 Processing helix chain 'N' and resid 117 through 121 Processing helix chain 'O' and resid 29 through 33 Processing helix chain 'O' and resid 117 through 121 Processing helix chain 'P' and resid 29 through 33 Processing helix chain 'P' and resid 117 through 121 Processing helix chain 'Q' and resid 29 through 33 Processing helix chain 'Q' and resid 117 through 121 Processing helix chain 'R' and resid 29 through 33 Processing helix chain 'R' and resid 117 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 130 removed outlier: 6.908A pdb=" N ILE A 74 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU A 102 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA A 76 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR A 104 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 78 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 170 removed outlier: 7.125A pdb=" N ILE B 127 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL B 150 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA B 129 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE B 101 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY B 130 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 103 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 74 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU B 102 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA B 76 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR B 104 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU B 78 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AA6, first strand: chain 'C' and resid 126 through 130 removed outlier: 6.701A pdb=" N ILE C 74 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLU C 102 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA C 76 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR C 104 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU C 78 " --> pdb=" O THR C 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 148 through 150 Processing sheet with id=AA8, first strand: chain 'C' and resid 172 through 173 Processing sheet with id=AA9, first strand: chain 'D' and resid 126 through 130 removed outlier: 6.850A pdb=" N ILE D 101 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY D 130 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE D 103 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALA D 76 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR D 104 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU D 78 " --> pdb=" O THR D 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 148 through 150 removed outlier: 6.972A pdb=" N ILE D 149 " --> pdb=" O MET D 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 172 through 173 Processing sheet with id=AB3, first strand: chain 'E' and resid 126 through 130 removed outlier: 7.258A pdb=" N ILE E 101 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLY E 130 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE E 103 " --> pdb=" O GLY E 130 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE E 74 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU E 102 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ALA E 76 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR E 104 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU E 78 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 148 through 150 Processing sheet with id=AB5, first strand: chain 'E' and resid 172 through 173 Processing sheet with id=AB6, first strand: chain 'F' and resid 126 through 130 removed outlier: 7.096A pdb=" N ILE F 101 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLY F 130 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE F 103 " --> pdb=" O GLY F 130 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE F 74 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLU F 102 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA F 76 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR F 104 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU F 78 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 148 through 150 Processing sheet with id=AB8, first strand: chain 'F' and resid 172 through 173 Processing sheet with id=AB9, first strand: chain 'G' and resid 6 through 9 Processing sheet with id=AC1, first strand: chain 'G' and resid 56 through 58 removed outlier: 5.169A pdb=" N GLY G 46 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG G 37 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 6 through 9 removed outlier: 3.626A pdb=" N SER H 23 " --> pdb=" O SER H 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 6 through 9 removed outlier: 3.626A pdb=" N SER H 23 " --> pdb=" O SER H 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 56 through 58 removed outlier: 6.602A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL H 33 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 6 through 9 Processing sheet with id=AC6, first strand: chain 'I' and resid 6 through 9 Processing sheet with id=AC7, first strand: chain 'I' and resid 12 through 15 removed outlier: 6.144A pdb=" N GLY I 12 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER I 119 " --> pdb=" O GLY I 12 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL I 14 " --> pdb=" O SER I 119 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG I 37 " --> pdb=" O GLY I 46 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY I 46 " --> pdb=" O ARG I 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 6 through 9 removed outlier: 3.771A pdb=" N SER J 23 " --> pdb=" O SER J 9 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 56 through 58 removed outlier: 6.714A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL J 33 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 6 through 9 removed outlier: 3.520A pdb=" N SER K 23 " --> pdb=" O SER K 9 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 12 through 15 removed outlier: 6.460A pdb=" N GLY K 12 " --> pdb=" O THR K 117 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N SER K 119 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL K 14 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL K 33 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL K 49 " --> pdb=" O VAL K 33 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP K 35 " --> pdb=" O VAL K 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 6 through 9 removed outlier: 3.754A pdb=" N SER L 23 " --> pdb=" O SER L 9 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 12 through 15 removed outlier: 6.213A pdb=" N GLY L 12 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER L 119 " --> pdb=" O GLY L 12 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL L 14 " --> pdb=" O SER L 119 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL L 33 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 8 through 10 removed outlier: 3.605A pdb=" N TYR M 8 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU M 36 " --> pdb=" O GLN M 55 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN M 55 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL M 38 " --> pdb=" O HIS M 53 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS M 53 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE M 40 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL M 51 " --> pdb=" O ARG M 67 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ARG M 67 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 8 through 10 removed outlier: 3.605A pdb=" N TYR M 8 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU M 36 " --> pdb=" O GLN M 55 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN M 55 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL M 38 " --> pdb=" O HIS M 53 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS M 53 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE M 40 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL M 51 " --> pdb=" O ARG M 67 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ARG M 67 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 107 through 113 removed outlier: 5.213A pdb=" N SER M 108 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL M 104 " --> pdb=" O SER M 108 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER M 18 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR M 19 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL M 137 " --> pdb=" O THR M 19 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR M 21 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE M 135 " --> pdb=" O THR M 21 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS M 23 " --> pdb=" O THR M 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 8 through 10 removed outlier: 3.501A pdb=" N TYR N 8 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE N 52 " --> pdb=" O PHE N 40 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N VAL N 51 " --> pdb=" O ARG N 67 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG N 67 " --> pdb=" O VAL N 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 8 through 10 removed outlier: 3.501A pdb=" N TYR N 8 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE N 52 " --> pdb=" O PHE N 40 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N VAL N 51 " --> pdb=" O ARG N 67 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG N 67 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL N 62 " --> pdb=" O SER N 78 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER N 78 " --> pdb=" O VAL N 62 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 107 through 113 removed outlier: 5.192A pdb=" N SER N 108 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL N 104 " --> pdb=" O SER N 108 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR N 110 " --> pdb=" O VAL N 102 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER N 18 " --> pdb=" O VAL N 95 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 8 through 10 removed outlier: 6.502A pdb=" N LEU O 36 " --> pdb=" O GLN O 55 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN O 55 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL O 38 " --> pdb=" O HIS O 53 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS O 53 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE O 40 " --> pdb=" O VAL O 51 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL O 51 " --> pdb=" O ARG O 67 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG O 67 " --> pdb=" O VAL O 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 8 through 10 removed outlier: 6.502A pdb=" N LEU O 36 " --> pdb=" O GLN O 55 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN O 55 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL O 38 " --> pdb=" O HIS O 53 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS O 53 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE O 40 " --> pdb=" O VAL O 51 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL O 51 " --> pdb=" O ARG O 67 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG O 67 " --> pdb=" O VAL O 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 108 through 113 removed outlier: 5.402A pdb=" N SER O 108 " --> pdb=" O VAL O 104 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL O 104 " --> pdb=" O SER O 108 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER O 18 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR O 19 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL O 137 " --> pdb=" O THR O 19 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR O 21 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE O 135 " --> pdb=" O THR O 21 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS O 23 " --> pdb=" O THR O 133 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 9 through 10 removed outlier: 3.579A pdb=" N MET P 123 " --> pdb=" O HIS P 41 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE P 52 " --> pdb=" O PHE P 40 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL P 51 " --> pdb=" O ARG P 67 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG P 67 " --> pdb=" O VAL P 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 9 through 10 removed outlier: 3.579A pdb=" N MET P 123 " --> pdb=" O HIS P 41 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE P 52 " --> pdb=" O PHE P 40 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL P 51 " --> pdb=" O ARG P 67 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG P 67 " --> pdb=" O VAL P 51 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 107 through 113 removed outlier: 5.010A pdb=" N SER P 108 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL P 104 " --> pdb=" O SER P 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR P 110 " --> pdb=" O VAL P 102 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER P 18 " --> pdb=" O VAL P 95 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR P 19 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL P 137 " --> pdb=" O THR P 19 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR P 21 " --> pdb=" O PHE P 135 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE P 135 " --> pdb=" O THR P 21 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS P 23 " --> pdb=" O THR P 133 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG P 25 " --> pdb=" O SER P 131 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 8 through 11 removed outlier: 3.781A pdb=" N PHE Q 52 " --> pdb=" O PHE Q 40 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL Q 51 " --> pdb=" O ARG Q 67 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG Q 67 " --> pdb=" O VAL Q 51 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 8 through 11 removed outlier: 3.781A pdb=" N PHE Q 52 " --> pdb=" O PHE Q 40 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL Q 51 " --> pdb=" O ARG Q 67 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG Q 67 " --> pdb=" O VAL Q 51 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 107 through 113 removed outlier: 5.410A pdb=" N SER Q 108 " --> pdb=" O VAL Q 104 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL Q 104 " --> pdb=" O SER Q 108 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR Q 19 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL Q 137 " --> pdb=" O THR Q 19 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR Q 21 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE Q 135 " --> pdb=" O THR Q 21 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS Q 23 " --> pdb=" O THR Q 133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 8 through 11 removed outlier: 3.509A pdb=" N TYR R 8 " --> pdb=" O VAL R 126 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET R 123 " --> pdb=" O HIS R 41 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE R 52 " --> pdb=" O PHE R 40 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL R 51 " --> pdb=" O ARG R 67 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG R 67 " --> pdb=" O VAL R 51 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 8 through 11 removed outlier: 3.509A pdb=" N TYR R 8 " --> pdb=" O VAL R 126 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET R 123 " --> pdb=" O HIS R 41 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE R 52 " --> pdb=" O PHE R 40 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL R 51 " --> pdb=" O ARG R 67 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG R 67 " --> pdb=" O VAL R 51 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 107 through 113 removed outlier: 5.424A pdb=" N SER R 108 " --> pdb=" O VAL R 104 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL R 104 " --> pdb=" O SER R 108 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR R 110 " --> pdb=" O VAL R 102 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR R 19 " --> pdb=" O VAL R 137 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL R 137 " --> pdb=" O THR R 19 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR R 21 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE R 135 " --> pdb=" O THR R 21 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS R 23 " --> pdb=" O THR R 133 " (cutoff:3.500A) 1230 hydrogen bonds defined for protein. 3372 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: 4.93 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7792 1.34 - 1.46: 5120 1.46 - 1.58: 11223 1.58 - 1.70: 0 1.70 - 1.81: 204 Bond restraints: 24339 Sorted by residual: bond pdb=" CA SER O 131 " pdb=" CB SER O 131 " ideal model delta sigma weight residual 1.532 1.453 0.079 1.74e-02 3.30e+03 2.06e+01 bond pdb=" N PRO C 171 " pdb=" CD PRO C 171 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" N PRO N 26 " pdb=" CD PRO N 26 " ideal model delta sigma weight residual 1.473 1.418 0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" N ASN L 82 " pdb=" CA ASN L 82 " ideal model delta sigma weight residual 1.458 1.499 -0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CA LYS C 254 " pdb=" C LYS C 254 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.30e-02 5.92e+03 9.86e+00 ... (remaining 24334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 31828 2.19 - 4.37: 841 4.37 - 6.56: 168 6.56 - 8.74: 35 8.74 - 10.93: 8 Bond angle restraints: 32880 Sorted by residual: angle pdb=" N VAL A 226 " pdb=" CA VAL A 226 " pdb=" C VAL A 226 " ideal model delta sigma weight residual 110.53 99.60 10.93 9.40e-01 1.13e+00 1.35e+02 angle pdb=" N ALA C 255 " pdb=" CA ALA C 255 " pdb=" C ALA C 255 " ideal model delta sigma weight residual 111.33 121.48 -10.15 1.21e+00 6.83e-01 7.04e+01 angle pdb=" N GLU D 260 " pdb=" CA GLU D 260 " pdb=" C GLU D 260 " ideal model delta sigma weight residual 112.54 102.38 10.16 1.22e+00 6.72e-01 6.93e+01 angle pdb=" N VAL K 47 " pdb=" CA VAL K 47 " pdb=" C VAL K 47 " ideal model delta sigma weight residual 111.67 118.87 -7.20 9.50e-01 1.11e+00 5.74e+01 angle pdb=" N ILE B 43 " pdb=" CA ILE B 43 " pdb=" C ILE B 43 " ideal model delta sigma weight residual 110.53 104.11 6.42 9.40e-01 1.13e+00 4.66e+01 ... (remaining 32875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12389 17.87 - 35.73: 1630 35.73 - 53.60: 548 53.60 - 71.47: 93 71.47 - 89.33: 52 Dihedral angle restraints: 14712 sinusoidal: 5817 harmonic: 8895 Sorted by residual: dihedral pdb=" CA VAL O 126 " pdb=" C VAL O 126 " pdb=" N TRP O 127 " pdb=" CA TRP O 127 " ideal model delta harmonic sigma weight residual -180.00 -154.90 -25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" C TRP O 127 " pdb=" N TRP O 127 " pdb=" CA TRP O 127 " pdb=" CB TRP O 127 " ideal model delta harmonic sigma weight residual -122.60 -110.37 -12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA VAL R 126 " pdb=" C VAL R 126 " pdb=" N TRP R 127 " pdb=" CA TRP R 127 " ideal model delta harmonic sigma weight residual 180.00 -159.47 -20.53 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 14709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3012 0.068 - 0.135: 567 0.135 - 0.203: 75 0.203 - 0.271: 24 0.271 - 0.339: 7 Chirality restraints: 3685 Sorted by residual: chirality pdb=" CA PHE O 54 " pdb=" N PHE O 54 " pdb=" C PHE O 54 " pdb=" CB PHE O 54 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ASN E 20 " pdb=" N ASN E 20 " pdb=" C ASN E 20 " pdb=" CB ASN E 20 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ASN A 20 " pdb=" N ASN A 20 " pdb=" C ASN A 20 " pdb=" CB ASN A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 3682 not shown) Planarity restraints: 4244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET M 81 " 0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO M 82 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO M 82 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO M 82 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 223 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C LEU A 223 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU A 223 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A 224 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR M 110 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C TYR M 110 " -0.047 2.00e-02 2.50e+03 pdb=" O TYR M 110 " 0.018 2.00e-02 2.50e+03 pdb=" N THR M 111 " 0.016 2.00e-02 2.50e+03 ... (remaining 4241 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2037 2.74 - 3.28: 23396 3.28 - 3.82: 40686 3.82 - 4.36: 48633 4.36 - 4.90: 83659 Nonbonded interactions: 198411 Sorted by model distance: nonbonded pdb=" OG SER K 69 " pdb=" OG SER K 78 " model vdw 2.200 3.040 nonbonded pdb=" O LEU D 78 " pdb=" OG1 THR D 104 " model vdw 2.204 3.040 nonbonded pdb=" NH2 ARG G 65 " pdb=" OD2 ASP G 88 " model vdw 2.205 3.120 nonbonded pdb=" O TRP O 127 " pdb=" CG TRP O 127 " model vdw 2.212 3.260 nonbonded pdb=" O ASN A 20 " pdb=" NE2 GLN A 54 " model vdw 2.212 3.120 ... (remaining 198406 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = (chain 'E' and resid 8 through 266) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.200 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.004 0.079 24351 Z= 0.217 Angle : 0.822 10.927 32904 Z= 0.517 Chirality : 0.057 0.339 3685 Planarity : 0.005 0.100 4244 Dihedral : 18.666 89.334 8950 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.78 % Allowed : 31.77 % Favored : 65.44 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -0.29 (0.15), residues: 3067 helix: 0.22 (0.17), residues: 897 sheet: 0.21 (0.18), residues: 896 loop : -0.67 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 21 TYR 0.029 0.001 TYR M 110 PHE 0.020 0.001 PHE B 94 TRP 0.014 0.001 TRP O 127 HIS 0.003 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00405 (24339) covalent geometry : angle 0.82266 (32880) SS BOND : bond 0.00165 ( 12) SS BOND : angle 0.36285 ( 24) hydrogen bonds : bond 0.23400 ( 1120) hydrogen bonds : angle 7.93341 ( 3372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 654 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8067 (tttt) cc_final: 0.7735 (tmtt) REVERT: A 73 LYS cc_start: 0.8462 (mttm) cc_final: 0.8245 (mttm) REVERT: A 120 LEU cc_start: 0.8546 (tp) cc_final: 0.8334 (mp) REVERT: A 245 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7885 (ttpp) REVERT: B 105 PHE cc_start: 0.8572 (m-10) cc_final: 0.8140 (m-80) REVERT: B 121 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8257 (ttpp) REVERT: B 256 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7633 (mmmt) REVERT: C 89 LYS cc_start: 0.7743 (mttp) cc_final: 0.7523 (mttp) REVERT: C 127 ILE cc_start: 0.8546 (mm) cc_final: 0.8337 (mp) REVERT: C 132 VAL cc_start: 0.8883 (t) cc_final: 0.8679 (m) REVERT: C 256 LYS cc_start: 0.7770 (ttpp) cc_final: 0.7491 (ttpp) REVERT: D 103 ILE cc_start: 0.8198 (mm) cc_final: 0.7946 (mp) REVERT: D 143 GLU cc_start: 0.7578 (tp30) cc_final: 0.7164 (tp30) REVERT: E 65 MET cc_start: 0.7262 (tpp) cc_final: 0.7037 (mmm) REVERT: E 105 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7866 (m-10) REVERT: E 207 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7825 (ttpt) REVERT: E 256 LYS cc_start: 0.8495 (mttp) cc_final: 0.8280 (mttp) REVERT: F 34 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7748 (mtpp) REVERT: H 98 SER cc_start: 0.8556 (m) cc_final: 0.8144 (t) REVERT: I 27 SER cc_start: 0.8564 (p) cc_final: 0.8259 (p) REVERT: M 102 VAL cc_start: 0.8476 (p) cc_final: 0.8271 (m) REVERT: N 56 VAL cc_start: 0.8115 (t) cc_final: 0.7905 (p) REVERT: P 62 VAL cc_start: 0.7981 (t) cc_final: 0.7660 (m) REVERT: Q 18 SER cc_start: 0.8651 (t) cc_final: 0.8393 (p) REVERT: Q 38 VAL cc_start: 0.7268 (OUTLIER) cc_final: 0.7061 (t) REVERT: Q 92 SER cc_start: 0.8137 (m) cc_final: 0.7872 (p) outliers start: 72 outliers final: 46 residues processed: 700 average time/residue: 0.6774 time to fit residues: 539.8256 Evaluate side-chains 682 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 634 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 105 PHE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 24 CYS Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 141 LYS Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 136 ASN Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 133 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.0010 chunk 298 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 GLN D 8 GLN G 42 ASN L 15 GLN N 32 ASN N 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.136105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129506 restraints weight = 35351.547| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.55 r_work: 0.3700 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24351 Z= 0.154 Angle : 0.573 8.425 32904 Z= 0.310 Chirality : 0.047 0.166 3685 Planarity : 0.005 0.061 4244 Dihedral : 6.035 59.332 3363 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.18 % Allowed : 29.69 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: 0.08 (0.15), residues: 3067 helix: 0.92 (0.17), residues: 907 sheet: 0.15 (0.18), residues: 899 loop : -0.55 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 252 TYR 0.028 0.001 TYR M 110 PHE 0.025 0.002 PHE B 161 TRP 0.015 0.001 TRP Q 127 HIS 0.006 0.001 HIS O 53 Details of bonding type rmsd covalent geometry : bond 0.00348 (24339) covalent geometry : angle 0.57291 (32880) SS BOND : bond 0.00164 ( 12) SS BOND : angle 0.59079 ( 24) hydrogen bonds : bond 0.04433 ( 1120) hydrogen bonds : angle 5.14594 ( 3372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 701 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8341 (mttm) cc_final: 0.8138 (mttm) REVERT: A 88 GLU cc_start: 0.6788 (mp0) cc_final: 0.6282 (mp0) REVERT: A 122 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6774 (tm-30) REVERT: A 136 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: A 157 GLU cc_start: 0.7296 (mp0) cc_final: 0.7066 (mp0) REVERT: A 196 GLU cc_start: 0.7589 (pm20) cc_final: 0.7252 (pm20) REVERT: A 245 LYS cc_start: 0.8235 (ttpp) cc_final: 0.8012 (ttpp) REVERT: A 256 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7711 (ttpp) REVERT: B 121 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8512 (ttpp) REVERT: B 256 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7670 (mmmt) REVERT: C 121 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8184 (ttmm) REVERT: C 132 VAL cc_start: 0.8856 (t) cc_final: 0.8596 (m) REVERT: C 256 LYS cc_start: 0.8021 (ttpp) cc_final: 0.7748 (ttpp) REVERT: D 143 GLU cc_start: 0.7740 (tp30) cc_final: 0.7284 (tp30) REVERT: D 164 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6558 (mm-30) REVERT: D 215 PHE cc_start: 0.8419 (m-80) cc_final: 0.8217 (m-80) REVERT: D 258 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7941 (t80) REVERT: E 121 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7898 (ttpp) REVERT: E 258 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8005 (t80) REVERT: E 262 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8393 (mt) REVERT: F 12 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: F 34 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7848 (mtpp) REVERT: F 65 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7420 (mmm) REVERT: F 87 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7955 (mp) REVERT: F 163 LYS cc_start: 0.8039 (tttp) cc_final: 0.7759 (tttp) REVERT: F 254 LYS cc_start: 0.8660 (ptmt) cc_final: 0.8422 (ptpp) REVERT: G 81 MET cc_start: 0.7807 (mtm) cc_final: 0.7517 (mtp) REVERT: H 98 SER cc_start: 0.8492 (m) cc_final: 0.8074 (t) REVERT: J 83 SER cc_start: 0.8187 (t) cc_final: 0.7886 (p) REVERT: Q 18 SER cc_start: 0.8578 (t) cc_final: 0.8275 (p) REVERT: R 76 VAL cc_start: 0.8362 (p) cc_final: 0.8052 (m) REVERT: R 108 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8484 (p) REVERT: R 126 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7800 (m) outliers start: 134 outliers final: 67 residues processed: 777 average time/residue: 0.6439 time to fit residues: 572.5761 Evaluate side-chains 742 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 666 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 258 PHE Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain F residue 12 PHE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 141 LYS Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain Q residue 134 LYS Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 96 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 141 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS D 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127492 restraints weight = 34948.385| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.54 r_work: 0.3644 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24351 Z= 0.277 Angle : 0.618 8.852 32904 Z= 0.330 Chirality : 0.050 0.228 3685 Planarity : 0.005 0.064 4244 Dihedral : 5.167 57.638 3301 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.95 % Allowed : 29.07 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -0.06 (0.15), residues: 3067 helix: 0.82 (0.17), residues: 942 sheet: -0.11 (0.17), residues: 977 loop : -0.54 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 263 TYR 0.048 0.002 TYR M 110 PHE 0.033 0.002 PHE C 148 TRP 0.022 0.002 TRP Q 127 HIS 0.008 0.001 HIS O 53 Details of bonding type rmsd covalent geometry : bond 0.00621 (24339) covalent geometry : angle 0.61761 (32880) SS BOND : bond 0.00156 ( 12) SS BOND : angle 0.80771 ( 24) hydrogen bonds : bond 0.04101 ( 1120) hydrogen bonds : angle 4.84313 ( 3372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 670 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7049 (mp0) cc_final: 0.6541 (mp0) REVERT: A 121 LYS cc_start: 0.8283 (tttm) cc_final: 0.8009 (tttm) REVERT: A 136 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: A 157 GLU cc_start: 0.7384 (mp0) cc_final: 0.7135 (mp0) REVERT: A 196 GLU cc_start: 0.7625 (pm20) cc_final: 0.7414 (pm20) REVERT: A 228 GLU cc_start: 0.7689 (tp30) cc_final: 0.7433 (tp30) REVERT: A 256 LYS cc_start: 0.8092 (ttpp) cc_final: 0.7843 (ttpp) REVERT: B 91 VAL cc_start: 0.8581 (m) cc_final: 0.8363 (p) REVERT: B 121 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8555 (ttpp) REVERT: B 122 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 157 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7057 (mm-30) REVERT: B 206 MET cc_start: 0.8484 (tpp) cc_final: 0.7954 (mpp) REVERT: B 256 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7787 (mmmt) REVERT: C 117 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8374 (mp) REVERT: C 122 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7547 (tm-30) REVERT: C 132 VAL cc_start: 0.8945 (t) cc_final: 0.8689 (m) REVERT: C 157 GLU cc_start: 0.7267 (mp0) cc_final: 0.7061 (mp0) REVERT: C 168 PHE cc_start: 0.8304 (t80) cc_final: 0.7840 (t80) REVERT: C 256 LYS cc_start: 0.8064 (ttpp) cc_final: 0.7788 (ttpp) REVERT: D 12 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: D 143 GLU cc_start: 0.7803 (tp30) cc_final: 0.7334 (tp30) REVERT: D 164 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6675 (mm-30) REVERT: D 258 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8190 (t80) REVERT: E 65 MET cc_start: 0.7425 (tpp) cc_final: 0.7085 (mmm) REVERT: E 87 ILE cc_start: 0.7999 (mm) cc_final: 0.7796 (mp) REVERT: E 88 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6701 (mp0) REVERT: E 121 LYS cc_start: 0.8293 (ttpp) cc_final: 0.7880 (ttpp) REVERT: E 148 PHE cc_start: 0.7908 (p90) cc_final: 0.7556 (p90) REVERT: E 207 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7975 (ttpt) REVERT: F 12 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: F 34 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7897 (mtpp) REVERT: F 65 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7433 (mmm) REVERT: F 67 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6871 (mm-30) REVERT: F 87 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8085 (mp) REVERT: F 88 GLU cc_start: 0.7069 (mp0) cc_final: 0.6805 (mp0) REVERT: H 23 SER cc_start: 0.8252 (t) cc_final: 0.7994 (m) REVERT: H 98 SER cc_start: 0.8515 (m) cc_final: 0.8067 (t) REVERT: J 83 SER cc_start: 0.8228 (t) cc_final: 0.7932 (p) REVERT: K 21 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7591 (ttt180) REVERT: K 33 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8190 (m) REVERT: K 63 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8226 (ttpp) REVERT: M 51 VAL cc_start: 0.8284 (t) cc_final: 0.8035 (t) REVERT: O 15 SER cc_start: 0.8141 (m) cc_final: 0.7921 (t) REVERT: O 92 SER cc_start: 0.8113 (OUTLIER) cc_final: 0.7782 (m) REVERT: Q 18 SER cc_start: 0.8619 (t) cc_final: 0.8332 (p) REVERT: R 76 VAL cc_start: 0.8411 (p) cc_final: 0.8128 (m) outliers start: 154 outliers final: 79 residues processed: 757 average time/residue: 0.6670 time to fit residues: 574.4464 Evaluate side-chains 762 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 672 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 12 PHE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 21 ARG Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain L residue 81 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 108 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain N residue 141 LYS Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 64 MET Chi-restraints excluded: chain P residue 123 MET Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 133 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 203 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 143 optimal weight: 0.4980 chunk 153 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 287 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 173 optimal weight: 0.0000 chunk 225 optimal weight: 0.4980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 GLN E 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129764 restraints weight = 34867.430| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.55 r_work: 0.3675 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24351 Z= 0.120 Angle : 0.537 6.964 32904 Z= 0.286 Chirality : 0.045 0.192 3685 Planarity : 0.004 0.060 4244 Dihedral : 4.919 59.986 3298 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.84 % Allowed : 30.58 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: 0.10 (0.15), residues: 3067 helix: 1.05 (0.17), residues: 942 sheet: -0.16 (0.17), residues: 933 loop : -0.39 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 263 TYR 0.012 0.001 TYR M 100 PHE 0.019 0.001 PHE B 161 TRP 0.014 0.001 TRP P 127 HIS 0.004 0.001 HIS O 53 Details of bonding type rmsd covalent geometry : bond 0.00278 (24339) covalent geometry : angle 0.53627 (32880) SS BOND : bond 0.00493 ( 12) SS BOND : angle 0.79061 ( 24) hydrogen bonds : bond 0.03337 ( 1120) hydrogen bonds : angle 4.53471 ( 3372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 664 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: A 121 LYS cc_start: 0.8170 (tttm) cc_final: 0.7931 (tttm) REVERT: A 136 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: A 157 GLU cc_start: 0.7283 (mp0) cc_final: 0.6998 (mp0) REVERT: A 163 LYS cc_start: 0.7961 (ttpp) cc_final: 0.7670 (ttpp) REVERT: A 196 GLU cc_start: 0.7596 (pm20) cc_final: 0.7345 (pm20) REVERT: A 228 GLU cc_start: 0.7566 (tp30) cc_final: 0.7270 (tp30) REVERT: A 256 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7702 (ttpp) REVERT: B 91 VAL cc_start: 0.8511 (m) cc_final: 0.8268 (p) REVERT: B 109 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6058 (t0) REVERT: B 157 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6968 (mm-30) REVERT: B 230 PHE cc_start: 0.8696 (m-80) cc_final: 0.8485 (m-80) REVERT: C 117 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8346 (mp) REVERT: C 122 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7500 (tm-30) REVERT: C 157 GLU cc_start: 0.7179 (mp0) cc_final: 0.6960 (mp0) REVERT: C 168 PHE cc_start: 0.8196 (t80) cc_final: 0.7836 (t80) REVERT: C 206 MET cc_start: 0.8503 (tpp) cc_final: 0.8072 (mpp) REVERT: C 230 PHE cc_start: 0.8671 (m-80) cc_final: 0.8366 (m-80) REVERT: C 256 LYS cc_start: 0.7921 (ttpp) cc_final: 0.7663 (ttpp) REVERT: C 258 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7978 (t80) REVERT: D 12 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: D 143 GLU cc_start: 0.7805 (tp30) cc_final: 0.7342 (tp30) REVERT: D 164 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6654 (mm-30) REVERT: D 258 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8056 (t80) REVERT: E 65 MET cc_start: 0.7354 (tpp) cc_final: 0.7120 (mmm) REVERT: E 88 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6743 (mp0) REVERT: E 120 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7771 (tp) REVERT: E 121 LYS cc_start: 0.8318 (ttpp) cc_final: 0.7897 (ttpp) REVERT: E 150 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7958 (p) REVERT: E 258 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7975 (t80) REVERT: E 262 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8477 (mt) REVERT: F 12 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: F 67 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6825 (mm-30) REVERT: F 87 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8050 (mp) REVERT: F 254 LYS cc_start: 0.8662 (ptmt) cc_final: 0.8336 (ptpp) REVERT: H 98 SER cc_start: 0.8452 (m) cc_final: 0.7996 (t) REVERT: I 98 SER cc_start: 0.8107 (p) cc_final: 0.7869 (t) REVERT: J 83 SER cc_start: 0.8118 (t) cc_final: 0.7849 (p) REVERT: J 93 TYR cc_start: 0.8082 (m-80) cc_final: 0.7159 (m-80) REVERT: M 63 VAL cc_start: 0.8262 (t) cc_final: 0.8019 (m) REVERT: O 15 SER cc_start: 0.8131 (m) cc_final: 0.7899 (t) REVERT: O 92 SER cc_start: 0.8087 (OUTLIER) cc_final: 0.7793 (m) REVERT: Q 18 SER cc_start: 0.8510 (t) cc_final: 0.8292 (p) REVERT: R 76 VAL cc_start: 0.8403 (p) cc_final: 0.8125 (m) outliers start: 151 outliers final: 81 residues processed: 738 average time/residue: 0.6404 time to fit residues: 538.3926 Evaluate side-chains 765 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 670 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 258 PHE Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain F residue 12 PHE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 136 ASN Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 133 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 190 optimal weight: 0.3980 chunk 177 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 265 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 297 optimal weight: 0.5980 chunk 205 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.135968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129367 restraints weight = 34743.941| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.54 r_work: 0.3667 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24351 Z= 0.144 Angle : 0.544 7.102 32904 Z= 0.287 Chirality : 0.046 0.202 3685 Planarity : 0.004 0.061 4244 Dihedral : 4.743 57.786 3292 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.22 % Allowed : 31.43 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: 0.17 (0.15), residues: 3067 helix: 1.13 (0.17), residues: 943 sheet: -0.15 (0.17), residues: 933 loop : -0.35 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 263 TYR 0.012 0.001 TYR L 58 PHE 0.036 0.002 PHE C 148 TRP 0.013 0.001 TRP Q 127 HIS 0.005 0.001 HIS O 53 Details of bonding type rmsd covalent geometry : bond 0.00333 (24339) covalent geometry : angle 0.54445 (32880) SS BOND : bond 0.00085 ( 12) SS BOND : angle 0.58934 ( 24) hydrogen bonds : bond 0.03276 ( 1120) hydrogen bonds : angle 4.42407 ( 3372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 681 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: A 121 LYS cc_start: 0.8197 (tttm) cc_final: 0.7965 (tttm) REVERT: A 136 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7255 (mm-30) REVERT: A 157 GLU cc_start: 0.7293 (mp0) cc_final: 0.7048 (mp0) REVERT: A 163 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7680 (ttpp) REVERT: A 196 GLU cc_start: 0.7653 (pm20) cc_final: 0.7397 (pm20) REVERT: A 228 GLU cc_start: 0.7596 (tp30) cc_final: 0.7301 (tp30) REVERT: A 256 LYS cc_start: 0.7997 (ttpp) cc_final: 0.7747 (ttpp) REVERT: B 91 VAL cc_start: 0.8543 (m) cc_final: 0.8288 (p) REVERT: B 109 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6058 (t0) REVERT: B 157 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6974 (mm-30) REVERT: B 256 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7696 (mmmt) REVERT: C 117 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8411 (mp) REVERT: C 121 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8364 (ttmm) REVERT: C 122 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7490 (tm-30) REVERT: C 157 GLU cc_start: 0.7283 (mp0) cc_final: 0.6995 (mp0) REVERT: C 168 PHE cc_start: 0.8159 (t80) cc_final: 0.7798 (t80) REVERT: C 230 PHE cc_start: 0.8635 (m-80) cc_final: 0.8385 (m-80) REVERT: D 12 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: D 69 PHE cc_start: 0.8404 (m-80) cc_final: 0.8035 (m-80) REVERT: D 143 GLU cc_start: 0.7825 (tp30) cc_final: 0.7344 (tp30) REVERT: D 164 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6650 (mm-30) REVERT: D 258 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8013 (t80) REVERT: E 88 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6721 (mp0) REVERT: E 109 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.5986 (t0) REVERT: E 120 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7763 (tp) REVERT: E 121 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7888 (ttpp) REVERT: E 150 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7980 (p) REVERT: E 251 VAL cc_start: 0.8091 (m) cc_final: 0.7823 (t) REVERT: E 258 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7996 (t80) REVERT: E 262 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8487 (mt) REVERT: F 12 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: F 65 MET cc_start: 0.7661 (mmm) cc_final: 0.7415 (mmm) REVERT: F 67 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6835 (mm-30) REVERT: F 87 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8098 (mp) REVERT: F 147 GLU cc_start: 0.7260 (mp0) cc_final: 0.7021 (mt-10) REVERT: F 223 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8271 (mp) REVERT: F 254 LYS cc_start: 0.8667 (ptmt) cc_final: 0.8406 (ptpp) REVERT: I 98 SER cc_start: 0.8109 (p) cc_final: 0.7863 (t) REVERT: K 63 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8140 (ttpp) REVERT: M 102 VAL cc_start: 0.8337 (m) cc_final: 0.8042 (p) REVERT: O 15 SER cc_start: 0.8155 (m) cc_final: 0.7855 (p) REVERT: O 92 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7786 (m) REVERT: P 45 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7948 (mtpp) REVERT: P 47 GLU cc_start: 0.8206 (pm20) cc_final: 0.7935 (pm20) REVERT: Q 18 SER cc_start: 0.8506 (t) cc_final: 0.8287 (p) REVERT: R 76 VAL cc_start: 0.8416 (p) cc_final: 0.8149 (m) outliers start: 135 outliers final: 85 residues processed: 755 average time/residue: 0.6375 time to fit residues: 550.5112 Evaluate side-chains 772 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 671 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 258 PHE Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain F residue 12 PHE Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 123 MET Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 18 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.136151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.129692 restraints weight = 34643.220| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.53 r_work: 0.3700 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24351 Z= 0.160 Angle : 0.549 7.728 32904 Z= 0.290 Chirality : 0.047 0.248 3685 Planarity : 0.004 0.062 4244 Dihedral : 4.725 55.268 3291 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.57 % Allowed : 31.47 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: 0.21 (0.15), residues: 3067 helix: 1.14 (0.17), residues: 948 sheet: -0.10 (0.18), residues: 901 loop : -0.33 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 65 TYR 0.012 0.001 TYR L 58 PHE 0.021 0.002 PHE B 202 TRP 0.015 0.001 TRP Q 127 HIS 0.004 0.001 HIS O 53 Details of bonding type rmsd covalent geometry : bond 0.00369 (24339) covalent geometry : angle 0.54873 (32880) SS BOND : bond 0.00081 ( 12) SS BOND : angle 0.56606 ( 24) hydrogen bonds : bond 0.03232 ( 1120) hydrogen bonds : angle 4.39107 ( 3372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 690 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: A 91 VAL cc_start: 0.8594 (m) cc_final: 0.8359 (p) REVERT: A 121 LYS cc_start: 0.8290 (tttm) cc_final: 0.8045 (tttm) REVERT: A 136 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: A 157 GLU cc_start: 0.7358 (mp0) cc_final: 0.7106 (mp0) REVERT: A 196 GLU cc_start: 0.7641 (pm20) cc_final: 0.7390 (pm20) REVERT: A 228 GLU cc_start: 0.7749 (tp30) cc_final: 0.7437 (tp30) REVERT: A 256 LYS cc_start: 0.8060 (ttpp) cc_final: 0.7797 (ttpp) REVERT: B 91 VAL cc_start: 0.8555 (m) cc_final: 0.8304 (p) REVERT: B 109 ASP cc_start: 0.6645 (OUTLIER) cc_final: 0.6052 (t0) REVERT: B 256 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7739 (mmmt) REVERT: C 122 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7493 (tm-30) REVERT: C 157 GLU cc_start: 0.7354 (mp0) cc_final: 0.7004 (mp0) REVERT: C 168 PHE cc_start: 0.8149 (t80) cc_final: 0.7792 (t80) REVERT: C 206 MET cc_start: 0.8552 (tpp) cc_final: 0.8073 (mpp) REVERT: C 256 LYS cc_start: 0.7981 (ttpp) cc_final: 0.7722 (ttpp) REVERT: D 12 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: D 143 GLU cc_start: 0.7861 (tp30) cc_final: 0.7358 (tp30) REVERT: D 147 GLU cc_start: 0.7370 (mp0) cc_final: 0.6793 (mp0) REVERT: D 258 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8071 (t80) REVERT: E 33 LEU cc_start: 0.8587 (mt) cc_final: 0.8381 (mm) REVERT: E 88 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6735 (mp0) REVERT: E 109 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.6017 (t0) REVERT: E 117 LEU cc_start: 0.8473 (mp) cc_final: 0.8235 (mm) REVERT: E 120 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7718 (tp) REVERT: E 121 LYS cc_start: 0.8309 (ttpp) cc_final: 0.7891 (ttpp) REVERT: E 150 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.7987 (p) REVERT: E 251 VAL cc_start: 0.8094 (m) cc_final: 0.7833 (t) REVERT: E 258 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7972 (t80) REVERT: F 12 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: F 65 MET cc_start: 0.7679 (mmm) cc_final: 0.7397 (mmm) REVERT: F 67 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6873 (mm-30) REVERT: F 87 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8153 (mp) REVERT: F 88 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: F 223 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8310 (mp) REVERT: F 254 LYS cc_start: 0.8668 (ptmt) cc_final: 0.8335 (ptpp) REVERT: G 9 SER cc_start: 0.8184 (p) cc_final: 0.7965 (t) REVERT: H 98 SER cc_start: 0.8401 (m) cc_final: 0.7990 (t) REVERT: I 98 SER cc_start: 0.8133 (p) cc_final: 0.7890 (t) REVERT: J 83 SER cc_start: 0.8112 (t) cc_final: 0.7823 (p) REVERT: K 21 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7575 (ttt180) REVERT: K 38 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: K 63 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8168 (ttpp) REVERT: K 81 MET cc_start: 0.7987 (mtt) cc_final: 0.7724 (mtt) REVERT: O 15 SER cc_start: 0.8134 (m) cc_final: 0.7866 (p) REVERT: O 92 SER cc_start: 0.8064 (OUTLIER) cc_final: 0.7780 (m) REVERT: P 45 LYS cc_start: 0.8326 (mtpp) cc_final: 0.8035 (mtpp) REVERT: P 47 GLU cc_start: 0.8172 (pm20) cc_final: 0.7944 (pm20) REVERT: Q 18 SER cc_start: 0.8501 (t) cc_final: 0.8292 (p) REVERT: R 76 VAL cc_start: 0.8412 (p) cc_final: 0.8155 (m) outliers start: 144 outliers final: 90 residues processed: 772 average time/residue: 0.6239 time to fit residues: 553.1101 Evaluate side-chains 785 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 678 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 258 PHE Chi-restraints excluded: chain F residue 12 PHE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain K residue 21 ARG Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 123 MET Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 258 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN B 72 HIS D 31 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS F 20 ASN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.133538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.127187 restraints weight = 34333.905| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.50 r_work: 0.3638 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 24351 Z= 0.346 Angle : 0.659 9.407 32904 Z= 0.347 Chirality : 0.052 0.329 3685 Planarity : 0.005 0.066 4244 Dihedral : 5.119 53.182 3291 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.30 % Allowed : 31.47 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: 0.01 (0.15), residues: 3067 helix: 0.97 (0.17), residues: 943 sheet: -0.29 (0.17), residues: 970 loop : -0.34 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 65 TYR 0.023 0.002 TYR L 58 PHE 0.029 0.002 PHE B 94 TRP 0.026 0.002 TRP Q 127 HIS 0.006 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00772 (24339) covalent geometry : angle 0.65931 (32880) SS BOND : bond 0.00184 ( 12) SS BOND : angle 0.84922 ( 24) hydrogen bonds : bond 0.03839 ( 1120) hydrogen bonds : angle 4.65000 ( 3372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 691 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7306 (mtm) REVERT: A 88 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: A 121 LYS cc_start: 0.8281 (tttm) cc_final: 0.8005 (tttm) REVERT: A 157 GLU cc_start: 0.7432 (mp0) cc_final: 0.7194 (mp0) REVERT: A 196 GLU cc_start: 0.7696 (pm20) cc_final: 0.7429 (pm20) REVERT: A 228 GLU cc_start: 0.7830 (tp30) cc_final: 0.7580 (tp30) REVERT: A 256 LYS cc_start: 0.8174 (ttpp) cc_final: 0.7928 (ttpp) REVERT: B 91 VAL cc_start: 0.8604 (m) cc_final: 0.8392 (p) REVERT: B 163 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8147 (ttmm) REVERT: B 165 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8338 (mtmm) REVERT: B 256 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7889 (mmmt) REVERT: C 85 GLU cc_start: 0.7142 (pm20) cc_final: 0.6931 (pm20) REVERT: C 122 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7533 (tm-30) REVERT: C 157 GLU cc_start: 0.7543 (mp0) cc_final: 0.7155 (mp0) REVERT: C 168 PHE cc_start: 0.8214 (t80) cc_final: 0.7816 (t80) REVERT: C 237 VAL cc_start: 0.8455 (m) cc_final: 0.8247 (p) REVERT: C 243 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7783 (tt) REVERT: C 254 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8196 (mtpp) REVERT: C 256 LYS cc_start: 0.8138 (ttpp) cc_final: 0.7890 (ttpp) REVERT: D 12 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: D 69 PHE cc_start: 0.8421 (m-80) cc_final: 0.8211 (m-80) REVERT: D 105 PHE cc_start: 0.8576 (m-80) cc_final: 0.8039 (m-80) REVERT: D 143 GLU cc_start: 0.7798 (tp30) cc_final: 0.7313 (tp30) REVERT: D 147 GLU cc_start: 0.7483 (mp0) cc_final: 0.6849 (mp0) REVERT: D 258 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8333 (t80) REVERT: E 84 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.5294 (pp20) REVERT: E 88 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6588 (mp0) REVERT: E 109 ASP cc_start: 0.6570 (OUTLIER) cc_final: 0.6169 (t0) REVERT: E 117 LEU cc_start: 0.8476 (mp) cc_final: 0.8245 (mm) REVERT: E 120 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7802 (tp) REVERT: E 121 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7869 (ttpp) REVERT: E 147 GLU cc_start: 0.6952 (mp0) cc_final: 0.6718 (mp0) REVERT: E 148 PHE cc_start: 0.7949 (p90) cc_final: 0.7621 (p90) REVERT: E 150 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.7932 (p) REVERT: E 196 GLU cc_start: 0.7327 (pm20) cc_final: 0.6944 (pm20) REVERT: E 207 LYS cc_start: 0.8243 (ttpt) cc_final: 0.8019 (ttpt) REVERT: F 12 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: F 65 MET cc_start: 0.7755 (mmm) cc_final: 0.7496 (mmm) REVERT: F 67 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6940 (mm-30) REVERT: F 88 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: F 223 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8484 (mp) REVERT: H 91 MET cc_start: 0.8099 (tpp) cc_final: 0.7802 (tpp) REVERT: H 98 SER cc_start: 0.8434 (m) cc_final: 0.8049 (t) REVERT: I 98 SER cc_start: 0.8141 (p) cc_final: 0.7892 (t) REVERT: J 83 SER cc_start: 0.8217 (t) cc_final: 0.7958 (p) REVERT: K 21 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7600 (ttt180) REVERT: K 38 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: K 63 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8232 (ttpp) REVERT: K 81 MET cc_start: 0.8129 (mtt) cc_final: 0.7922 (mtt) REVERT: M 123 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7961 (ttm) REVERT: O 15 SER cc_start: 0.8130 (m) cc_final: 0.7879 (p) REVERT: O 92 SER cc_start: 0.8048 (OUTLIER) cc_final: 0.7770 (m) REVERT: P 45 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8058 (mtpp) REVERT: P 47 GLU cc_start: 0.8199 (pm20) cc_final: 0.7905 (pm20) REVERT: P 62 VAL cc_start: 0.8178 (t) cc_final: 0.7847 (m) REVERT: Q 18 SER cc_start: 0.8564 (t) cc_final: 0.8343 (p) REVERT: Q 36 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8305 (tt) REVERT: R 76 VAL cc_start: 0.8467 (p) cc_final: 0.8209 (m) outliers start: 163 outliers final: 103 residues processed: 781 average time/residue: 0.6271 time to fit residues: 560.5318 Evaluate side-chains 813 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 690 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 258 PHE Chi-restraints excluded: chain F residue 12 PHE Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 21 ARG Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 108 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 123 MET Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 123 MET Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain Q residue 134 LYS Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 145 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 292 optimal weight: 0.5980 chunk 247 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 251 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.135650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129098 restraints weight = 34279.706| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.52 r_work: 0.3672 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24351 Z= 0.145 Angle : 0.583 11.789 32904 Z= 0.303 Chirality : 0.047 0.279 3685 Planarity : 0.004 0.063 4244 Dihedral : 4.913 53.402 3291 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.99 % Allowed : 33.13 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: 0.07 (0.15), residues: 3067 helix: 1.09 (0.17), residues: 943 sheet: -0.28 (0.17), residues: 966 loop : -0.36 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 263 TYR 0.011 0.001 TYR J 92 PHE 0.045 0.002 PHE A 148 TRP 0.015 0.001 TRP Q 127 HIS 0.004 0.001 HIS O 53 Details of bonding type rmsd covalent geometry : bond 0.00338 (24339) covalent geometry : angle 0.58340 (32880) SS BOND : bond 0.00083 ( 12) SS BOND : angle 0.47336 ( 24) hydrogen bonds : bond 0.03235 ( 1120) hydrogen bonds : angle 4.47168 ( 3372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 690 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: A 103 ILE cc_start: 0.8594 (mm) cc_final: 0.8040 (pp) REVERT: A 121 LYS cc_start: 0.8262 (tttm) cc_final: 0.7986 (tttm) REVERT: A 131 THR cc_start: 0.8033 (p) cc_final: 0.7778 (t) REVERT: A 157 GLU cc_start: 0.7310 (mp0) cc_final: 0.7059 (mp0) REVERT: A 196 GLU cc_start: 0.7667 (pm20) cc_final: 0.7369 (pm20) REVERT: A 228 GLU cc_start: 0.7772 (tp30) cc_final: 0.7495 (tp30) REVERT: A 256 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7857 (ttpp) REVERT: B 91 VAL cc_start: 0.8543 (m) cc_final: 0.8298 (p) REVERT: B 165 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8229 (mtmm) REVERT: B 193 PHE cc_start: 0.8304 (t80) cc_final: 0.8047 (t80) REVERT: B 256 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7801 (mmmt) REVERT: C 122 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7509 (tm-30) REVERT: C 157 GLU cc_start: 0.7401 (mp0) cc_final: 0.7021 (mp0) REVERT: C 168 PHE cc_start: 0.8153 (t80) cc_final: 0.7797 (t80) REVERT: C 243 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7886 (tt) REVERT: C 256 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7794 (ttpp) REVERT: D 12 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: D 105 PHE cc_start: 0.8537 (m-80) cc_final: 0.8070 (m-80) REVERT: D 143 GLU cc_start: 0.7843 (tp30) cc_final: 0.7325 (tp30) REVERT: D 147 GLU cc_start: 0.7375 (mp0) cc_final: 0.6852 (mp0) REVERT: D 258 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7991 (t80) REVERT: E 65 MET cc_start: 0.7360 (tpp) cc_final: 0.7113 (mmm) REVERT: E 84 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5193 (pp20) REVERT: E 88 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6470 (mp0) REVERT: E 109 ASP cc_start: 0.6531 (OUTLIER) cc_final: 0.6138 (t0) REVERT: E 120 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7724 (tp) REVERT: E 121 LYS cc_start: 0.8290 (ttpp) cc_final: 0.7897 (ttpp) REVERT: E 196 GLU cc_start: 0.7339 (pm20) cc_final: 0.6967 (pm20) REVERT: E 251 VAL cc_start: 0.8116 (m) cc_final: 0.7860 (t) REVERT: E 258 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7866 (t80) REVERT: F 12 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: F 65 MET cc_start: 0.7690 (mmm) cc_final: 0.7463 (mmm) REVERT: F 67 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6898 (mm-30) REVERT: F 88 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: F 223 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8333 (mt) REVERT: H 98 SER cc_start: 0.8414 (m) cc_final: 0.8016 (t) REVERT: I 98 SER cc_start: 0.8094 (p) cc_final: 0.7840 (t) REVERT: J 23 SER cc_start: 0.8142 (t) cc_final: 0.7852 (p) REVERT: K 21 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7515 (ttt180) REVERT: K 38 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: K 63 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8050 (ttpp) REVERT: K 81 MET cc_start: 0.8065 (mtt) cc_final: 0.7827 (mtt) REVERT: M 102 VAL cc_start: 0.8351 (m) cc_final: 0.8086 (p) REVERT: N 53 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.8259 (t-90) REVERT: N 81 MET cc_start: 0.8186 (tpp) cc_final: 0.7898 (tpp) REVERT: P 45 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8064 (mtpp) REVERT: P 47 GLU cc_start: 0.8139 (pm20) cc_final: 0.7921 (pm20) REVERT: R 76 VAL cc_start: 0.8429 (p) cc_final: 0.8173 (m) outliers start: 129 outliers final: 89 residues processed: 763 average time/residue: 0.6545 time to fit residues: 573.2258 Evaluate side-chains 792 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 687 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 258 PHE Chi-restraints excluded: chain F residue 12 PHE Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain K residue 21 ARG Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 53 HIS Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 123 MET Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 136 ASN Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 134 LYS Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 121 optimal weight: 0.0870 chunk 152 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 295 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 GLN J 42 ASN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.135846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.129402 restraints weight = 34457.083| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.54 r_work: 0.3672 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24351 Z= 0.155 Angle : 0.588 10.912 32904 Z= 0.305 Chirality : 0.047 0.265 3685 Planarity : 0.005 0.063 4244 Dihedral : 4.811 52.997 3289 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.37 % Allowed : 33.67 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: 0.11 (0.15), residues: 3067 helix: 1.13 (0.17), residues: 943 sheet: -0.21 (0.17), residues: 931 loop : -0.39 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 263 TYR 0.013 0.001 TYR J 92 PHE 0.040 0.002 PHE C 148 TRP 0.015 0.001 TRP Q 127 HIS 0.004 0.001 HIS O 53 Details of bonding type rmsd covalent geometry : bond 0.00364 (24339) covalent geometry : angle 0.58759 (32880) SS BOND : bond 0.00086 ( 12) SS BOND : angle 0.50906 ( 24) hydrogen bonds : bond 0.03213 ( 1120) hydrogen bonds : angle 4.41034 ( 3372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 681 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: A 103 ILE cc_start: 0.8626 (mm) cc_final: 0.8055 (pp) REVERT: A 121 LYS cc_start: 0.8284 (tttm) cc_final: 0.7997 (tttm) REVERT: A 131 THR cc_start: 0.8042 (p) cc_final: 0.7807 (t) REVERT: A 157 GLU cc_start: 0.7324 (mp0) cc_final: 0.7078 (mp0) REVERT: A 196 GLU cc_start: 0.7684 (pm20) cc_final: 0.7412 (pm20) REVERT: A 228 GLU cc_start: 0.7803 (tp30) cc_final: 0.7519 (tp30) REVERT: A 256 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7862 (ttpp) REVERT: B 91 VAL cc_start: 0.8552 (m) cc_final: 0.8293 (p) REVERT: B 109 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6118 (t0) REVERT: B 256 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7809 (mmmt) REVERT: C 122 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7502 (tm-30) REVERT: C 157 GLU cc_start: 0.7399 (mp0) cc_final: 0.7008 (mp0) REVERT: C 163 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7977 (ttpp) REVERT: C 168 PHE cc_start: 0.8138 (t80) cc_final: 0.7833 (t80) REVERT: C 191 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7687 (tttp) REVERT: C 206 MET cc_start: 0.8576 (tpp) cc_final: 0.8099 (mpp) REVERT: C 243 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7877 (tt) REVERT: C 256 LYS cc_start: 0.8085 (ttpp) cc_final: 0.7812 (ttpp) REVERT: D 143 GLU cc_start: 0.7871 (tp30) cc_final: 0.7340 (tp30) REVERT: D 147 GLU cc_start: 0.7413 (mp0) cc_final: 0.6884 (mp0) REVERT: D 258 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8016 (t80) REVERT: E 65 MET cc_start: 0.7359 (tpp) cc_final: 0.7073 (mmm) REVERT: E 84 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.5158 (pp20) REVERT: E 88 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6505 (mp0) REVERT: E 109 ASP cc_start: 0.6547 (OUTLIER) cc_final: 0.6137 (t0) REVERT: E 117 LEU cc_start: 0.8465 (mp) cc_final: 0.8233 (mm) REVERT: E 120 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7744 (tp) REVERT: E 121 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7890 (ttpp) REVERT: E 196 GLU cc_start: 0.7359 (pm20) cc_final: 0.6957 (pm20) REVERT: E 251 VAL cc_start: 0.8127 (m) cc_final: 0.7865 (t) REVERT: E 258 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.7854 (t80) REVERT: F 12 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: F 65 MET cc_start: 0.7702 (mmm) cc_final: 0.7451 (mmm) REVERT: F 67 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6829 (mm-30) REVERT: F 88 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: F 223 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8351 (mt) REVERT: H 98 SER cc_start: 0.8439 (m) cc_final: 0.8038 (t) REVERT: I 98 SER cc_start: 0.8086 (p) cc_final: 0.7829 (t) REVERT: J 23 SER cc_start: 0.8139 (t) cc_final: 0.7849 (p) REVERT: K 21 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7552 (ttt180) REVERT: K 38 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: K 63 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8099 (ttpp) REVERT: K 81 MET cc_start: 0.8093 (mtt) cc_final: 0.7847 (mtt) REVERT: N 81 MET cc_start: 0.8216 (tpp) cc_final: 0.7952 (tpp) REVERT: O 123 MET cc_start: 0.8019 (ppp) cc_final: 0.7744 (ppp) REVERT: P 45 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8108 (mtpp) REVERT: Q 36 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8292 (tt) REVERT: R 76 VAL cc_start: 0.8429 (p) cc_final: 0.8163 (m) outliers start: 113 outliers final: 83 residues processed: 743 average time/residue: 0.6611 time to fit residues: 561.5988 Evaluate side-chains 772 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 672 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 258 PHE Chi-restraints excluded: chain F residue 12 PHE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 263 ARG Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain K residue 21 ARG Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 123 MET Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 136 ASN Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 249 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 152 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 70 optimal weight: 0.0000 chunk 216 optimal weight: 0.9980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.129500 restraints weight = 34534.578| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.54 r_work: 0.3705 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24351 Z= 0.133 Angle : 0.584 10.714 32904 Z= 0.303 Chirality : 0.046 0.171 3685 Planarity : 0.004 0.063 4244 Dihedral : 4.682 52.253 3287 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.98 % Allowed : 34.29 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: 0.17 (0.15), residues: 3067 helix: 1.19 (0.17), residues: 943 sheet: -0.19 (0.17), residues: 931 loop : -0.37 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 263 TYR 0.010 0.001 TYR G 93 PHE 0.037 0.002 PHE C 94 TRP 0.013 0.001 TRP P 127 HIS 0.005 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00314 (24339) covalent geometry : angle 0.58389 (32880) SS BOND : bond 0.00077 ( 12) SS BOND : angle 0.43668 ( 24) hydrogen bonds : bond 0.03111 ( 1120) hydrogen bonds : angle 4.35720 ( 3372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6134 Ramachandran restraints generated. 3067 Oldfield, 0 Emsley, 3067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 657 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: A 103 ILE cc_start: 0.8614 (mm) cc_final: 0.8036 (pp) REVERT: A 121 LYS cc_start: 0.8288 (tttm) cc_final: 0.7988 (tttm) REVERT: A 126 ILE cc_start: 0.8470 (mm) cc_final: 0.8243 (mp) REVERT: A 157 GLU cc_start: 0.7288 (mp0) cc_final: 0.7039 (mp0) REVERT: A 196 GLU cc_start: 0.7657 (pm20) cc_final: 0.7381 (pm20) REVERT: A 228 GLU cc_start: 0.7777 (tp30) cc_final: 0.7480 (tp30) REVERT: A 256 LYS cc_start: 0.8092 (ttpp) cc_final: 0.7832 (ttpp) REVERT: B 91 VAL cc_start: 0.8536 (m) cc_final: 0.8286 (p) REVERT: B 109 ASP cc_start: 0.6638 (OUTLIER) cc_final: 0.6072 (t0) REVERT: B 256 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7764 (mmmt) REVERT: C 121 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8103 (ttmm) REVERT: C 122 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7543 (tm-30) REVERT: C 157 GLU cc_start: 0.7357 (mp0) cc_final: 0.6965 (mp0) REVERT: C 168 PHE cc_start: 0.8124 (t80) cc_final: 0.7797 (t80) REVERT: C 191 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7697 (tttp) REVERT: C 206 MET cc_start: 0.8558 (tpp) cc_final: 0.8091 (mpp) REVERT: C 243 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7863 (tt) REVERT: C 256 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7749 (ttpp) REVERT: D 105 PHE cc_start: 0.8339 (m-80) cc_final: 0.7909 (m-80) REVERT: D 143 GLU cc_start: 0.7872 (tp30) cc_final: 0.7350 (tp30) REVERT: D 147 GLU cc_start: 0.7381 (mp0) cc_final: 0.6948 (mp0) REVERT: D 258 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7923 (t80) REVERT: E 65 MET cc_start: 0.7324 (tpp) cc_final: 0.7090 (mmm) REVERT: E 84 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5087 (pp20) REVERT: E 88 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6469 (mp0) REVERT: E 109 ASP cc_start: 0.6545 (OUTLIER) cc_final: 0.6094 (t0) REVERT: E 117 LEU cc_start: 0.8459 (mp) cc_final: 0.8231 (mm) REVERT: E 120 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7720 (tp) REVERT: E 121 LYS cc_start: 0.8296 (ttpp) cc_final: 0.7916 (ttpp) REVERT: E 196 GLU cc_start: 0.7342 (pm20) cc_final: 0.6938 (pm20) REVERT: E 251 VAL cc_start: 0.8079 (m) cc_final: 0.7810 (t) REVERT: E 258 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7945 (t80) REVERT: F 12 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: F 65 MET cc_start: 0.7659 (mmm) cc_final: 0.7423 (mmm) REVERT: F 67 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6878 (mm-30) REVERT: F 88 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: F 223 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8286 (mp) REVERT: F 254 LYS cc_start: 0.8680 (ptpt) cc_final: 0.8441 (pttt) REVERT: H 23 SER cc_start: 0.8252 (t) cc_final: 0.7948 (m) REVERT: H 98 SER cc_start: 0.8424 (m) cc_final: 0.8021 (t) REVERT: I 98 SER cc_start: 0.8076 (p) cc_final: 0.7822 (t) REVERT: J 23 SER cc_start: 0.8128 (t) cc_final: 0.7840 (p) REVERT: K 38 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: K 63 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8121 (ttpp) REVERT: K 81 MET cc_start: 0.8039 (mtt) cc_final: 0.7796 (mtt) REVERT: N 81 MET cc_start: 0.8194 (tpp) cc_final: 0.7939 (tpp) REVERT: O 123 MET cc_start: 0.8017 (ppp) cc_final: 0.7751 (ptp) REVERT: P 47 GLU cc_start: 0.8299 (pm20) cc_final: 0.7919 (pm20) REVERT: R 76 VAL cc_start: 0.8417 (p) cc_final: 0.8162 (m) outliers start: 103 outliers final: 83 residues processed: 715 average time/residue: 0.6632 time to fit residues: 539.6814 Evaluate side-chains 753 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 655 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 258 PHE Chi-restraints excluded: chain F residue 12 PHE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 263 ARG Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 123 MET Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 136 ASN Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 109 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 269 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 263 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129560 restraints weight = 34355.018| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.53 r_work: 0.3706 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24351 Z= 0.135 Angle : 0.580 10.483 32904 Z= 0.301 Chirality : 0.046 0.180 3685 Planarity : 0.004 0.063 4244 Dihedral : 4.648 51.362 3287 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.33 % Allowed : 34.17 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: 0.20 (0.15), residues: 3067 helix: 1.23 (0.17), residues: 943 sheet: -0.18 (0.17), residues: 933 loop : -0.34 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 21 TYR 0.011 0.001 TYR M 110 PHE 0.034 0.002 PHE A 148 TRP 0.013 0.001 TRP P 127 HIS 0.004 0.001 HIS O 53 Details of bonding type rmsd covalent geometry : bond 0.00320 (24339) covalent geometry : angle 0.58035 (32880) SS BOND : bond 0.00077 ( 12) SS BOND : angle 0.43984 ( 24) hydrogen bonds : bond 0.03092 ( 1120) hydrogen bonds : angle 4.31583 ( 3372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11485.46 seconds wall clock time: 195 minutes 39.80 seconds (11739.80 seconds total)